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Bioinformática : Aplicaciones a la proteómica y genómica
Provedor de dados: 32
Autores: Riaño Pachón, Diego Mauricio; González Estrada, Elizabeth; Alexa, Adrian; Ramírez, Fidel; Vischi Winck, Flavia; Gómez Merino, Fernando, Coord.; Silva Rojas, Hilda Victoria, Coord.; Pérez Rodríguez, Paulino, Coord.
En esta publicación intitulada “Bioinformática: aplicaciones a la genómica y proteómica” se detallan algunos de los avances más sobresalientes de los temas de genómica y proteómica, derivados de un curso internacional sobre el tema, organizado por el Colegio de Postgraduados. Estos avances incluyen aspectos de las dos ciencias ómicas, incluyendo genómica y biología estructural, código R, análisis comparativo y evolución, agrupamiento y minería de datos en R, redes de interacciones entre proteínas y proteómica bioinformática. BIOINFORMATICS : APPLICATIONS TO GENOMICS AND PROTEOMICS. ABSTRACT : In this publication entitled "Bioinformatics: applications to genomics and proteomics" are some of the most salient issues of genomics and proteomics, derived from an...
Tipo: Libro
Palavras-chave: Bioinformática; Proteómica; Genómica; ADN; Proteínas; Modelación; Simulación; Análisis de genómas; Biología estructural; Código R; Análisis comparativo; Minería de datos; Computación aplicada; Bioinformatics; Proteomics; DNA; Proteins; Models; Genomics; Simulation; R Code; Data mining; Computing; Genome analysis.
Ano: 2010
URL: http://hdl.handle.net/10521/313

Base de datos para factores de transcripción de Glycine max, Triticum aestivum y Zea maiz.
Provedor de dados: 32
Autores: Ramírez Sánchez, Obed.
Los factores de transcripción (FTs) son proteínas que incrementan o disminuyen la tasa transcripcional de uno o varios genes. Los FTs desempeñan un papel fundamental en el control de casi todos los procesos biológicos: crecimiento, metabolismo, respuesta a factores ambientales, etc. En plantas cultivadas, son de particular importancia aquellos relacionados con la respuesta al estrés (sequía, salinidad, bajas temperaturas, plagas, enfermedades, etc.). La identificación de FTs, su posterior anotación y la construcción de bases de datos públicas constituye un importante recurso para el estudio de los procesos que controlan la expresión génica. Se construyó la base de datos FT-MTS que contiene información de 13,975 genes identificados como FTs en los genomas...
Palavras-chave: Regulación transcripcional; Anotación funcional; Bioinformática; Transcriptional regulation; Functional annotation; Bioinformatics; Cómputo aplicado; Maestría.
Ano: 2012
URL: http://hdl.handle.net/10521/689

Electronic Field Guides and User Communities in the Eco-informatics Revolution
Provedor de dados: 7
Autores: Stevenson, R. D.; University of Massachusetts Boston; robert.stevenson@umb.edu; Haber, William A; Missouri Botanical Garden; whaber@racsa.co.cr; Morris, Robert; UMASS Boston; ram@cs.umb.edu.
The recognition that taxonomy is central to the conservation of biodiversity has reestablished the critical role of taxonomy in biology. However, many of the tools taxonomists produce for the identification and characterization of species, e.g., dichotomous keys, have been difficult to use and largely ignored by the general public in favor of field guides, which are essentially browsable picture guides. We review the role of field guides in species identification and discuss the application of a host of digital technologies to produce user-friendly tools for identification that are likely to greatly enhance species identification in the field by nonspecialists. We suggest that wider adoption of the citizen science model and the use of electronic field...
Tipo: Peer-Reviewed Reports
Palavras-chave: Bioinformatics; Birding; Citizen science; Ecoinformatics; Field biology; Field guides; Species identification; Taxonomic keys; Taxonomy.
Ano: 2003

Experimental and bioinformatic approaches for analyzing and visualizing cyanobacterial nitrogen and hydrogen metabolism
Provedor de dados: 69
Autores: Wünschiers,Röbbe; Axelsson,Rikard; Vellguth,Martin; Lindblad,Peter.
Many cyanobacteria are capable of utilizing light energy for nitrogen fixation. As a by-product of this nitrogenase mediated catalysis, hydrogen gas is produced. Several approaches to increase hydrogen production from cyanobacteria exist. Usually, these approaches are non-targeted. Here we exemplify how DNA-microarray based gene-expression analysis and bioinformatic visualization techniques can be used to analyze nitrogen and hydrogen metabolism from the filamentous, heterocyst forming cyanobacterium Nostoc PCC 7120. We analyzed the expression of 1249 genes from major metabolic categories under nitrogen fixing and non-nitrogen fixing growth. Of the selected genes, 494 show a more than 2-fold expression difference in the two conditions analyzed. Under...
Tipo: Journal article
Palavras-chave: Bioinformatics; Cyanobacteria; DNA-microarrays; Gene expression; Metabolic pathways; Nitrogen availability; Nitrogen fixation.
Ano: 2007
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000400008

Cloning and analysis of a NBS-LRR disease resistance gene candidate PnAG1 from peanut (Arachis hypogaea L.)
Provedor de dados: 69
Autores: Shan,Shi-hua; Zhang,Ting-ting; Li,Chun-juan; Yang,Chen; Yan,Cai-xia; Wan,Shu-bo.
Background: Based on the conserved sequences of a known NBS resistance gene, a pair of degenerate primers was designed to amplify the NBS-LRR resistance gene from peanut using PCR and RACE methods. Results: Analyzing the amino acid sequence by BLAST on NCBI, which was deduced from the 1088bp-long gene named PnAG1-2, showed that it had a certain homology with some resistance proteins, among which Arachis cardenasii resistance protein gene had the highest homology (66%). Relative quantification PCR analysis indicated that PnAG1-2 gene expresses more in J11 (an A. flavus-resistant variety) than in JH1012 (an A. flavus-susceptible variety) when the harvest time was coming. Conclusions: In this study, the NBS-LRR resistance sequence was successfully cloned from...
Tipo: Journal article
Palavras-chave: Bioinformatics; NBS-LRR; Peanut; Real-time fluorescence quantitative PCR.
Ano: 2011
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000600006

Expression analysis in response to drought stress in soybean: shedding light on the regulation of metabolic pathway genes
Provedor de dados: 74
Autores: Guimarães-Dias,Fábia; Neves-Borges,Anna Cristina; Viana,Antonio Americo Barbosa; Mesquita,Rosilene Oliveira; Romano,Eduardo; Grossi-de-Sá,Maria de Fátima; Nepomuceno,Alexandre Lima; Loureiro,Marcelo Ehlers; Alves-Ferreira,Márcio.
Metabolomics analysis of wild type Arabidopsis thaliana plants, under control and drought stress conditions revealed several metabolic pathways that are induced under water deficit. The metabolic response to drought stress is also associated with ABA dependent and independent pathways, allowing a better understanding of the molecular mechanisms in this model plant. Through combining an in silico approach and gene expression analysis by quantitative real-time PCR, the present work aims at identifying genes of soybean metabolic pathways potentially associated with water deficit. Digital expression patterns of Arabidopsis genes, which were selected based on the basis of literature reports, were evaluated under drought stress condition by Genevestigator. Genes...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Glycine max; Drought resistance; QPCR; Metabolic pathway; Bioinformatics.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200004

An overall evaluation of the resistance (R) and pathogenesis-related (PR) superfamilies in soybean, as compared with Medicago and Arabidopsis
Provedor de dados: 74
Autores: Wanderley-Nogueira,Ana C.; Belarmino,Luis C.; Soares-Cavalcanti,Nina da M.; Bezerra-Neto,João P.; Kido,Ederson A.; Pandolfi,Valesca; Abdelnoor,Ricardo V.; Binneck,Eliseu; Carazzole,Marcelo F.; Benko-Iseppon,Ana M.
Plants have the ability to recognize and respond to a multitude of pathogens, resulting in a massive reprogramming of the plant to activate defense responses including Resistance (R) and Pathogenesis-Related (PR) genes. Abiotic stresses can also activate PR genes and enhance pathogen resistance, representing valuable genes for breeding purposes. The present work offers an overview of soybean R and PR genes present in the GENOSOJA (Brazilian Soybean Genome Consortium) platform, regarding their structure, abundance, evolution and role in the plantpathogen metabolic pathway, as compared with Medicago and Arabidopsis. Searches revealed 3,065 R candidates (756 in Soybean, 1,142 in Medicago and 1,167 in Arabidopsis), and PR candidates matching to 1,261 sequences...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Pathogen response; Biotic stress; Bioinformatics; Glycine max; Medicago truncatula.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200007

Clustering and artificial neural networks: classification of variable lengths of Helminth antigens in set of domains
Provedor de dados: 74
Autores: Rodrigues,Thiago de Souza; Pacífico,Lucila Grossi Gonçalves; Teixeira,Santuza Maria Ribeiro; Oliveira,Sérgio Costa; Braga,Antônio de Pádua.
A new scheme for representing proteins of different lengths in number of amino acids that can be presented to a fixed number of inputs Artificial Neural Networks (ANNs) speel-out classification is described. K-Means's clustering of the new vectors with subsequent classification was then possible with the dimension reduction technique Principal Component Analysis applied previously. The new representation scheme was applied to a set of 112 antigens sequences from several parasitic helminths, selected in the National Center for Biotechnology Information and classified into fourth different groups. This bioinformatic tool permitted the establishment of a good correlation with domains that are already well characterized, regardless of the differences between...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Artificial neural networks; Clustering; Helminth antigen; Domain.
Ano: 2004
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400032

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases
Provedor de dados: 74
Autores: Alvarenga,Samuel Mazzinghy; Caixeta,Eveline Teixeira; Hufnagel,Bárbara; Thiebaut,Flávia; Maciel-Zambolim,Eunize; Zambolimand,Laércio; Sakiyama,Ney Sussumu.
Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Coffea; Data mining; ESTs; Genomics; In silico; Bioinformatics.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000400031

ABC transporters in Mycoplasma hyopneumoniae and Mycoplasma synoviae: insights into evolution and pathogenicity
Provedor de dados: 74
Autores: Nicolás,Marisa Fabiana; Barcellos,Fernando Gomes; Nehab Hess,Pablo; Hungria,Mariangela.
ABC transporters represent one of the largest superfamilies of active membrane transport proteins (MTPs) with a highly conserved ATPase domain that binds and hydrolyzes ATP, supplying energy for the uptake of a variety of nutrients and for the extrusion of drugs and metabolic wastes. The complete genomes of a non-pathogenic (J) and pathogenic (7448) strain of Mycoplasma hyopneumoniae, as well as of a pathogenic (53) strain of Mycoplasma synoviae have been recently sequenced. A detailed study revealed a high percentage of CDSs encoding MTPs in M. hyopneumoniae strains J (13.4%), 7448 (13.8%), and in M. synoviae 53 (11.2%), and the ABC systems represented from 85.0 to 88.6% of those CDSs. Uptake systems are mainly involved in cell nutrition and some might be...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: ABC transporters; Bioinformatics; Genomes of microorganisms; Membrane transport proteins; Mycoplasma; Phylogeny of prokaryotes.
Ano: 2007
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000200006

Overall picture of expressed Heat Shock Factors in Glycine max, Lotus japonicus and Medicago truncatula
Provedor de dados: 74
Autores: Soares-Cavalcanti,Nina M.; Belarmino,Luís C; Kido,Ederson A.; Pandolfi,Valesca; Marcelino-Guimarães,Francismar C.; Rodrigues,Fabiana A.; Pereira,Gonçalo A.G.; Benko-Iseppon,Ana M.
Heat shock (HS) leads to the activation of molecular mechanisms, known as HS-response, that prevent damage and enhance survival under stress. Plants have a flexible and specialized network of Heat Shock Factors (HSFs), which are transcription factors that induce the expression of heat shock proteins. The present work aimed to identify and characterize the Glycine max HSF repertory in the Soybean Genome Project (GENOSOJA platform), comparing them with other legumes (Medicago truncatula and Lotus japonicus) in view of current knowledge of Arabidopsis thaliana. The HSF characterization in leguminous plants led to the identification of 25, 19 and 21 candidate ESTs in soybean, Lotus and Medicago, respectively. A search in the SuperSAGE libraries revealed 68...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: HSF; Fabaceae; Bioinformatics; Abiotic stress; Transcription factor.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200006

Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: an example using soybean
Provedor de dados: 74
Autores: Belarmino,Luis C.; Oliveira,Ana R. da S.; Brasileiro-Vida,Ana C.; Bortoleti,Kyria C. de A.; Bezerra-Neto,João Pacífico; Abdelnoor,Ricardo V.; Benko-Iseppon,Ana M.
Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical mapping, providing also a general overview and examples...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Gene families; FISH; BAC; SSR; Aquaporin; Bioinformatics.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200015

Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy
Provedor de dados: 74
Autores: Boulila,Moncef.
A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Phylogeny; Recombination; Positive selection; Tombusviridae; Sequence; Taxonomy.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400018

Ribosome binding site recognition using neural networks
Provedor de dados: 74
Autores: Oliveira,Márcio Ferreira da Silva; Mendes,Daniele Quintella; Ferrari,Luciana Itida; Vasconcelos,Ana Tereza Ribeiro.
Pattern recognition is an important process for gene localization in genomes. The ribosome binding sites are signals that can help in the identification of a gene. It is difficult to find these signals in the genome through conventional methods because they are highly degenerated. Artificial Neural Networks is the approach used in this work to address this problem.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Neural networks; Ribosome binding site.
Ano: 2004
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400028

Complex networks: the key to systems biology
Provedor de dados: 74
Autores: Costa,Luciano da F.; Rodrigues,Francisco A.; Cristino,Alexandre S.
Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Complex networks; Metabolic networks; Protein-protein networks; Systems biology; Transcription networks.
Ano: 2008
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000400001

Translational selection on SHH genes
Provedor de dados: 74
Autores: Hajjari,Mohammadreza; Saffar,Behnaz; Khoshnevisan,Atefeh.
Codon usage bias has been observed in various organisms. In this study, the correlation between SHH genes expression in some tissues and codon usage features was analyzed by bioinformatics. We found that translational selection may act on compositional features of this set of genes.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Codon usage bias; Correlation; Translational selection.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000200033

A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor
Provedor de dados: 74
Autores: Cheng,Xiao; Jiang,Haiyang; Zhao,Yang; Qian,Yexiong; Zhu,Suwen; Cheng,Beijiu.
A large set of candidate nucleotide-binding site (NBS)-encoding genes related to disease resistance was identified in the sorghum (Sorghum bicolor) genome. These resistance (R) genes were characterized based on their structural diversity, physical chromosomal location and phylogenetic relationships. Based on their N-terminal motifs and leucine-rich repeats (LRR), 50 non-regular NBS genes and 224 regular NBS genes were identified in 274 candidate NBS genes. The regular NBS genes were classified into ten types: CNL, CN, CNLX, CNX, CNXL, CXN, NX, N, NL and NLX. The vast majority (97%) of NBS genes occurred in gene clusters, indicating extensive gene duplication in the evolution of S. bicolor NBS genes. Analysis of the S. bicolor NBS phylogenetic tree revealed...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Disease resistance gene; Nucleotide binding site; Sorghum bicolor.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000200016

A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines
Provedor de dados: 74
Autores: Nascimento,Leandro Costa do; Costa,Gustavo Gilson Lacerda; Binneck,Eliseu; Pereira,Gonçalo Amarante Guimarães; Carazzolle,Marcelo Falsarella.
The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Database; Gene expression; Soybean; Genosoja.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200002

Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases
Provedor de dados: 74
Autores: Michels,Marcus; Matte,Ursula; Fraga,Lucas Rosa; Mancuso,Aline Castello Branco; Ligabue-Braun,Rodrigo; Berneira,Elias Figueroa Rodrigues; Siebert,Marina; Sanseverino,Maria Teresa Vieira.
Abstract Pathogenic variants in the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) are responsible for cystic fibrosis (CF), the commonest monogenic autosomal recessive disease, and CFTR-related disorders in infants and youth. Diagnosis of such diseases relies on clinical, functional, and molecular studies. To date, over 2,000 variants have been described on CFTR (~40% missense). Since few of them have confirmed pathogenicity, in silico analysis could help molecular diagnosis and genetic counseling. Here, the pathogenicity of 779 CFTR missense variants was predicted by consensus predictor PredictSNP and compared to annotations on CFTR2 and ClinVar. Sensitivity and specificity analysis was divided into modeling and validation phases using...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: CFTR; Missense variant; Prediction; Bioinformatics; Cystic fibrosis.
Ano: 2019
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000400560

Biomolecular computers with multiple restriction enzymes
Provedor de dados: 74
Autores: Sakowski,Sebastian; Krasinski,Tadeusz; Waldmajer,Jacek; Sarnik,Joanna; Blasiak,Janusz; Poplawski,Tomasz.
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton that was subsequently extended by using two restriction enzymes. In...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; DNA; DNA computer; Restriction enzymes.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000500860

Resumos...
Provedor de dados: 14
Autores: MOSTRA DE ESTAGIÁRIOS E BOLSISTAS DA EMBRAPA INFORMÁTICA AGROPECUÁRIA, 8., 2012, Campinas.
Desde a primeira edição do evento, em 2005, até a sétima edição, 2011, já foram apresentados 309 trabalhos. Em sua 8a edição, realizada em novembro de 2012, a Mostra contou com a participação de 47 trabalhos inscritos em três categorias: Pesquisa, Pós-graduação e Suporte à Pesquisa, em que 14 trabalhos foram selecionados para apresentação oral e 33 trabalhos para apresentação na seção de pôsteres.
Tipo: Outras publicações técnicas (INFOTECA-E)
Palavras-chave: Agroinformática; Mudanças climáticas; Bioinformática.; Tecnologia da Informação.; Information technology; Bioinformatics; Climate change.
Ano: 2012
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/954471

Imputação de genótipos em bovinos: um guia passo a passo.
Provedor de dados: 14
Autores: MUDADU, M. de A.; CARVALHO, H. G. de; YOKOO, M. J. I.; CARDOSO, F. F.
O programa de melhoramento genético no Brasil está implementando o uso de marcadores genéticos, um procedimento chamado seleção genômica (SG). SG consiste em genotipar uma população de referência com fenótipos conhecidos e na descoberta de marcadores genéticos associados. O efeito dos marcadores são estimados e validados de forma a tornar possível predizer os valores genéticos dos cadidatos à seleção baseado nos seus genótipos. A genotipagem de alta densidade tem custo elevado, de forma que usa-se genotipar a população de referência usando chips de alta densidade de marcadores e genotipar com menor custo os candidatos a seleção usando chips de baixa densidade de marcadores. A imputação de genótipos é então aplicada para expandir os dados de genotipagem dos...
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Genotipagem em alta densidade; Imputação de genótipos; Bioinformática; Genotyping; Bioinformatics.
Ano: 2016
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1064163

Análise de conjunto de genes de dados de expressão gênica na Rede Genômica Animal.
Provedor de dados: 14
Autores: HIGA, R. H.; IBELLI, A. M. G.; CARDOSO, F. F.; REGITANO, L. C. de A.
O objetivo deste trabalho é apresentar a análise de conjuntos de genes para dados de experssão gênica, conforme utilizada no escopo da RGA. Na seção 2 é apresentado o procedimento correspondente à análise de GSA proposta por (EFRON; TIBSHIRANI, 2007), utilizado na RGA. Um exemplo completo, incluindo principais comandos do correspondente script R é apresentado na seção 3.
Tipo: Comunicado Técnico (INFOTECA-E)
Palavras-chave: Bioinformática; Expressão gênica; Rede Genômica Animal; Análise de genes; Bioinformatics; Gene expression.
Ano: 2011
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/920185

Instruções para uso do Open Grid Engine no Laboratório Multiusuário de Bioinformática.
Provedor de dados: 14
Autores: CINTRA, L. C.
O presente trabalho tem sua relevância no treinamento dos recursos humanos que estão atuando no âmbito de projetos da Embrapa que exigem o processamento intenso e, por isso, demandam recursos computacionais especiais para a obtenção de seus resultados. No entanto, problemas similares ocorrem em outras organizações de ensino e pesquisa no País; e a discussão apresentada pode ser útil também para profissionais dessas, que queiram ampliar a sua capacidade de processamento utilizando clusters computacionais.
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Bioinformática; Processamento de dados biológicos; Cluster; Bioinformatics.
Ano: 2016
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1066147

Análise de dados de RNA-Seq utilizando o Galaxy.
Provedor de dados: 14
Autores: ZERLOTINI NETO, A.; CINTRA, L. C.
Neste documento, serão apresentados métodos computacionais para facilitar o processo de análise de dados de RNA-Seq, por meio de ferramentas acessíveis via navegadores. Esta metodologia possibilita o processamento distribuído e o compartilhamento de grandes volumes de dados de RNA-Seq, com o objetivo de efetivamente identificarmos as diferenças de expressão de genes para elucidar mecanismos biológicos ligados à produtividade e a doenças.
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Bioinformática; Plataforma Galaxy; RNA-Seq; Expressão gênica; Bioinformatics; Gene expression.
Ano: 2016
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1064217

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards
Provedor de dados: 5
Autores: Ten Hoopen, Petra; Pesant, Stephane; Kottmann, Renzo; Kopf, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick M. A.; Bowler, Chris; Gloeckner, Frank Oliver; Cochrane, Guy.
Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be...
Tipo: Text
Palavras-chave: Data standard; Marine; Molecular; Biodiversity; Microbial; Bioinformatics; Reporting; Interoperability.
Ano: 2015
URL: http://archimer.ifremer.fr/doc/00311/42266/41588.pdf

Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations
Provedor de dados: 5
Autores: Genitsaris, Savvas; Monchy, Sebastien; Breton, Elsa; Lecuyer, Eric; Christaki, Urania.
The aim of this study was to analyze planktonic protistan assemblages under different environmental pressures at 2 adjacent coastal stations (inshore and offshore; similar to 6.4 km apart) in the eastern English Channel (EEC). Samples were collected between March 2012 and June 2013, and analyzed using bioinformatic analysis and tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. In addition to the taxonomic composition of the protistan communities, the detected operational taxonomic units (OTUs) were sorted into 6 major functional groups based on their trophic roles in marine systems. Comparisons of 13 environmental factors, including physical and chemical variables, indicated significant differences between the 2 stations. However,...
Tipo: Text
Palavras-chave: Unicellular eukaryotes; Community organization; Environmental parameters; Biotic interactions; 18S rRNA; Pyrosequencing; Bioinformatics; Ecological tools.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00373/48450/48765.pdf

AMIS, The Article Minimum Information Standard
Provedor de dados: 17
Autores: Delphine Dauga.
The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, _Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al....
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5054/version/1

Detection of Nonlinear Effects in Gene Expression Pathways
Provedor de dados: 17
Autores: Andreas Mayr; Djork-Arne Clevert; Sepp Hochreiter.
One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present, gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be distinguished.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We propose an algorithm to infer nonlinear network elements in pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by one single latent factor. We...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4715/version/1

Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics
Provedor de dados: 17
Autores: Michel Dumontier; James R. Green; Ashkan Golshani; Myron L. Smith; Nadereh  Mir-Rashed; Md  Alamgir; Veronika  Eroukova; Frank Dehne; James  J. Cheetham.
Background&amp;#xd;&amp;#xa;High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2311/version/1

Mizoribin as a inhibitor for leukocyte immunoglobulin receptor sub family A member3
Provedor de dados: 17
Autores: Varala Sravani; I Vani Priyadarshini; Amineni Umamaheswari.
The Leukocyte Immunoglobulin-like Receptors (LILRs) are a family of receptors that was broadly expressed on all leukocytes and have the ability to regulate their function. The increased levels of human LILRA3 in rheumatoid arthritis patients leads to stroke. In quest of designing novel inhibitors against LILRA3 an accurate homology model for the protein was based on crystal structures of 1GOX and 3P2T using Modeller 9V9. The use of multiple templates for structure prediction led us to propose a structure comprising all 439 amino acids of human LILRA3 for the first time.  The best model was selected based on GA341 and DOPE score and further assessed through ProSA and PROCHECK. The validated structure was subjected to CASTp analysis ligand binding site...
Tipo: Presentation
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6532/version/1

Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data
Provedor de dados: 17
Autores: Valentina Carapella; Vicente Grau; Pras Pathmanathan; Kevin Burrage.
Cardiac motion is a vital process as it sustains the pumping of blood in the body. For this reason motion abnormalities are often associated with severe cardiac pathologies. Clinical imaging techniques, such as MRI, are powerful in assessing motion abnormalities but their connection with pathology often remains unknown.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Computational models of cardiac motion, integrating imaging data, would thus be of great help in linking tissue structure (i.e. cells organisation into fibres and sheets) to motion abnormalities and to pathology. Current models, though, are not able yet to correctly predict realistic cardiac motion in the healthy or diseased heart.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our hypothesis is that a more realistic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6594/version/1

Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics
Provedor de dados: 17
Autores: Kentaro Hayashi; Vincent  Piras; Masaru  Tomita; Masa  Tsuchiya; Kumar Selvarajoo.
The Tumor Necrosis Factor-&amp;#x3b1; (TNF-&amp;#x3b1;), a cytokine produced during the innate immune response to invading pathogens, is involved in numerous fundamental cellular processes. Here, to understand the temporal activation profiles of the TNF-&amp;#x3b1; regulated signaling network, we developed a dynamic computational model based on the perturbation-response approach and the law of information (signaling flux) conservation. Our simulations show that the temporal average population response of the TNF-&amp;#x3b1; stimulated transcription factors NF-&amp;#x3ba;B and AP-1, and 3 groups of 180 downstream gene expressions follow first-order equations. Using the model, in contrast to a well-known previous study, our model suggests that the continuous...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6495/version/1

Ontology-based Assisted Curation of Biomedical Data
Provedor de dados: 17
Autores: Conrad Plake.
Manual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3122/version/1

Biological taxonomy and ontology development: scope and limitations
Provedor de dados: 17
Autores: Nico M. Franz; David M. Thau.
The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static &amp;#x27;snapshot&amp;#x27; hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4593/version/1

Towards an Ontological Representation of Resistance: The Case of MRSa
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. Resistance terms from various existing ontologies are examined and found to be either overly narrow, inconsistent, or&amp;#xd;&amp;#xa;otherwise problematic. We propose a more coherent ontological representation using the antibiotic resistance in Methicillin-Resistant _Staphylococcus aureus_ (MRSa) as a case study.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3475/version/1

Using the Gene Ontology to Annotate Biomedical Journal Articles
Provedor de dados: 17
Autores: Michael Bada; Lawrence Hunter.
We are creating a gold-standard corpus of manually annotated full-text biomedical journal articles toward natural-language-processing applications.  Central to this is our use of entire ontologies of the Open Biomedical Ontologies initiative as well as other terminologies as term sources, in contrast to most other such annotation projects, which have used small, ad hoc schemas.  In addition to the standard difficulties in such annotation projects, each of the terminologies we have used has idiosyncrasies and ambiguities that present further challenges to consistent, high-quality annotation of these articles.  In this paper we present and discuss the most salient of these with regard to the Gene Ontology that we have encountered and addressed in our...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3556/version/1

Cross-Product Extensions of the Gene Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Michael Bada; Tanya Z. Berardini; Jennifer Deegan; Amelia Ireland; Midori A. Harris; David P. Hill; Jane Lomax.
The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3496/version/1

CASIMIR &amp;#x26; ENFIN
Provedor de dados: 17
Autores: John Hancock.
I review the development of draft database registries in the CASIMIR and ENFIN projects and the development of the CASIMIR Database Description Framework.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6158/version/1

Evaluation of diversity, specialization, and gene specificity in transcriptomes
Provedor de dados: 17
Autores: Octavio Martinez; Humberto Reyes-Vald&amp;#xe9;s.
The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. Recently we proposed an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. This approach can be useful for the determination and measure of transcriptional networks. We defined transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3012/version/1

Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection
Provedor de dados: 17
Autores: Ricardo Franco-Duarte; Lan Umek; Blaz Zupan; Dorit Schuller.
The objective of the present study was to compare genetic and phenotypic variation of 103 Saccharomyces cerevisiae strains isolated from winemaking environments. We used bioinformatics approaches to identify genetically similary strains with specific phenotypes and to estimate a strain&amp;#x27;s biotechnological potential.  &amp;#xd;&amp;#xa;A S. cerevisiae collection, comprising 440 strains that were obtained from winemaking environments in Portugal has been constituted during the last years. All strains were genetically characterized by a set of eleven highly polymorphic microsatellites and showed unique allelic combinations. Using neural networks, a subset of 103 genetically most diverse strains was chosen for phenotypic analysis, that included growth...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2288/version/1

Integration of Co-expression Networks for Gene Clustering
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
Simultaneous overexpression or underexpression of multiple genes, used in various forms as probes in the high-throughput microarray experiments, facilitates the identification of their underlying functional proximity. This kind of functional associativity (or conversely the separability) between the genes can be represented proficiently using co-expression networks. The extensive repository of diversified microarray data encounters a recent problem of multi-experimental data integration for the aforesaid purpose. This paper highlights a novel integration method of  gene co-expression networks, based on the search for their consensus network, derived from diverse microarray experimental data for the purpose of clustering. The proposed methodology avoids the...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7126/version/1

GMOD for Evolutionary Biology
Provedor de dados: 17
Autores: Robert Buels; Dave Clements.
The Generic Model Organism Database (GMOD, &amp;#x22;http://gmod.org&amp;#x22;:http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data.  GMOD is also a community of people addressing common challenges with biological data.  Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk will focus on three areas of particular interest to iEvoBio participants.  &amp;#xd;&amp;#xa;1) GBrowse_syn comparative genomics viewer&amp;#xd;&amp;#xa;2)...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4611/version/1

YeastMed: An XML-Based System for Biological Data Integration of Yeast
Provedor de dados: 17
Autores: Abdelaali Briache; Kamar Marrakchi; Amine Kerzazi; Ismael Navas-Delgado; Jos&amp;#xe9; F. Aldana Montes; Badr Din Rossi Hassani; Khalid Lairini.
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of biological data.  SGD, Yeastract, CYGD-MIPS, BioGrid and PhosphoGrid are five of the most visited databases by the yeast community. These sources provide complementary data on biological entities. Biologists are brought systematically to query these data sources in order to analyse the results of their experiments. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned result is a complex and laborious task. To provide transparent and simultaneous access to these...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5396/version/1

Openness as Infrastructure
Provedor de dados: 17
Autores: John Wilbanks.
Openness at the layer of cultural works and data is the key to the data infrastructure we need to accelerate science. This article lays out three key elements of data infrastructure - collaboration, classification, and openness - which draw us inevitably towards the long-claimed, but rarely-achieved, goal of the scientific method: to make claims that are reproducible under similar circumstances by someone other than the claimant, to be reproducible.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6032/version/1

Evidence attribution in the UniProt Knowledgebase
Provedor de dados: 17
Autores: Michele Magrane; UniProt Consortium.
UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3129/version/1

Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping
Provedor de dados: 17
Autores: Scott L. Carter; Matthew Meyerson; Gad Getz.
Interpretation of allelic copy measurements at polymorphic markers in cancer samples presents distinctive challenges and opportunities. Due to frequent gross chromosomal alterations occurring in cancer (aneuploidy), many genomic regions are present at homologous-allele imbalance. Within such regions, the unequal contribution of alleles at heterozygous markers allows for direct phasing of the haplotype derived from each individual parent. In addition, genome-wide estimates of homologue specific copy- ratios (HSCRs) are important for interpretation of the cancer genome in terms of fixed integral copy-numbers. We describe HAPSEG, a probabilistic method to interpret bi- allelic marker data in cancer samples. HAPSEG operates by partitioning the genome into...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6494/version/1

On the exotic fishes given to... geometry
Provedor de dados: 17
Autores: Yury L. Voytekhovsky.
Polyhedral forms are extremely widespread both in animate and inanimate nature. Thus,  crystals occur as polyhedra only. Besides, these forms are quite common with various primitive organisms, i.e. icosahedral viruses, radiolaria and algae. Here we discuss the cases of exotic Boxfish and Porcupinefish. The specific morphology of the Boxfish reveals in polygonal osseous blades, covering its body. As for the Porcupinefish, its polyhedral approximation was observed via certain geometrical techniques applied. Namely, their spine bases were considered the Delaunay point (R, r)-systems. Consequently, the respective Dirichlet tiling proved to be quasifullerenes and analogous to the Boxfish morphology. This unexpected geometrical dualism of the two families...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2191/version/1

Dynamic is-a Hierarchy Generation from a Clinical Medical Ontology
Provedor de dados: 17
Autores: Hiroko Kou; Jun Zhou; Mamoru Ohta; Kouji Kozaki; Ken Imai; Kazuhiko Ohe; Riichiro Mizoguchi.
This article discusses an ontology-handling technology to provide on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physicians might have. It is one of the important benefits of our medical ontology which is developed as a Japanese national project. This technology tackles with the multi-perspective issues of medical knowledge.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3501/version/1

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases
Provedor de dados: 17
Autores: Gil-Mi Ryu; Pamela Song; Kyu-Won Kim; Kyung-Soo Oh; Jong Hun Kim.
We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2079/version/1

Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget
Provedor de dados: 17
Autores: Huilei Xu; Avi Ma&amp;#x27;ayan.
Results from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3074/version/1

Towards realising Darwin&amp;#x2019;s dream: setting the trees free
Provedor de dados: 17
Autores: Roderic Page.
The fact that all living organisms are related by common descent is one of the central principles of modern biology.  Since the early 1990&amp;#x27;s the amount of data available to evolutionary biologists has exploded, and Elsevier&amp;#x2019;s journal _Molecular Phylogenetics and Evolution_, has become the largest single publisher of evolutionary trees (phylogenies). These trees and their supporting data potentially form a tremendous resource for biologists, with applications in genomics, evolutionary biology, biodiversity, and public health. However, most published trees are not available in any public database, but instead languish as images, &amp;#x22;locked up&amp;#x22; in the pages of journals. A long term solution to this problem is to invert the...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2217/version/1

Prediction of Evolutionarily important catalytic amino acid of Mycobacterium tuberculosis O-Succinylbenzoate synthase through in silico mutational analysis
Provedor de dados: 17
Autores: Babajan B; Chaitanya M; Anuradha CM; Suresh Kumar Chitta.
The emergence of tuberculosis resistant to multiple, first- and second-line antibiotics poses challenges to a global control strategy that relies on standard drug treatment regimens. The high drug-resistant strains of Mycobacterium tuberculosis (Mtb) have been implicated in outbreaks and have been found throughout the world; a comprehensive understanding, the magnitude of this threat requires an accurate assessment of the worldwide burden of resistance. In an attempt to design anti-TB drugs, the target chosen is a key enzyme of Mtb, O-Succinylbenzoate synthase (OSBS), which is an attractive target for its role in electron transport chain as OSBS is not available in humans.  An attempt has been to built the 3-D structure of Mtb-OSBS using online Swiss model...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3776/version/1

The Teleost Taxonomy Ontology
Provedor de dados: 17
Autores: Peter E. Midford; James P. Balhoff; Wasila Dahdul; Cartik R. Kothari; Hilmar Lapp; John Lundberg; Paula Mabee; Todd J. Vision; Monte Westerfield.
The Teleost Taxonomy Ontology (TTO) is an ontology of taxonomic groups and associated names for fish (not just teleosts). This ontology has served as a source of names and taxonomic structure within the Phenoscape project since early 2008. Although the TTO is based on Eschmeyer&amp;#x27;s Catalog of Fishes (CoF) and incorporates all valid species and genus names, it is also extended by the curation needs of the Phenoscape project. Names of fossil taxa not included in the CoF as well as references to specimens identi&amp;#xc;ed only to genus (e.g., _Eigenmannia sp._ (Fink and Fink 1981)) are incorporated into the TTO as required by the curation needs of the Phenoscape project. As Phenoscape receives updates to the CoF, a tool called TTOUpdate merges the...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4629/version/1

Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1&amp;#x3bc;^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/2

NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0
Provedor de dados: 17
Autores: Tiefeng You; I. C. Baianu.
The soybean-derived products are among the most important agricultural products in the USA and the world. Conventional analytical methods for soybean composition analysis are both time consuming and costly. Faster and less expensive methods are required for most practical applications. To improve the accuracy, reliability and sensitivity of NIR, major advancements in instrumentation, as well as, data analysis / calibration methodology are required. Novel NIR instruments, such as DA-NIR and FT-NIR spectrometers developed in recent years have the potential for improving significantly the quantification of soybean composition at a reasonable cost. We present representative calibrations and data for intact soybean composition analysis obtained at the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6253/version/1

The association between having a household member with a cancer-related limitation and human papillomavirus vaccine uptake
Provedor de dados: 17
Autores: Tabatha N. Offutt-Powell; Rohit P. Ojha; Joseph Tota; Karan P. Singh.
OBJECTIVE: To evaluate the association between having a household member with a cancer-related limitation (physical, mental, or emotional) and human papillomavirus (HPV) vaccine uptake among females aged 9 &amp;#x2013; 17 years. &amp;#xd;&amp;#xa;METHODS: We analyzed 2008 National Health Interview Survey for our cross-sectional analysis. All households with females aged 9 &amp;#x2013; 17 years were eligible for inclusion in our analysis. Our outcomes of interest included HPV vaccine initiation (&amp;#x2265;1 dose) and series completion (full 3 doses). A dichotomous variable indicating a cancer-related limitation for a household member was created if at least one adult in the household responded to having a limitation caused by cancer. We used...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4925/version/1

Epigrass: a tool to study disease spread in complex networks.
Provedor de dados: 17
Autores: Fl&amp;#xe1;vio Code&amp;#xe7;o Coelho; Claudia Codeco; Oswaldo Cruz.
The construction of complex statial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most if not all these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior.&amp;#xd;&amp;#xa;...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/378/version/1

A science metrics based citation for tagging the biomedical researchers
Provedor de dados: 17
Autores: Adeilton Brandao.
With the thousands of scientific papers being produced every month, picking an authors name, associate it to a research field and right evaluate his or her performance is in most of times a cumbersome task. I am proposing here that science indexes as h-index, g-index, total citations and published papers  could be added to biomedical bibliographic citation in order to create a unique identifier for a given researcher.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/794/version/1

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/3721/version/3

Suggested actions from the Melbourne HVP Information Seminar
Provedor de dados: 17
Autores: Richard Cotton; Myles Axton; Agnes Bankier; Bernard Brais; Lawrence Cavedon; Desir&amp;#xe9;e du Sart; Peter George; David Goldgar; Terence Harrison; Marienne Hibbert; John Hopper; Finlay Macrae; Christine M. O&amp;#x2019;Keefe; David Ravine; Ravi Savarirayan; Les Sheffield; Tim Smith; Nicola Stokes; Vijaya Sundararajan; David Thorburn; Ingrid Winship.
The Human Variome Project (HVP; www.humanvariomeproject.org) was initiated at a meeting in June 2006 and addressed the problems of collecting genetic information and generated 96 recommendations (http://www.nature.com/ng/journal/v39/n4/full/ng0407-423.html) to overcome these, with the focus on Mendelian disease. A considerable number of projects have been added, to those that have been ongoing for a number of years, since that meeting. Also, a planning meeting is to be held May 25-29, 2008 in Spain (http://www.humanvariomeproject.org/HVP2008/).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A dramatic boost has been given to the HVP by the preparedness and action of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org), to,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1784/version/1

Decoding Sequence Classification Models for Acquiring  New Biological Insights
Provedor de dados: 17
Autores: Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter.
Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In this contribution, we propose a new approach to analyzing...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4708/version/1

Improved prediction of protein interaction from microarray data using asymmetric correlation
Provedor de dados: 17
Autores: Kojiro Yano.
Background:Detection of correlated gene expression is a fundamental process in the characterization of gene functions using microarray data. Commonly used methods such as the Pearson correlation can detect only a fraction of interactions between genes or their products. However, the performance of correlation analysis can be significantly improved either by providing additional biological information or by combining correlation with other techniques that can extract various mathematical or statistical properties of gene expression from microarray data. In this article, I will test the performance of three correlation methods-the Pearson correlation, the rank (Spearman) correlation, and the Mutual Information approach-in detection of protein-protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4430/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/1

Self-organization of intrinsically disordered proteins with folded N-termini
Provedor de dados: 17
Autores: Philip C. Simister; Fred Schaper; Nicola O&amp;#x27;Reilly; Simon McGowan; Stephan M. Feller.
Thousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions.
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5124/version/1

Organising metabolic networks: cycles in flux distributions
Provedor de dados: 17
Autores: Maur&amp;#xed;cio V. Kritz; Marcelo T. dos Santos; Sebasti&amp;#xe1;n Urrita; Jean-Marc Schwartz.
Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3932/version/1

The Latest Information and Perspective of Human Gene and Protein Database (HGPD) as Human Proteome Study
Provedor de dados: 17
Autores: Yukio Maruyama; Yoshifumi Kawamura; Takao Isogai; Nobuo Nomura; Naoki Goshima.
HGPD (&amp;#x22;http://www.HGPD.jp/&amp;#x22;:http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression data. HGPD was launched in November 2008 and, since then, 33,275 human Gateway entry clones have been constructed from ORFs of full-length cDNAs, thus representing the largest collection in the world. Sequence information and protein expression of Gateway entry clones can also be retrieved from HGPD. The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (&amp;#x22;http://flj.hinv.jp/v01/cgi/index.cgi&amp;#x22;:http://flj.hinv.jp/v01/cgi/index.cgi), which was constructed as human cDNA sequence analysis database focusing on mRNA...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5070/version/1

The model of proteolysis
Provedor de dados: 17
Autores: Piotr Dittwald; Anna Gambin.
This document presents the original approach for estimating parameters of proteolysis process. Data used to fit the model are taken from mass&amp;#xd;&amp;#xa;spectrometric experiments. For parameters estimation the Levenberg-Marquadt algorithm is used. The motivation for model is a hypothesis&amp;#xd;&amp;#xa;that discrimination between cancer patients and healthy donors can be based on activity of peptide cleaving enzymes (i.e. peptidases).
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4400/version/1

Top-down and bottom-up informatics: who has the high ground?
Provedor de dados: 17
Autores: Vincent S. Smith; Dave Roberts.
Recent years have seen the emergence of several major initiatives supporting the development of biodiversity informatics infrastructures. In Europe examples include: EDIT &amp;#x2013; the European Distributed Institute of Taxonomy; LifeWatch &amp;#x2013; a biodiversity analytical platform integrating observatories, databases, processing and computational capacity; and SYNTHESYS &amp;#x2013; funding researcher access to a network of taxonomic collections, laboratories and libraries. These European projects alone represent a spend of approximately 35 Million Euros, with funding contingent on the collaboration of numerous geographically dispersed institutional partners. In this presentation we will review the major informatics products of these initiatives;...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4592/version/1

Systems Biology Ontology: Update
Provedor de dados: 17
Autores: Nick Juty.
The Systems Biology Ontology (SBO) is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling, providing an additional layer of semantic information. We present recent developments in SBO, including the ontology&amp;#x27;s OBO Foundry status, its relationship to SBGN, and detail some of the restructuring work that has been undertaken.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5121/version/1

SPARQL Assist Language Neutral Query Composer
Provedor de dados: 17
Autores: Luke McCarthy; Ben Vandervalk; Mark D. Wilkinson.
SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar.    Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task.  We present SPARQL Assist: a web application that  addresses these issues by providing context-sensitive type-ahead completion to existing web forms.  Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5382/version/1

New checksum functions for Biopython
Provedor de dados: 17
Autores: Sebastian Bassi; Virginia Gonzalez.
Checksum algorithms are used in biological databases for integrity check and identification purposes. CRC64 is the only checksum algorithm already included in Biopython. This work proposes two new implementation of known algorithms (GCG Checksum and SEGUID). There is also an application based on SEGUID: Looking for redundancy between two FASTA files full of protein sequences based only in sequence information, by comparing the SEGUIDs of both files.&amp;#xd;&amp;#xa;The code is shown in the manuscript and may be available at Biopython.org.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/278/version/1

Aptamer-based multiplexed proteomic technology for biomarker discovery
Provedor de dados: 17
Autores: Larry Gold; Deborah Ayers; Jennifer Bertino; Christopher Bock; Ashley Bock; Edward N. Brody; Jeff Carter; Virginia Cunningham; Andrew Dalby; Bruce E. Eaton; Tim Fitzwater; Dylan Flather; Ashley Forbes; Trudi Foreman; Cate Fowler; Bharat Gawande; Meredith Goss; Magda Gunn; Shashi Gupta; Dennis Halladay; Jim Heil; Joe Heilig; Brian Hicke; Gregory Husar; Nebojsa Janjic; Thale Jarvis; Susan Jennings; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Terese Kaske; Tad Koch; Stephan Kraemer; Luke Kroiss; Ngan Le; Daniel Levine; Wes Lindsey; Bridget Lollo; Wes Mayfield; Mike Mehan; Robert Mehler; Michele Nelson; Sally K. Nelson; Dan Nieuwlandt; Malti Nikrad; Urs Ochsner; Rachel M. Ostroff; Matt Otis; Thomas Parker; Steve  Pietrasiewicz; Dan Resnicow; John Rohloff; Glenn Sanders; Sarah Sattin; Dan Schneider; Britta Singer; Martin Stanton; Alana Sterkel; Alex Stewart; Suzanne Stratford; Jonathan D. Vaught; Mike Vrkljan; Jeffrey J. Walker; Mike Watrobka; Sheela Waugh; Allison Weiss; Sheri Wilcox; Alexey Wolfson; Steve Wolk; Chi Zhang; Dom Zichi.
Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology.  We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma).  Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation.  This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected.  Proteins in complex...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4538/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (v.3)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/3

Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis
Provedor de dados: 17
Autores: Bin-Guang Ma.
The emergence of &amp;#x201c;Systems Biology&amp;#x201d; in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function....
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2223/version/1

Virtual screening for NS5B inhibitors of Hepatitis C virus
Provedor de dados: 17
Autores: Amjesh  R; Achuthsankar  S. Nair; Sugunan V.S.
Hepatitis C Virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at a risk of developing significant morbidity and mortality. To date there is no effective drug for the treatment or vaccine to prevent this infection. The present study aims to discover novel inhibitors which target an allosteric binding site of RNA dependent RNA polymerase enzyme of HCV. A structure based virtual screening of Zinc database by computational docking and the post docking analysis of energy calculations and interactions followed by ADMET studies were conducted. Our study revealed 10 compounds which has more potential than the existing inhibitor to be considered as lead compounds.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7055/version/1

PocketMatch: A new algorithm to compare binding sites in protein structures
Provedor de dados: 17
Autores: Yeturu Kalidas; Nagasuma Chandra.
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental&amp;#xd;&amp;#xa;requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring  functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of&amp;#xd;&amp;#xa;the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2142/version/1

MUEGANO: A divide and conquer algorithm to overcome memory limitations when assembling shotgun projects
Provedor de dados: 17
Autores: Octavio Martinez; Araceli Fernandez-Cortes.
When assembling a large quantity of reads in a genomic shotgun project a serious limitation is the amount of random access memory (RAM) of the computers used in the project. This arises because all assembling programs must look at all the overlaps between reads at the same time, using RAM in order to construct contigs, and the memory of the computer can be filled up during this step, causing the abortion of the assembling process.&amp;#xd;&amp;#xa;Here we propose an algorithm that is capable of overcoming any memory limitation by using redundancy of processing and thus producing an increase in computing time but overcoming the memory limitation.&amp;#xd;&amp;#xa;The proposed algorithm consists in dividing the reads in a set of groups which size is half the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3712/version/1

SED-ML Script Language
Provedor de dados: 17
Autores: Frank Bergmann.
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6105/version/1

Lengthening of 3&amp;#x27;UTR Increases Morphological Complexity in Animal Evolution
Provedor de dados: 17
Autores: Cho-Yi Chen; Shui-Tein Chen; Hsueh-Fen Juan; Hsuan-Cheng Huang.
By analyzing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3&amp;#x27; untranslated regions (3&amp;#x27;UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3&amp;#x27;UTRs together with a commensurate expansion in post-transcriptional regulation can contribute to the emergence of new cell types during animal evolution.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4915/version/1

PlnTFDB: Plant Transcription Factor Database &amp;#x2013; Update
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Luiz Gustavo Guedes Correa; Bernd Mueller-Roeber.
PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss _Physcomitrella patens_ and the rice _Oryza sativa_ spp _indica_. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1094/version/1

NPO:  Ontology for Cancer Nanotechnology Research
Provedor de dados: 17
Autores: Dennis Thomas; Rohit Pappu; Nathan Baker.
We present the design and development of NanoParticle Ontology (NPO). The ontology is implemented in the Ontology Web Language (OWL).  The domain terms in NPO currently represent entities, which describe knowledge about physical, chemical, and functional properties of nanoparticles characterized in cancer nanotechnology research. The upper-level of NPO is formed using terms from the Basic Formal Ontology (BFO).
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3515/version/1

Inverse relationship between genetic diversity and epigenetic complexity
Provedor de dados: 17
Autores: Shi Huang.
Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence.  This observation provoked the molecular clock hypothesis and in turn the &amp;#x2018;Neutral Theory&amp;#x2019;, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year.  Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence.  It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets.  Here, an inverse relationship between genetic diversity and epigenetic...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1751/version/1

Signaling Flux Redistribution concept can switch survival to apoptosis in cancer cells
Provedor de dados: 17
Autores: Daiki Yamada; Kentaro Hayashi; Vincent Piras; Masaru  Tomita; Masa Tsuchiya; Kumar  Selvarajoo.
The tumor necrosis factor related apoptosis-inducing ligand (TRAIL) induces apoptosis in certain types of carcinoma. However, in majority of malignant tumors, it has no effect. Here we analyzed cell survival and apoptotic pathways triggered by TRAIL.  A computational model based on perturbation-response approach with mass-action equations was developed. All 48 parameter values of the model were selected by genetic algorithm that minimizes deviation between experimental and simulation data for human fibrosarcoma cells. Subsequently, we show in silico knock-down of a cell survival pathway molecule could potentially enhance the activation of apoptosis through Signaling Flux Redistribution (SFR).
Tipo: Poster
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4375/version/1

On the nucleotide distribution in bacterial DNA sequences
Provedor de dados: 17
Autores: Marcelo Sobottka; Andrew Glenn Hart.
It is probable that the distributional structure of DNA sequences arises from the accumulation of many successive stochastic events such as nucleotide deletions, insertions, substitutions and elongations [1, 2, 3, 4, 5, 6, 7]. Although the existence of long-range correlations in non-coding portions of DNA sequences is well established [8, 9, 10, 11], first order Markov chains might well capture aspects of their nucleotide distributions [12]. Here we propose a hidden Markov model based on a coupling of an urn process with a Markov chain to approximate the distributional structure of primitive DNA sequences. Then, by supposing that a bacterial DNA sequence can be derived from uniformly distributed mutations of some primitive DNA, we use the model to explain...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5245/version/1

Counting absolute number of molecules using unique molecular identifiers
Provedor de dados: 17
Autores: Teemu Kivioja; Anna V&amp;#xe4;h&amp;#xe4;rautio; Kasper Karlsson; Martin Bonke; Sten Linnarsson; Jussi Taipale.
Advances in molecular biology have made it easy to identify different DNA or RNA species and to copy them. Identification of nucleic acid species can be accomplished by reading the DNA sequence; currently millions of molecules can be sequenced in a single day using massively parallel sequencing. Efficient copying of DNA-molecules of arbitrary sequence was made possible by molecular cloning, and the polymerase chain reaction. Differences in the relative abundance of a large number of different sequences between two or more samples can in turn be measured using microarray hybridization and/or tag sequencing. However, determining the relative abundance of two different species and/or the absolute number of molecules present in a single sample has proven much...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5903/version/1

Manual annotation of the mouse genome: HAVANA and EUCOMM
Provedor de dados: 17
Autores: Mark Thomas.
The European Conditional Mouse Mutagenesis (EUCOMM) project aims to establish a mutant resource containing up to 13,000 conditional mouse mutations in C57BL/6N embryonic stem cells. As part of this resource, up to 8,000 targeted conditional mutations will be generated for genes that can not be readily trapped by random gene trapping methods. Non-symmetrical critical exons are identified as part of the targeting approach, which when deleted produce a knockout (KO) transcript that is susceptible to nonsensemediated decay (NMD). The success of this approach is dependent on detailed and accurate genome annotation, which is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute. Based on a combination...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3181/version/1

Metabolic Network Representation in SBGN PD: EC and Identity Gate
Provedor de dados: 17
Autores: Alexander Mazein.
This presentations describes proposed changes in SBGN PD that would allow this language to be better adopted for representing metabolic network.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4974/version/1

Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules
Provedor de dados: 17
Autores: Karuna  J. Jaya Sai; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4902/version/1

Querying Drosophila In-Situ Expression Data using SPARQL and D2RQ
Provedor de dados: 17
Autores: Chris Mungall.
I describe a SPARQL endpoint for a database containing annotated images of gene expression in fruitfly embryogenesis. The images depict the actual expression of genes at a microscopic level using a technique called insitu hybridisation. The results were recorded in a relational database, and the images were annotated using the fly anatomy ontology.
Tipo: Marker Paper / Data Plan
Palavras-chave: Developmental Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5522/version/1

Desiderata for an ontology of diseases for the annotation of biological datasets.
Provedor de dados: 17
Autores: Olivier Bodenreider; Anita Burgun.
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3531/version/1

Trans-Disciplinary Protein Binding Of Drug: Docking Approach
Provedor de dados: 17
Autores: Ajeet Ajeet.
The purpose of present work is to introduce the binding of existing drugs to the trans-disciplinary protein with the help of docking procedures. Docking procedures allows virtually screening a database of compounds and predict the strongest binder based on various scoring functions. This work has been performed with the help of Molegro Virtual docker, in which two drugs are docked with their corresponding and non-corresponding (trans-disciplinary) protein. Results reveals that the protein-ligand interaction energy, hydrogen bond energy and  MolDock scores provided by molegro virtual docker, between legands (Levodopa and Acyclovir) and trans-disciplinary proteins have been equivalent or even better than that of between legands and corresponding proteins.
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6702/version/1

Towards Context Driven Modularization of Large Biomedical Ontologies
Provedor de dados: 17
Autores: Pinar Wennerberg; Sonja Zillner.
Formal knowledge about human anatomy, radiology or diseases is necessary to support clinical applications such as medical image search. This machine processable knowledge can be acquired from biomedical domain ontologies, which however, are typically very large and complex models.  Thus, their straightforward incorporation into the software applications becomes difficult. In this paper we discuss first ideas on a statistical approach for modularizing large medical ontologies and we prioritize the practical applicability aspect. The underlying assumption is that the application relevant ontology fragments, i.e. modules, can be identified by the statistical analysis of the ontology concepts in the domain corpus. Accordingly, we argue that most frequently...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3522/version/1

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) &amp;#x2013; a Genome Project funded by a Local Community Effort
Provedor de dados: 17
Autores: Taras K. Oleksyk.
The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico.  This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled.  A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (&amp;#x3c;500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6552/version/1

Plasma amino acid profile is altered by visceral fat accumulation and is a predictor of visceral obesity in humans
Provedor de dados: 17
Autores: Takayuki Tanaka; Yuko Ishizaka; Toru Mitushima; Mizuki Tani; Akiko Toda; Eiichi Toda; Minoru Okada; Hiroshi Yamamoto; Minoru Yamakado.
Background: The plasma amino acid profile can be a useful indicator in clinical settings because it changes in response to various metabolic alternations. However, the association between the plasma amino acid profile and body fat accumulation has not been evaluated in humans.Objective: This study aimed to relate plasma amino acids to visceral fat accumulation in humans because excess visceral fat raises the odds ratio of developing metabolic syndrome.Design: A total of 1,449 subjects (985 males and 464 females) who had undergone a comprehensive health screening were enrolled in this study. The visceral fat area (VFA) was determined in each subject using CT imaging. Subjects were then divided into two groups according to VFA: high-VFA (&amp;#x2265;100 cm2,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5560/version/1

Association Analysis Techniques for Discovering Functional Modules from Microarray Data
Provedor de dados: 17
Autores: Gaurav Pandey; Gowtham Atluri; Michael Steinbach; Vipin Kumar.
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the data set. The techniques in this field attempt to find groups of data objects that contain coherent values...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2184/version/1

Identification of transcription regulation associated proteins in plants and stramenopiles
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o Pach&amp;#xf3;n; Silvia Restrepo; Bernd Mueller-Roeber; Francisco Buitrago Florez.
The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7000/version/1

In Silico Characterization of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A Proteins
Provedor de dados: 17
Autores: Rajneesh  Prajapat; Avinash  Marwal; Anurag  Sahu; Rajarshi Kumar  Gaur.
We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI (ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and 13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the model. Findings of the present study provide a base...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6658/version/1

Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns.
Provedor de dados: 17
Autores: Drew Schwartz.
This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3834/version/1

BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations
Provedor de dados: 17
Autores: Rafal Woycicki; Wojciech Gutman; Zbigniew Przybecki.
Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3900/version/1

Capturing lost research
Provedor de dados: 17
Autores: Rebecca Lawrence.
A very significant proportion of valuable research conducted is lost, either after presentation at a meeting or even at the stage of the creation of the initial dataset; _F1000 Posters_ and _F1000 Research_ aim to capture this valuable information.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6175/version/1

Specificity and Evolvability in Eukaryotic Protein Interaction Networks
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10?5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 103 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/26/version/1

MIRIAM Resources: a robust annotation and cross referencing framework
Provedor de dados: 17
Autores: Camille Laibe; Nick Juty; Nicolas Le Nov&amp;#xe8;re.
_Background_&amp;#xd;&amp;#xa;More than ever, the era of data integration has highlighted the key requirement to reference specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes, these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM, &amp;#x22;http://biomodels.net/miriam/&amp;#x22;:http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Objectives_&amp;#xd;&amp;#xa;To...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5128/version/1

Ontology (Science)
Provedor de dados: 17
Autores: Barry Smith.
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type &amp;#x2013; the Gene Ontology (GO) being the most conspicuous example &amp;#x2013; are a _part of science_. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology develop&amp;#xac;ment work being undertaken in support of scientific research. Ontologies created by...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2027/version/2

PocketMatch: A new algorithm to compare binding sites in protein structures
Provedor de dados: 17
Autores: Yeturu Kalidas; Nagasuma Chandra.
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental&amp;#xd;&amp;#xa;requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring  functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of&amp;#xd;&amp;#xa;the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2142/version/2

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)
Provedor de dados: 17
Autores: Michael Hucka; Frank Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; Darren J. Wilkinson.
This is the specification for _Release 1 Candidate_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa; More information about SBML and this specification is available online at &amp;#x22;http://sbml.org/Documents/Specifications/...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4123/version/1

Overview of BioSharing
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends in both the regulatory arena and commercial science.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioSharing catalogue (www.biosharing.org) aims...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6151/version/1

Virtual Fly Brain: An ontology-linked schema of the Drosophila Brain
Provedor de dados: 17
Autores: David J. Osumi-Sutherland; Mark Longair; J. Douglas Armstrong.
Drosophila neuro-anatomical data is scattered across a large, diverse literature dating back over 75 years and a growing number of community databases. Lack of a standardized nomenclature for neuro-anatomy makes comparison and searching this growing data-set extremely arduous. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A recent standardization effort (BrainName; Manuscript in preparation) has produced a segmented, 3D model of the Drosophila brain annotated with a controlled vocabulary.  We are formalizing these developments to produce a web-based ontology-linked atlas in which gross brain anatomy is defined, in part, by labeled volumes in a standard reference brain.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed new relations that allow us to use this...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3980/version/1

OntoCAT - an integrated programming toolkit for common ontology application tasks
Provedor de dados: 17
Autores: Tomasz Adamusiak; Natalja Kurbatova; Morris A. Swertz; Helen  Parkinson.
OntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6121/version/1

Hexose-6-phosphate dehydrogenase modulates the effect of inhibitors and alternative substrates of 11[beta]-hydroxysteroid dehydrogenase 1
Provedor de dados: 17
Autores: Zolt&amp;#xe1;n Bal&amp;#xe1;zs; Lyubomir G. Nashev; Charlie Chandsawangbhuwana; Michael E. Baker; Alex Odermatt.
Intracellular glucocorticoid reactivation is catalyzed by 11[beta]-hydroxysteroid dehydrogenase 1 (11[beta]-HSD1), which functions predominantly as a reductase in cells expressing hexose-6-phosphate dehydrogenase (H6PDH). We recently showed that the ratios of cortisone to cortisol and 7-keto- to 7-hydroxy-neurosteroids are regulated by 11[beta]-HSD1 and very much depend on co-expression with H6PDH, providing cosubstrate NADPH. Here, we investigated the impact of H6PDH on the modulation of 11[beta]-HSD1-dependent inter-conversion of cortisone and cortisol by inhibitors and alternative substrates. Using HEK-293 cells expressing 11[beta]-HSD1 or co-expressing 11[beta]-HSD1 and H6PDH, we observed significant differences of 11[beta]-HSD1 inhibition by natural...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2430/version/1

FReD: The floral reflectance spectra database
Provedor de dados: 17
Autores: Sarah E. J. Arnold; Vincent Savolainen; Lars Chittka.
Floral reflectance measurements are of great value to researchers who need consider the real colour of flowers, for example in the context of how the flowers appear to their pollinators. We have thus developed the Floral Reflectance Database (FReD) to assist these researchers, gathering together floral reflectance data in a publicly available, searchable online database. The first version of the database is now available online at &amp;#x22;http://www.reflectance.co.uk&amp;#x22;:http://www.reflectance.co.uk. We anticipate that this resource will be of interest to researchers working on flower colour and animal vision.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1846/version/1

Molecular modelling and Function Prediction of hABH7, human homologue  of _E. coli_ ALKB7
Provedor de dados: 17
Autores: Mr. Shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Human homologues of ALKB protein have shown the prime role in DNA damaging drugs, used for cancer therapy. Little is known about structure and function of hABH7, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeller 9v7 to predict the 3D structure of the hABH7 protein. The tertiary structure model of hABH7, ALKBH7.B99990002.pdb was predicted and evaluated. Validation results showed 97.8% residues in favored and additional allowed regions of Ramachandran plots. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, presence of a Phe120-Gly121-Gly122 conserved pattern in...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5841/version/1

Molecular phylogenies and evolutionary behavior of AhR (aryl hydrocarbon receptor) pathway genes in aquatic animals
Provedor de dados: 17
Autores: Hailong Zhou; Ying Qu; Qinzhao Xue.
Phylogenetic analysis of AhR pathway genes and their evolutionary rate variations were studied on aquatic animals. The gene sequences for the proteins involved in this pathway were obtained from major phylogenetic groups of mollusc, amphibian, fish and aquatic mammal. These genes were distributed under four major steps of toxicology regulation: formation of cytosolic complex, translocation of AhR, heterodimerization of AhR and induction of CYP1A. The NJ, MP and ML algorithm were used on protein coding DNA sequences to deduce the evolutionary relationship for the respective AhR pathway gene among different aquatic animals. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d~N~) and synonymous nucleotide substitutions per synonymous...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2928/version/1

Generating Homology Relationships by Alignment of Anatomical Ontologies
Provedor de dados: 17
Autores: Frederic B. Bastian; Gilles Parmentier; Marc Robinson-Rechavi.
The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at &amp;#x22;http://bgee.unil.ch/.&amp;#x22;:http://bgee.unil.ch/
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3547/version/1

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The genetic equidistance result shows that sister species are approximately equidistant to an outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when different species can...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/1

The GABI Primary Database: GABIPD - Integration of Plant &amp;#x27;Omics&amp;#x27;-Data in Gene Context
Provedor de dados: 17
Autores: Diego Mauricio  Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Jost Neigenfind; Robert Wagner; Rico Basekow; Elke Weber; Sabrina Kleessen; Birgit Kersten.
GabiPD (&amp;#x22;http://www.gabipd.org/&amp;#x22;:http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data provided by the GABI community (Ria&amp;#xf1;o-Pach&amp;#xf3;n et al., 2009). Beside the data, current versions of useful tools are being made accessible via GabiPD, such as MapMan (Usadel et al., 2005) and SATlotyper (Neigenfind et al., 2008). Access to GabiPD is provided via either the web interface or WebServices.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In GabiPD, twenty different plant species are currently represented with the model plant A. thaliana on top followed by the crop plants S. tuberosum and H. vulgare....
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3218/version/1

How do we quantify biodiversity? All the evidence in one place.
Provedor de dados: 17
Autores: Olga Lyashevska.
Biodiversity is a multi-dimensional concept that is represented by a large variety of measures. This complexity and lack of consistency limits the development of a coherent scientific understanding of biodiversity and how properties, such as ecosystem services, may depend on it. Here, I demonstrate that the formal discipline of creating a relational database (RDB) for information about biodiversity and its measures,  is a useful tool in organising such knowledge into coherent sense. Following steps of the logical database design and data normalization to build a RDB, results in a formal definition of biodiversity within a well defined concept structure; mapping rules between the concepts of biodiversity and entities of RDB and a consistent information...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3327/version/1

The Open Practises E-Science Network (OPEN)
Provedor de dados: 17
Autores: Cameron  Neylon.
A grant proposal submitted for support to fund a research network focussed on identifying and dealing with the practical issues of enabling open practise in research. The text of the proposal was written by a large number of people and coordinated by Cameron Neylon.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1370/version/1

PID: The Pathway Interaction Database
Provedor de dados: 17
Autores: Carl F. Schaefer; Kira Anthony; Shiva Krupa; Jeffrey Buchoff; Matthew Day; Timo Hannay; Kenneth H. Buetow.
The Pathway Interaction Database (PID, &amp;#x22;http://pid.nci.nih.gov&amp;#x22;:http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2243/version/1

Finding Bicliques in Digraphs: Application into Viral-host Protein Interactome
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay; Ujjwal Maulik.
We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein interaction graphs. Strong and significant bicliques of HIV-1 and human proteins are derived using the proposed methodology, which provides insights into some novel regulatory functionalities in case of the acute immunodeficiency syndrome in human.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7148/version/1

OntoFox:
Provedor de dados: 17
Autores: Zuoshuang Xiang; Yongqun He.
OntoFox (&amp;#x22;http://ontofox.hegroup.org/&amp;#x22;:http://ontofox.hegroup.org/) is a web server that facilitates ontology development by automatically fetching ontology terms and their annotations from existing ontologies and saving the results in importable RDF/OWL format. OntoFox is developed based on the MIREOT principle. Currently OntoFox can fetch ontology annotations from &amp;#x3e;10 existing ontologies. OntoFox provides an efficient approach to promote ontology sharing and interoperability.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3528/version/1

Structural requirements for the binding affinity of some small, non&amp;#x2013;peptide C5a receptor antagonists
Provedor de dados: 17
Autores: Haiying Xie; Weiming  Wang; Ziqiang  Xie; Hong  Chen; Kexian  Chen.
Complement anaphylatoxin 5a (C5a) has been recognized as a potent therapeutic target for anti-inflammatory therapy, thus, blocking the action of C5a on its binding receptors may provide an effective treatment of a variety of inflammatory diseases. However, there have been few clinically available non-peptide C5a receptor antagonists disclosed at present. In pursuit of better anti-inflammatory drugs, quantitative structure&amp;#x2013;activity relationship studies were carried out in a series of non-peptide C5a receptor antagonists with binding activity using different physicochemical descriptors. The conventional best 2D-QSAR models were developed using a training set of 35 molecules and an external test set of 8 molecules by genetic function approximation...
Tipo: Manuscript
Palavras-chave: Chemistry; Immunology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6630/version/1

The NCI-Nature Pathway Interaction Database: A cell signaling resource.
Provedor de dados: 17
Autores: Shiva Krupa; Kira Anthony; Jeffrey  R. Buchoff; Matthew Day; Timo Hannay; Carl  F. Schaefer.
The Pathway Interaction Database (*PID*, http://pid.nci.nih.gov) is a freely available&amp;#xd;&amp;#xa;collection of curated and peer-reviewed signaling pathways composed of human&amp;#xd;&amp;#xa;biomolecular interactions and cellular processes. Created in a collaboration between the&amp;#xd;&amp;#xa;U.S. National Cancer Institute and Nature Publishing Group, the database is a research&amp;#xd;&amp;#xa;tool for cell biologists, biochemists, computational biologists and bioinformaticians.&amp;#xd;&amp;#xa;The PID offers a range of tools to facilitate pathway exploration. Users can browse the&amp;#xd;&amp;#xa;pre-defi ned set of pathways and also create interaction network maps centered on&amp;#xd;&amp;#xa;a single molecule of interest or an extensive list...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1311/version/1

The Gene Ontology&amp;#x27;s Reference Genome Project: &amp;#xb;A Unified Framework for Functional Annotation across Species
Provedor de dados: 17
Autores: Pascale Gaudet; Reference Genome Group.
Complete functional annotation of genomes is a powerful tool for researchers; however, such annotation is a time-consuming task limited by the availability of experimental data. The function of genes for which there is no experimental data can often be predicted via comparison to related, annotated sequences of known function. We describe here the Reference Genome project, an effort from the Gene Ontology (GO) Consortium to fully annotate twelve genomes to rigorous standards: human, plus eleven organisms that are important models in biomedical research, including mouse, fly, zebrafish, yeast and _E. coli_. To achieve this, we examine existing experimentally based annotations in a phylogenetic context in order to infer the function(s) of ancestral proteins...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3150/version/1

Docking and QSAR Studies of Camptothecin Derivatives as Inhibitor of DNA Topoisomerase-I
Provedor de dados: 17
Autores: Dharmendra  K. Yadav; Feroz  Khan; Santosh K. Srivastava.
Camptothecin (CPT) is a cytotoxic quinoline alkaloid which inhibits the DNA enzyme Topoisomerase-I (Topo-I) and has shown remarkable anticancer activity in preliminary clinical trials. The major limitation is its low solubility and high adverse reaction. In the studied work, we performed molecular docking of CPT derivatives against Topo-I and developed the quantitative structure activity relationship (QSAR) model for anticancer activity screening. For QSAR, we used CPT and other anticancer drugs with its IC50 values. We used a total of forty seven anticancer drugs as training set and eight compounds as test set and thirty derivatives of CPT as query set. Total of fifty two chemical descriptors were used for the quantitative data calculation. Only four...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5773/version/1

Reflect: Augmented Browsing for the Life Scientist
Provedor de dados: 17
Autores: Evangelos Pafilis; Se&amp;#xe1;n I. O&amp;#x27;Donoghue; Lars J. Jensen; Heiko Horn; Michael Kuhn; Nigel P. Brown; Reinhard Schneider.
Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect (&amp;#x22;http://reflect.ws&amp;#x22;:http://reflect.ws) that can be installed as a plug-in to Firefox or Internet Explorer. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds, and without affecting document layout. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. Clicking on a tagged small...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3212/version/1

Changes in Scholarly Communication and the Potential Impact on Biocuration
Provedor de dados: 17
Autores: Philip Bourne.
Open access in particular and changes in on-line scholarship have the potential to impact biocuration which often involves translating information currently read in papers to knowledge that is found in a variety of biological resources. The implication of these changes in scholarly communication to the biocuration process will be discussed with references to our work and that of others.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3229/version/1

Progress report: SBML  Level 3 package FBA
Provedor de dados: 17
Autores: Brett G. Olivier; Frank T. Bergmann.
The SBML Level 3 &amp;#x22;FBA&amp;#x22; package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5033/version/1

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates
Provedor de dados: 17
Autores: Bjoern Peters; Alan Ruttenberg; Jason Greenbaum; Melanie Courtot; Ryan Brinkman; Patricia Whetzel; Daniel Schober; Susanna Assunta Sansone; Richard Scheuerman; Philippe Rocca-Serra.
The developers of the Ontology of Biomedical Investigations (OBI) primarily use Prot&amp;#xe9;g&amp;#xe9; for editing. However, adding many classes with similar patterns of logical definition is time consuming, error prone, and requires the editor to have some expertise in OWL. Therefore, the process is poorly suited for a large number of domain experts who have limited experience Prot&amp;#xe9;g&amp;#xe9; and ontology development. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions yet requires minimal manual intervention by OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format which is...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3970/version/1

Modeling Resting-State Brain Functional Integration
Provedor de dados: 17
Autores: Xi-Nian Zuo.
During the past 15 years, resting state fMRI has rapidly emerged as a powerful and reliable approach to explore the human brain architecture. There are two concepts of human brain working mechanism: functional segregation and integration. In this report, I mainly focused on functional integration. Relevant mathematics and statistics in this &amp;#xfb01;eld are reviewed including both seed-based and independent component analysis (ICA) resting state functional connectivity. Moreover, ICA was applied to study the abnormalities of a fronto-striatal-insular network in ADHD. First, mathematical methods to investigate the functional integration by using rs-fMRI were reviewed as well as more details on ICA. Two topics have been addressed: ranking components and...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4380/version/1

Signi&amp;#xfb01;cance tests for comparing digital gene  expression pro&amp;#xfb01;les
Provedor de dados: 17
Autores: Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira.
Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/2

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.&amp;#xd;&amp;#xa;Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4068/version/1

Hierarchical Model Composition updates
Provedor de dados: 17
Autores: Lucian Smith.
A summary of the status of the hierarchical model composition package for SBML Level 3, and of its current implementation.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6402/version/1

Slug-based epithelial-mesenchymal transition gene signature is associated with prolonged time to recurrence in glioblastoma
Provedor de dados: 17
Autores: Wei-Yi Cheng; Jessica J. Kandel; Darrell J. Yamashiro; Peter Canoll; Dimitris Anastassiou.
Background&amp;#xd;&amp;#xa;We previously identified a precise stage-associated gene expression signature of coordinately expressed genes, including the transcription factor Slug (SNAI2) and other epithelial mesenchymal transition (EMT) markers, present in samples from publicly available gene expression datasets in multiple cancer types. The expression levels of the co-expressed genes vary in a continuous and coordinate manner across the samples, ranging from absence of expression to strong co-expression of all genes. These data suggest that tumor cells may pass through an EMT like process of mesenchymal transition to varying degrees.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Findings&amp;#xd;&amp;#xa;Here we show that this signature in glioblastoma multiforme...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6544/version/1

IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels
Provedor de dados: 17
Autores: Joanna L. Sharman; Valerie A. Hale; Rebecca Hills; Edward M. Rosser; Martin Jones; Stuart D. Greenhill; Anthony J. Harmar; NC - IUPHAR.
The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry.  Individual gene pages provide a comprehensive description of the genes and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays and biologically...
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3230/version/1

F1000 and data publishing
Provedor de dados: 17
Autores: Rebecca Lawrence.
Utility of the BioSharing standards and the BioDBCore registry in F1000 journal publishing.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6172/version/1

The human genome is composed of viral DNA: Viral homologues of the protein products cause Alzheimer&amp;#x27;s disease and others via autoimmune mechanisms.
Provedor de dados: 17
Autores: Christopher J. Carter.
The human genome is composed of millions of fragmented contiguous viral DNA sequences, dating from the dawn of evolution and reflecting retroviral insertions over millions of years of coexistence. Herpes and other viral insertion points correspond to the locations of over 120 Alzheimer&amp;#x27;s disease susceptibility genes and to linkage hotspots. The greater the number of pathogen matches, the more important the gene. These DNA sequences are translated into short contiguous 5-12 amino acid stretches (vatches), identical in viruses and man, and in other pathogens implicated in Alzheimer&amp;#x27;s disease (_Borrelia_, _Chlamydia_, _Helicobacter_, _C. Neoformans_ , _P. Gingivalis_). _C. Neoformans_, which has been associated with a rare but curable form...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4765/version/1

Evaluation of the Cell Ontology (CL)
Provedor de dados: 17
Autores: Lindsay G. Cowell.
An ontological representation of the entities relevant to biological research is urgently needed.  The cell ontology developed by Bard and colleagues (CL) (Bard et al. 2005) makes a significant contribution towards fulfilling this need by providing an ontology of cell types.  The CL has already proven useful for data annotation (e.g. Grumbling et al. 2006), although the ontology&amp;#x2019;s potential utility goes well beyond that specific application.  For example, using the number of distinct cell types in an organism as a measure of biological complexity, Vogel and Chothia (2006) compared the proteomes of 38 organisms of varying complexity and identified patterns in the evolution and expansion of protein domain superfamilies.  This work has implications...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3971/version/1

GOAssay: from Gene Ontology to Assays IDentifiers - Towards Automatic Functional Annotation of PubChem BioAssays
Provedor de dados: 17
Autores: Rajarshi Guha; Julien Gobeill; Patrick Ruch.
OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;METHODS and MATERIALS: The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;AVAILABILITIES: the database is hosted by the...
Tipo: Poster
Palavras-chave: Chemistry; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3176/version/1

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: Mr. Shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/2

SBML Level 3 Brief Update
Provedor de dados: 17
Autores: Michael Hucka.
SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional &amp;#x22;packages&amp;#x22; that add topic-specific features to the Core to support more specialized models and application areas.  In this presentation, I provide a very brief overview of SBML Level 3 activity areas.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5011/version/2

Cluster Analysis of Breast Cancer Microarray Data
Provedor de dados: 17
Autores: Kirtan  P. Dave.
High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. The recent development gene expression microarray and related technology provide to an opportunity to perform more detail profiling of the disease However, whole-genome approaches are still relatively new and critics have been quick to highlight, non-overlapping results from groups testing similar hypotheses. In this canopy, cluster analysis helps to reduce complex multivariate data and may be used to devise in the development of classification systems or taxonomies by gene ontology.
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4936/version/1

Protein Regge Trajectories, Phase Coexistence and Loop Aetiology in Alzheimers Disease
Provedor de dados: 17
Autores: Antti Niemi; Andrey Krokhotin.
Alzheimer&amp;#x27;s disease has a devastating impact on its victims by causing severe neurodegeneration in the brain that leads to a certain death. Only in a small number of cases can the origin be traced to a variety of genetic mutations, for the greater part the reasons for its onset are unclear.The defining factor is the formation of extracellular senile amyloid plaques in the brain, but therapeutic approaches to remove them remain to be shown effective in humans. Here we investigate physical processes that are involved in the release of the extracellular amyloid, by scrutinizing the intracellular domain of its precursor protein. We identify a phenomenon that has never before been discussed in the context of protein research: Like ice and water...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6030/version/1

Process Makna - A Semantic Wiki for Scientific Workflows
Provedor de dados: 17
Autores: Adrian Paschke; Zhili Zhao.
Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5633/version/1

Underlying Mathematics in Diversification of Human Olfactory Receptors in Different Loci
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Arunava Goswami.
As per conservative estimate, approximately (51-105) Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pair of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for huge number of pure and complex odorants. ORs form the largest known multi-gene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5475/version/1

Foregut microbiome in development of esophageal adenocarcinoma
Provedor de dados: 17
Autores: Liying Yang; William  E. Oberdorf; Erika Gerz; Tamasha  Parsons; Pinak  Shah; Sukhleen Bedi; Carlos W. Nossa; Stuart  M. Brown; Yu Chen; Mengling Liu; Michael Poles; Fritz Francois; Morris Traube; Navjeet  Singh; Todd Z. DeSantis; Gary L. Andersen; Monika  Bihan; Les Foster; Aaron  Tenney; Daniel  Brami; Mathangi  Thiagarajan; Indresh K. Singh; Manolito   Torralba; Shibu  Yooseph; Yu-Hui  Rogers; Eoin L. Brodie; Karen E. Nelson; Zhiheng Pei.
Esophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years.  This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett&amp;#x2019;s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are &amp;#x3e;15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5026/version/1

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/version/2

Text mining for Swiss-Prot curation: A story of success and failure
Provedor de dados: 17
Autores: Anne-Lise Veuthey; Violaine Pillet; Yum Lina Yip; Patrick Ruch.
A text mining group has been set up at the Swiss Institute of Bioinformatics, with objective to develop and adapt information retrieval and extraction tools to help Swiss-Prot curators in their daily annotation work.  After over 7 year activities, this group has gathered a significant amount of experience about the need in text mining for biocuration.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The first observation we made is that there is no &amp;#x201c;in-a-box&amp;#x201d; solution which can satisfy every needs. Each curator has his/her own strategy to find information from the literature and none of the existing information retrieval systems is able to compete with it, more for reason of habits than for reason of performance. Second observation: to be...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3166/version/1

Enhanced display of scienti&amp;#xfb01;c articles using extended metadata
Provedor de dados: 17
Autores: Roderic D. M. Page.
Although the Web has transformed science publishing, scientific papers themselves are still essentially &amp;#x22;black boxes&amp;#x22;, with much of their content intended for human readers only.  Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article  metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical  coordinates,  publishers could greatly  increase the scientific value of their digital content. At the same time this will provide  novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3173/version/1

Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm
Provedor de dados: 17
Autores: M. S. Jeevitesh; Narayan Behera; Justin Jose; Krishna Kant; Alpana Dey.
Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4258/version/1

Current State of JUMMP
Provedor de dados: 17
Autores: Martin Gr&amp;#xe4;&amp;#xdf;lin.
In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment there is no tool available to bring a model from development in the lab directly to the peer-reviewed online resource.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The JUMMP (JUst a Model Management Platform) project aims at providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models can be developed and shared privately and later on be made available to the curation process and the broader community. Each change to a model is recorded in a version...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6371/version/1

Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.
Provedor de dados: 17
Autores: Kentaro Onizuka.
The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3043/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5272/version/1

A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel M&amp;#xf6;ller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and (c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a terminology on radiology.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/2

Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.  Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner.  A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/2

SBRML Interoperability
Provedor de dados: 17
Autores: Frank T. Bergmann.
This presentation summarizes an initial meeting of SED-ML and SBRML editors in order to facilitate reuse and sharing of components of each language.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6329/version/1

Extending libSedML to support CellML models
Provedor de dados: 17
Autores: David Nickerson; Dongxue Amy You.
libSedML is a collection of libraries and tools developed in support of the Simulation Experiment Markup Language (&amp;#x22;SED-ML&amp;#x22;:http://sed-ml.org/). &amp;#x22;libSedML&amp;#x22;:http://libsedml.sourceforge.net/ is implemented in C# and provides libraries for processing SED-ML documents and for running the numerical simulations required for the encoded simulation experiment(s). SED-ML supports models encoded in any encoding format, although predominantly expected to be an XML based encoding. To date, however, libSedML has only supported performing simulations using models encoded in the Systems Biology Markup Language (&amp;#x22;SBML&amp;#x22;:http://sbml.org/). The presented project looked at using the &amp;#x22;CellML...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5897/version/1

COMBINE - What it is, what it could be
Provedor de dados: 17
Autores: Nicolas Le Novere.
The &amp;#x27;COmputational Modeling in BIology&amp;#x27; NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6332/version/1

A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices
Provedor de dados: 17
Autores: Andras Gelencser; Themistoklis Prodromakis; Christofer Toumazou; Tamas Roska.
In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6664/version/1

Evolution of the Protein Universe. Time Scales and Selection
Provedor de dados: 17
Autores: Marco Cosentino Lagomarsino; Alessandro Sellerio; Philip Heijning; Bruno Bassetti.
The availability of many genome sequences gives us abundant information, which is, however, very difficult to decode. As a consequence, in order to advance our understanding of biological processes at the whole-cell scale, it becomes very important to develop higher-level, synthetic descriptions of the contents of a genome. At the protein level, an effective scale of description is provided by protein domains. Domains are independent unit-shapes (or &amp;#x22;folds&amp;#x22;) forming proteins. They are structurally stable and have thermodynamic origin. A domain determines a set of potential functions and interactions for the protein that carries it, for example DNA- or protein-binding capability or catalytic sites. Protein domains are found on genomes with...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1376/version/1

Ontology-&amp;#xad;based Tools to Enhance the Curation Workflow
Provedor de dados: 17
Autores: Trish Whetzel.
In order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms.  However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation.  We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator.  The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology.  The widgets provide a variety of functionality including term autocompletion and ontology visualization.  The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5213/version/1

Study Of Phenothiazine On p53 Core Domain Mutant Y220C: Finding The Anti-tumor Activity Of Phenothiazine
Provedor de dados: 17
Autores: Asif Husain Naqvi; Hardik H. Sheth; Vijay Kumar; Suchindran H S; Vivek Gupta.
The tumor suppressor protein p53 is a transcription factor that plays a key role in the prevention of cancer development. The p53 cancer mutation Y220C induces formation of a cavity on the protein&amp;#x27;s surface that can accommodate stabilizing small molecules. We have attempted with the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm to elucidate the extent of specificity of p53 cancer mutation Y220C towards different class of Phenothiazines (an anti-cancer agent). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The 393 residue p53 tumor suppressor protein exists in a dynamic equilibrium to form homotetramers. Each chain comprises several functional domains. The N terminal part of the protein consists of the...
Tipo: Presentation
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6135/version/1

Valid and efficient formula for free energy difference from nonequilibrium work
Provedor de dados: 17
Autores: Liao Y. Chen.
Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1911/version/1

Publishing Interactive Articles: Integrating Journals And Biological Databases
Provedor de dados: 17
Autores: Karen Yook; Arun  Rangarajan; Hans-Michael Muller; Paul Sternberg; Tracey DePellegrin-Connelly; Tim Schedl; Mike Cherry; William  Gelbart; Juancarlos Chan; Stephen  Haenel; Lolly  Otis; Sharon Faelten; Marek S. Skrzypek; Steven Marygold.
In collaboration with the journal GENETICS, we&amp;#x27;ve developed and launched a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities linked to corresponding resource pages in &amp;#x22;WormBase&amp;#x22;:http://www.wormbase.org/ (WB). Our interactive articles allow a reader to click on over ten different data type objects (gene, protein, transgene, etc.) and be directed to the relevant webpage. This seamless connection from the article to summaries of data types promotes a deeper level of understanding for the na&amp;#xef;ve reader, and incisive evaluation for the sophisticated reader. Further, this collaboration allows us to identify and collect information before the publication of the article. The...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5146/version/1

Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case
Provedor de dados: 17
Autores: Jos&amp;#xe9; Luiz Rybarczyk; Mauro A. A. Castro; Rodrigo J. S. Dalmolin; Jos&amp;#xe9; C. F. Moreira; Leonardo G. Brunnet; Rita M. C. de Almeida.
A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3869/version/1

SBML layout and render news
Provedor de dados: 17
Autores: Ralph Gauges.
This presentation gives a short overview on the layout and render extension to SBML and on recent software updates we did that support those two extensions.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5117/version/1

The BRIF (Bioresource Research Impact Factor) as a tool for improving bioresource sharing in biomedical research
Provedor de dados: 17
Autores: Laurence Mabile; Raymond Dalgleish; Gudmundur  A. Thorisson; Myl&amp;#xe8;ne Desch&amp;#xea;nes; Robert Hewitt; Jane Carpenter; Elena Bravo; Pierre-Antoine Gourraud; Paul Hofman; Jennifer Harris; Maria Angeles Munoz-Fernandes; Anne Cambon-Thomsen.
The central aim of the BRIF (Bioresource Research Impact Factor) initiative is to construct a quantitative parameter to evaluate bioresources, modeled to some degree on the Journal Impact Factor (JIF), and to provide guidance and methodology for optimizing recognition of bioresources, their use and their sharing at international level. To implement this concept an international working group has been set up. Specific tasks have been assigned to several sub-groups: BRIF digital identifier schemes; BRIF parameters, measures and indicators; journal guidelines for resource citing and referencing; policies for bioresource access and sharing. These are discussed in the present manuscript.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6568/version/1

Is your phylogeny informative? Measuring the power of comparative methods
Provedor de dados: 17
Autores: Peter Ralph; Graham Coop; Carl Boettiger.
Phylogenetic comparative methods have become all but ubiquitous in only a few decades, forcing us to reconsider if information from a phylogenetic tree can justify the results. Existing approaches to this question have been inadequate and do not scale with tree size or the ability to resolve branches. For instance, selection between phylogenetic models typically based on information criteria fails to adequately reflect this uncertainty, and can lead to preference for arbitrarily complicated models. Common measures of phylogenetic signal tend to characterize the goodness-of-fit of a Brownian motion model to the data, rather than indicate whether the data is sufficient to confidently distinguish between different hypotheses. We present a Monte Carlo based...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6453/version/1

SBML Level 3 Brief Update
Provedor de dados: 17
Autores: Michael Hucka.
SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional &amp;#x22;packages&amp;#x22; that add topic-specific features to the Core to support more specialized models and application areas.  In this presentation, I provide a very brief overview of SBML Level 3 activity areas.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5011/version/1

A Systems Biology Approach towards Deciphering the Unfolded Protein Response in Huntington&amp;#x27;s Disease
Provedor de dados: 17
Autores: Kameshwar R. Ayasolla; Ravi K. R. Kalathur; Matthias  E. Futschik.
Although the disease causing gene huntingtin has been known for some time, the exact cause of neuronal cell death during _Huntington&amp;#x27;s disease_ (HD) remains unknown. One potential mechanism contributing to the massive loss of neurons in HD brains might be the _Unfolded Protein Response_ (UPR) which is activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response, UPR upregulates transcription of chaperones, temporarily attenuating new translation and activates protein degradation via the proteasome. However, at high levels of ER stress, UPR signalling can contribute to neuronal apoptosis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our primary aims include (a) construction of the UPR signalling network, (b)...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7078/version/1

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/2

Broadening Pfam Protein Sequence Annotations
Provedor de dados: 17
Autores: Jaina Mistry; Penny Cogghill; Sean Eddy; Rob Finn; John  Tate; Alex Bateman.
Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It comprises two parts: (1) Pfam-A families, which are fully annotated and consist of a representative seed alignment, HMMs, and a full alignment comprising all sequences that score above the curated threshold; (2) Pfam-B families, which are automatically generated clusters of domains not matched by Pfam-A but that often indicate conserved sequence regions. Pfam release 23.0 predicts at least one Pfam-A domain on 74% of the sequences in UniProtKB, and predicts either a Pfam-A or Pfam-B domain on 93% of the sequences in UniProtKB.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the ever increasing rate of deposition of new proteins of all...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3194/version/1

Treemap Versus BPA (Again): A Response to Dowling
Provedor de dados: 17
Autores: Roderic Page; Michael Charleston.
TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling&amp;#x2019;s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling&amp;#x2019;s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1030/version/1

SBFC - The Systems Biology Format Converter Framework
Provedor de dados: 17
Autores: Martina Kutmon; Nicolas Rodriguez.
The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable.  Recently a prototype has been developed with OSGi to achieve a more modular framework structure. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6370/version/1

Two &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a &amp;#x27;normal&amp;#x27; globular and a &amp;#x27;pathological&amp;#x27; amyloid version. The underlying normal &amp;#x27;protein folding code error network&amp;#x27; is found to have one major, highly dominant, &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/1

Development of Java based graphical user interface for Diagnosis of Hepatitis UsingI Mixture of Expert
Provedor de dados: 17
Autores: M Shankaracharya; Suchitra Kumari; Ambarish S. Vidyarthi.
Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7093/version/1

GabiPD: Gabi Primary Database - a plant integrative &amp;#x2018;omics&amp;#x2019; database in GABI-FUTURE
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Robert Wagner; Elke Weber; Birgit Kersten.
GabiPD (&amp;#x22;http://gabi.rzpd.de&amp;#x22;:http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species.  Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1684/version/1

Better Analysis, Better Acceptance &amp;#x2010;Take up the Challenge of Publishing in Bioinformatics
Provedor de dados: 17
Autores: Malay Bhattacharyya.
This presentation teaches the novice in bioinformatics research to publish quality analysis in good venues.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7124/version/1

The likelihood that two proteins interact might depend on the proteins&amp;#x27; age
Provedor de dados: 17
Autores: Pedro Beltrao.
It has been previously shown [1] that _S. cerevisiae_ proteins preferentially interact with proteins of the same estimated likely time of origin.  To study this observation further, the protein interaction networks of _S. cerevisiae_ and _H. sapiens_ were analyzed taking into account an estimate for the age of the proteins in these species.  These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins&amp;#x2019; age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/22/version/1

A Universal Carrier Test for the Long Tail of Mendelian Disease
Provedor de dados: 17
Autores: Balaji S. Srinivasan; Jason Flannick; A. Scott Patterson; Christopher C. Chang; Tuan Pham; Sharon Young; Amit Kaushal; James J. Lee; Pasquale Patrizio; Eric A. Evans.
*Background:* &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Mendelian disorders are individually rare but collectively common, forming a &amp;#x22;long tail&amp;#x22; of genetic disease. More than 20 million people worldwide suffer from a disease in this long tail before the age of 25, with minorities and developing countries at highest risk and with the number of carriers far in excess of this figure. Importantly, the Jewish community&amp;#x2019;s campaign for universal Tay-Sachs screening shows that these incurable diseases can nevertheless be prevented if carrier status is known before conception. A single highly-accurate assay for the long tail of Mendelian disease would allow us to scale this successful campaign up to the general population, thereby improving...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4192/version/1

Alignment of Linear Biochemical Pathways Using Protein Structural Classification
Provedor de dados: 17
Autores: Sridhar Hariharaputran; Thoralf T&amp;#xf6;pel; Timm Oberwahrenbrock; Ralf Hofest&amp;#xe4;dt.
Metabolic, signaling and regulatory pathways form the basis of biological processes and are important for the analysis of cellular behavior and evolution. This paper presents an approach of aligning biochemical pathways on the basis of the structure of involved proteins and their classification. The suitable information is retrieved from an integrated database system.&amp;#xd;&amp;#xa;SIGNALIGN is available at: http://agbi.techfak.uni-bielefeld.de/signalign/index.jsp  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1943/version/1

QSAR and Docking Studies of Gallic Acid Derivatives for Anticancer and Immunomodulatory Activity
Provedor de dados: 17
Autores: Dharmendra Kumar Yadav; Feroz Khan; Arvind Singh  Negi.
Immuno-modulation is the process of alteration in immune response due to foreign intrusion of molecules inside the body. In the present communication QSAR and molecular docking studies for immuno-modulatory activity of derivatives of gallic acid were performed. Molecular docking studies showed higher binding affinity with INF&amp;#x3b1;-2, IL-6, and IL-4 receptors. Binding site residues indicate hydrogen bonds formation with gallic acid derivative compounds G-3, G-4, G-5, G-6, G-7 and G-10. Further screening through quantitative structure activity relationship model establishes the immuno-modulatory activity of the compounds G-4, G-7, G-9, G-10, G-12 and G-13. Activity was predicted through a robust statistical model, developed by forward feed multiple...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6620/version/1

Applying Biomedical Ontologies on Semantic Query Expansion
Provedor de dados: 17
Autores: Andre Bechara; Maria Luiza C. Machado; Vanessa Braganholo.
*1- Introduction*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The interpretation of a question (or information need) depends, among other things, of a series of lexicalsemantic relations that complement and help the cognitive process of answering that information need. Despite this fact, currently used information retrieval mechanisms take few advantages of the semantic interpretation of users&amp;#x2019; information needs (usually specified through keywords). In most of the cases, those mechanisms are based on keyword matching, and thus are excessively dependant on the query and document terms.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;There are several past results showing that, in general, information retrieval based on domain knowledge decreases the accuracy of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3550/version/1

Structural and functional validation of Microsystin synthetases
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6835/version/1

An optimized energy potential can predict SH2 domain-peptide interactions
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families.  Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains.  The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family.  Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically.  Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1881/version/1

Malaria Diagnosis and the Plasmodium Life Cycle: the BFO Perspective
Provedor de dados: 17
Autores: Werner Ceusters; Barry Smith.
Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We address a challenge to this realist approach relating to the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3960/version/1

Improving metabolite evaluation in integrated pathway analysis
Provedor de dados: 17
Autores: Rasanpreet Kaur; Anwesha  Dutta; Martina Kutmon; Martijn Iersel; Chris Evelo.
Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6970/version/1

Diagnostic robustness of DNA microarrays in the classification of acute leukemia
Provedor de dados: 17
Autores: Marie Loh; Adrian Mondry.
Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This raises the question whether DNA microarrays are robust diagnostic tools.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In order to address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was calculated using Cohen&amp;#x27;s &amp;#x3ba;-score.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The inter-test agreement scores were 0.15 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.68 for gene selection, and 0.60 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.89 for sample classification....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1056/version/1

CellML: current status and future directions
Provedor de dados: 17
Autores: David Nickerson.
An overview of the current status of the CellML project and some ideas on where things are heading.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6417/version/1

Ontology Mapping of PATO to YATO for the improvement of interoperability of quality description
Provedor de dados: 17
Autores: Hiroshi Masuya; Nobuhiko Tanaka; Kazunori Waki; Tatsuya Kushida; Kouji Kozaki; Riichiro Mizoguchi.
To facilitate broad interoperability for phenotype information between different ontological frameworks, we developed a reference ontology, PATO2YATO_Quality, with the careful mapping of terms of PATO which is a quality ontology commonly used for biological phenotype annotation to the latest top-level ontology, YATO, which represents advanced modeling of quality-related concepts.  As a result, YATO framework enabled to describe changes of phenotypic qualities along the courses of time in ontologically correct way and sophisticated classification and representation of interrelationships among quality-related concepts to provide fully integration of qualitative values and quantitative values obtained from phenotyping experiments and advanced representation...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3508/version/1

neXtProt, a new knowledgebase  on human proteins
Provedor de dados: 17
Autores: Lydie Lane.
In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from ~20&amp;#x27;300 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5104/version/1

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6^-10^9^ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/2

Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies
Provedor de dados: 17
Autores: Benoit H. Dessailly; Oliver C. Redfern; Christine A. Orengo.
The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.&amp;#xd;&amp;#xa;A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes.  These large superfamilies are generally very diverse, spanning a wide range of functions,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2214/version/1

Sequence-specific Solution Structures of the Four Isosequential Pairs of Single-stranded DNAs and RNAs
Provedor de dados: 17
Autores: Subhrangsu  Chatterjee; Wimal  Pathmasiri; Jyoti Chattopadhyaya.
The role of the sequence-context in the self-organization of four single-stranded (ss) isosequential pairs of DNAs (1 &amp;#x2013; 4) and RNAs (5 &amp;#x2013; 8), [d/r-(5&amp;#x27;C^1^A^2^X^3^G^4^Y^5^A^6^C^7^): X^3^ = A or C, Y^5^ = A or C; sequence variations: 2^2^ = 4], has been elucidated by NMR-constrained Molecular Dynamics (MD) simulations (2 ns). Following sequence-specific observations have been made from the solution NMR and the NMR constrained MD simulation study: (i) Analysis of the NOESY footprints, mainly (H8/H6)~n~ to (H1&amp;#x27; and H3&amp;#x27;)~n-1~ contacts, of ssDNAs (1 - 4) and ssRNAs (5 &amp;#x2013; 8) in the aqueous medium have shown that all ssDNAs (1 - 4) and ssRNAs (5 - 8) adopt right handed stacked helical structures in the NMR...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1685/version/1

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems
Provedor de dados: 17
Autores: Jyl Boline; Michael Hawrylycz; Robert W. Williams.
The goal of this workshop was to survey current activities and plans related to development of mouse and rat brain digital atlasing systems. The workshop discussed needs for and types of coordinated action that will ensure rapid progress, compatibility, and dissemination with use of novel technological approaches. The report summarizes the state-of-the-art in the field and provides recommendations for actions.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1046/version/1

Nanoconfinement of spider silk fibrils begets superior strength, extensibility and toughness
Provedor de dados: 17
Autores: Tristan Giesa; Melis Arslan; Nicola Pugno; Markus J. Buehler.
Silk is an exceptionally strong, extensible and tough material made from simple protein building blocks. The molecular structure of dragline spider silk repeat units consists of semi-amorphous and nanocrystalline beta-sheet protein domains. Here we show by a series of computational experiments how the nanoscale properties of silk repeat units are scaled up to create macroscopic silk fibers with outstanding mechanical properties despite the presence of cavities, tears and cracks. We demonstrate that the geometric confinement of silk fibrils to diameters of 50&amp;#xb1;30 nm width is critical to facilitate a powerful mechanism by which hundreds of thousands of protein domains synergistically resist deformation and failure to provide enhanced strength,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5916/version/2

Lead identification and docking studies of metastatic protein human mitogen activated protein kinase kinase4
Provedor de dados: 17
Autores: Harika  Meduru; Dibyabhaba Pradhan; Manne  Munikumar; Amineni Umamaheswari.
Human dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4) is a direct activator of MAP kinases in response to various environmental stresses or mitogenic stimuli. Upon phosphorylation, MAP2K4 has been shown to activate MAPK8, MAPK9 and MAPK14/p38 but not MAPK1/ERK2 or MAPK3/ERK1. Over expression of MAP2K4 causes carcinogenic effects, such as ovarian cancer, colorectal cancer, prostate cancer and pancreatic cancer. Our present study was carried out to design a potent drug molecule against MAP2K4 to control over expression. As there is no experimentally determined structure for MAP2K4, the homology modeling technique of Modeller9v7 was implemented to generate a MAP2K4 3D model based on the co-crystal structure of MAP2K6 (PDB ID: 3FME) with...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5457/version/1

Ten thousand times faster: Classifying multidimensional data on a spiking neuromorphic hardware system.
Provedor de dados: 17
Autores: Michael Schmuker; Daniel Br&amp;#xfc;derle; Sven Schrader; Martin Nawrot.
Discrimination of sensory inputs is a computational task that biological neuronal systems perform very efficiently. Assessing the principles in those systems is a promising approach to develop technical solutions for many problems, such as data classification. A particular problem here is to train a classifier in a supervised fashion to discriminate classes in multidimensional data. We implemented a network of spiking neurons that solves this task using a neuromorphic hardware system, that is, analog neuronal circuits on a silicon substrate. This system enables us to do high-performance computation in a biologically inspired way, with spiking neurons as computational units. In this contribution, we illustrate solutions to technical challenges that occur...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6547/version/1

Co-expression Toggling of MicroRNAs in Alzheimer&amp;#x2019;s Brain
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present the findings on how microRNA expression profiles changes in Alzheimer&amp;#x27;s brain.
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7123/version/1

Geographical and chronological origin and evolution of Hepatitis C Virus.
Provedor de dados: 17
Autores: amjesh revikumar; Achuthsankar  S. Nair; Sugunan V.S.
Hepatitis C Virus (HCV) infection is a major health problem that leads to cirrhosis and hepatocellular carcinoma. World over, more than 270-300 million people are estimated to be infected with the virus. HCV is a positive sense single stranded RNA virus and replicates within the cytoplasm of the hepatocyte using its own RNA dependent RNA polymerase (RdRp). RdRp does not have proof reading capacity, and hence generates mutants of the virus, resulting in a chronic infection, which ultimately ends in hepatocellular carcinoma.  Such mutations have given rise to several genotypes, subtypes, strains and variants with significant difference in disease outcomes.  The mutation rate varies among genotypes, subtypes, strains or even in different sites of the genome....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6710/version/1

QSAR &amp;#x26; DOCKING APPROACH - POTENTIAL WAY TO NEW DRUG  DEVELOPMENT
Provedor de dados: 17
Autores: Ajeet Ajeet.
With today&amp;#x27;s need for discovering and developing new drug molecules, it is necessary to accept ways to save time and wet lab essentials.  To this end, the QSAR and molecular docking approach is used widely by us.  This poster describes steps for developing a new or modified moiety of a drug molecule.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7071/version/1

Computational binding mechanism of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (MurA) with inhibitors fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine analog RWJ-110192, purine analog  RWJ-140998, 5-sulfonoxy-anthranilic aci
Provedor de dados: 17
Autores: C. M. Anuradha; B. Babajan; M. Chaitanaya; C. Rajasekhar; Suresh Kumar Chitta.
Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world&amp;#x27;s population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial cell wall biosynthesis.  In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by homology modeling and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3731/version/1

Protein and DNA evolution: Statistics and combinatorics are the rules of the game
Provedor de dados: 17
Autores: Arunava Goswami; Srimoyee Duttagupta; Chirantan Chakraborty; Amita Pal; Pabitra Pal Choudhury; Sk Sarif Hassan.
Let us assume AVMAYDRYVAIC or MAYDRYVAICCP, most important signature domain of&amp;#xd;&amp;#xa;olfactory receptor (OR) gene family assembled in evolution following simplest possible laws of statistics which says the addition of V after A in AVMAYDRYVAIC or addition of A after M are independent events. There are 20 amino acids present in nature so the probability of joint occurrence of such events is 1/400. Therefore for making a contiguous string of&amp;#xd;&amp;#xa;AVMAYDRYVAIC or MAYDRYVAICCP, the probability would be 1 out of 2012. Over millions of years of evolution this has certainly happened and that is why we see such a signature sequence in OR1D2, OR1D subfamily member 2 as per &amp;#x22;HORDE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4859/version/1

3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone
Provedor de dados: 17
Autores: Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone.  Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol.  To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone.  These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol.  Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR].  Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5.  Mutant...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6216/version/1

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value.   With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial.  While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains.  In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/1

Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor
Provedor de dados: 17
Autores: Abhishek Kumar.
Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7016/version/1

SBGN support in BIOCHAM
Provedor de dados: 17
Autores: Dragana Jovanovska; Fran&amp;#xe7;ois Fages; Sylvain Soliman.
BIOCHAM - BioChemical Abstract Machine is an environment for modeling biological systems and formalizing experimental knowledge. Mainly, it is  composed of:&amp;#xd;&amp;#xa;* a rule-based language for modeling biochemical systems (compatible with SBML)&amp;#xd;&amp;#xa;* several simulators (boolean, differential, stochastic)&amp;#xd;&amp;#xa;* a temporal logic based language to formalize the temporal properties of a biological system and validate models with respect to such specifications,&amp;#xd;&amp;#xa;* unique features for developing/correcting/completing/reducing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;BIOCHAM is presented with a user...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5189/version/1

NPO:  Ontology for Cancer Nanotechnology Research
Provedor de dados: 17
Autores: Dennis Thomas; Rohit Pappu; Nathan Baker.
We present the design and development of NanoParticle Ontology (NPO). The ontology is implemented in the Ontology Web Language (OWL).  The domain terms in NPO currently represent entities, which describe knowledge about physical, chemical, and functional properties of nanoparticles characterized in cancer nanotechnology research. The upper-level of NPO is formed using terms from the Basic Formal Ontology (BFO).
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3514/version/1

OpenCell - Status and plans
Provedor de dados: 17
Autores: Alan Garny.
Update on the current status of OpenCell (&amp;#x22;www.opencell.org&amp;#x22;:http://www.opencell.org) and discussion of our plans for a new version of OpenCell.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5131/version/1

Towards Context Driven Modularization of Large Biomedical Ontologies
Provedor de dados: 17
Autores: Pinar Wennerberg; Sonja S. Zillner; Alexander Cavallaro.
Formal knowledge about human anatomy, radiology or diseases is necessary to support clinical applications such as medical image search. This machine processable knowledge can be acquired from biomedical domain ontologies, which however, are typically very large and complex models.  Thus, their straightforward incorporation into the software applications becomes difficult. In this paper we discuss first ideas on a statistical approach for modularizing large medical ontologies and we prioritize the practical applicability aspect. The underlying assumption is that the application relevant ontology fragments, i.e. modules, can be identified by the statistical analysis of the ontology concepts in the domain corpus. Accordingly, we argue that most frequently...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3523/version/1

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees
Provedor de dados: 17
Autores: Amelia G. White; Avi Ma&amp;#x27;ayan.
Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that &amp;#x201c;connect&amp;#x201d; the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1768/version/1

Hierarchical nanomechanics of collagen microfibrils
Provedor de dados: 17
Autores: Alfonso Gautieri; Simone  Vesentini; Alberto Redaelli; Markus J. Buehler.
Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to connective tissues. Collagen is also the dominating material in the extracellular matrix (ECM) and is thus crucial for cell differentiation, growth and pathology. However, fundamental questions remain with respect to the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response. By using x-ray diffraction data of a collagen fibril reported by Orgel et al. (Proceedings of the National Academy of Sciences USA, 2006) in combination with protein structure identification methods, here we present an experimentally validated model of the nanomechanics of a...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4995/version/1

The &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) specification
Provedor de dados: 17
Autores: Pelin  Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette  Johnston; Guy Cochrane; Robert  Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine  A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn  Maguire; Barbara A. Meth&amp;#xe9;; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; J&amp;#xf6;rg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aym&amp;#xe9; Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Gl&amp;#xf6;ckner.
We present the Genomic Standards Consortium&amp;#x2019;s (GSC) &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5252/version/1

Towards an Ontological Representation of Resistance: The Case of MRSa
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. Resistance terms from various existing ontologies are examined and found to be either overly narrow, inconsistent, or&amp;#xd;&amp;#xa;otherwise problematic. We propose a more coherent ontological representation using the antibiotic resistance in Methicillin-Resistant _Staphylococcus aureus_ (MRSa) as a case study.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3474/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (Version 2.0)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/2

Biological networks and epistasis in genome-wide association studies
Provedor de dados: 17
Autores: Mathieu Emily; Leif  Schauser; Thomas Mailund; Mikkel H. Schierup.
Over the last few years, technological improvements have made possible the genotyping of hundreds of thousands of SNPs, enabling whole-genome association studies. The first genome-wide association studies have recently been completed to detect causal variant for complex traits. Although increasing evidence suggests that interaction between loci, such as epistasis between two loci, should be considered, most of these studies proceed by considering each SNP independently. One reason for this choice is that looking at all pairs of SNPs increases dramatically the number of tests (approximatively 50 billions of tests for a 300,000 SNPs data set) that faces with computational limitation and strong multiple testing correction.&amp;#xd;&amp;#xa;We proposed to...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/466/version/1

D2RQ Platform &amp;#x2013; Treating Non-RDF Databases as Virtual RDF Graphs
Provedor de dados: 17
Autores: Radoslaw Oldakowski.
D2RQ is a complete solution to map and expose relational databases as RDF.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5660/version/1

Reading the Secrets of Biological Fluctuations
Provedor de dados: 17
Autores: Carl Boettiger.
I explore tools and applications of the van Kampen expansion of the stochastic master equation in several areas of population biology.  I highlight fluctuation-dissipation and fluctuation-enhancement regimes, using information from noise to help model choice, and examples where noise changes the macroscopic dynamics of a system.
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4949/version/1

Identification and correction of systematic error in high-throughput sequence data
Provedor de dados: 17
Autores: Frazer Meacham; Dario Boffelli; Joseph Dhahbi; David I. K. Martin; Meromit Singer; Lior Pachter.
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed &amp;#x201c;next-gen&amp;#x201d; sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5989/version/1

Function, Role, and Disposition in Basic Formal Ontology
Provedor de dados: 17
Autores: Robert Arp; Barry Smith.
Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO&amp;#x2019;s general structure and use.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1941/version/1

DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences
Provedor de dados: 17
Autores: Xiaolong Wang; Shuang-yong  Xu; Deming  Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4898/version/1

BRIF and Variant Databases
Provedor de dados: 17
Autores: Raymond Dalgleish.
Databases of sequence variation in human genes (LSDBs) are an important resource for biology and medicine. Currently, the measurement of importance is not as objective as it might be and the establishment of impact factors would be of benefit to those who curate LSDBs. Specific issues relating to such databases are discussed.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5586/version/1

Deterministic individual-based cellular automata modelling of single species population dynamics
Provedor de dados: 17
Autores: Lev Kalmykov; Vyacheslav Kalmykov.
This presentation was created to characterise foundations of cellular automata modelling of single species population dynamics. We show models of single species population growth based on deterministic birth-death-regeneration process and demonstrate a relationship between fecundity rate and population growth rate. Our models provide mechanistic simulation of logistic-like and double logistic-like curves of population growth that is not possible in the classical Verhulst model (logistic growth model). This method is deterministic individual-based and is based on logical &amp;#x201c;if-then&amp;#x201d; statements only. As this method is bottom-up mechanistic and provides a direct visual insight into dynamics of complex systems, we used it to study...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6661/version/1

R tools for MicroRNA pathway analysis
Provedor de dados: 17
Autores: Anwesha Dutta; Pooja Mandaviya; Rasanpreet Kaur; Sandeep  Mallya.
In the early 2000s, microRNAs (miRNAs) were discovered as segments of a new class of highly conserved and small non-coding RNA molecules of 20-25 nucleotides that are transcribed from DNA.&amp;#xd;&amp;#xa;They do not translation into proteins, rather they inhibit protein expression by binding to the 3&amp;#x2019;untranslated regions (3&amp;#x2019; UTRs) of specific mRNA targets (that is/are complementary to them) and guiding their translational repression or complete degradation and gene silencing. With this, miRNAs provide a second level of regulation beyond primary gene expression. Integrative study of cellular pathways is pivotal to understanding the functions of individual genes and proteins in terms of systems and processes that contribute to normal...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5918/version/1

The Jena Library of Biological Macromolecules - JenaLib
Provedor de dados: 17
Autores: Rolf Huehne; Juergen Suehnel.
The JenaLib database (&amp;#x22;www.fli-leibniz.de/IMAGE.html&amp;#x22;:http://www.fli-leibniz.de/IMAGE.html) offers value-added information for all Protein Data Bank (PDB) and Nucleic Acid Database (NDB) entries. This includes:&amp;#xd;&amp;#xa;(1) atlas pages and entry lists, (2) PDB sequence information extracted from atomic coordinates, (3) PDB/UniProt sequence alignments that clearly indicate gaps, mutations, numbering irregularities and modified residues, (4) integration of data on single amino acid polymorphisms (SAPs), PROSITE motifs, exon structure and SCOP/CATH/Pfam domains with PDB, GO and taxonomy information, (5) display of these data in the sequence/alignment viewer and in the Jmol-based molecule viewer Jena3D...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3114/version/1

A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model, a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006).  It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/2

A Reaction Route Approach to Flux Balance Analysis
Provedor de dados: 17
Autores: Ilie  Fishtik.
Background: Flux balance and network-based pathway analyses are theoretical tools aimed to find optimal steady state flux distributions in a metabolic network subject to additional constraints on the rates of the reaction steps. Although these methods are mathematically accurate, there are several physicochemical and computational aspects that are questionable and misleading. In particular, it is well known that the flux balance analysis may result in multiple flux distributions for the same objective function.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The flux balance and network-based pathway analyses are reformulated in terms of reaction routes (RRs), a theoretical framework that has been developed by Horiuti over 50 years ago. Not only does the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2788/version/1

Standards and infrastructure for managing experimental metadata
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra.
*See also &amp;#x22;related poster&amp;#x22;:http://precedings.nature.com/documents/3144/version/1*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Today&amp;#x2019;s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as &amp;#x2018;omics&amp;#x2019;). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Standards initiatives normally cater to particular domains. However, several synergistic...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3145/version/1

Towards a Modelling Ecosystem for Libraries of Modular, Reusable Components
Provedor de dados: 17
Autores: Michael T. Cooling.
CellML 1.1 [1] is an XML-based model exchange protocol with inherent support for modularity.&amp;#xd;&amp;#xa;To assist in answering complex biomedical research questions, we are developing libraries of modular model components that facilitate mathematical model construction. &amp;#xd;&amp;#xa;Stored in the online, publicly accessible CellML Repository [2], the libraries vary from genetic and associated regulatory components for Synthetic Biology [3] to quantifying the Systems Biology of cardiovascular wall mal-adaptation [4,5].&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Currently however, using the libraries is not as easy as it should be. Here I describe progress towards a modelling ecosystem to encompasses component search and retrieval,...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6392/version/1

Lightning Talk: Biopython (bio) Geography Module
Provedor de dados: 17
Autores: Nicholas J. Matzke.
For Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython.  The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank.  Application of the tool to a historical biogeography study on bivalves will be illustrated.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:&amp;#xd;&amp;#xa;&amp;#x22;http://www.biopython.org/DIST/LICENSE&amp;#x22;:http://www.biopython.org/DIST/LICENSE&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The module is described, and a tutorial is presented, on the Biopython...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4676/version/1

A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Provedor de dados: 17
Autores: Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6391/version/1

Variability In The Ecoraces Of Tropical Tasar Sillkworm Antheraea Mylitta  Drury
Provedor de dados: 17
Autores: Ajit Kumar Sinha.
Tropical tasar silkworm, Antheraea mylitta Drury is exploited in countries for commercial silk production and improved varieties of these silkworms can be evolved by employing various breeding techniques. As the insect has established itself in various forms of ecological populations (Commonly called as ecoraces) in different geographical niches of the country depending on food plants and micro-environmental conditions available to them, the species exists in the form of nearly 44 ecoraces (Singh and Srivastava,1997, Srivastava,2002 and Srivastava et at. 2007) distributed over different states. However, due to free interbreeding in nature for centuries, the fauna is highly heterogeneous.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Tasar culture is a forest based...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6161/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/1

Cardiovascular Gene Ontology Annotation Initiative
Provedor de dados: 17
Autores: Varsha K. Khodiyar; Daniel G. Barrell; Peter Scambler; Mike Hubank; Rolf Apweiler; Philippa J. Talmud; Ruth C. Lovering.
Gene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional annotation to proteins across a wide range of species (&amp;#x22;www.geneontology.org&amp;#x22;:http://www.geneontology.org).  The BHF-UCL team is funded by the British Heath Foundation to supply GO annotation specifically for human proteins involved in cardiovascular (CV) processes.  This is the first time that a physiological process-centered approach has been used for human protein GO annotation.  Experienced GO curators from the BHF-UCL team work alongside the bench scientists from the CV genetics group at University College London. By working in a CV dedicated environment the GO curators are able to build up their expertise in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3135/version/1

Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Provedor de dados: 17
Autores: T. Michael Keesey.
_Names on Nodes_^1^ is an open&amp;#x2011;source^2^ Flex application which utilizes a mathematical approach to automate the application of phylogenetically&amp;#x2011;defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (NEXUS, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. _Names on Nodes_ stores hypotheses as MathML, an XML&amp;#x2011;based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4653/version/1

Identification of small molecule inhibitor of cyclophilin-A using high throughput virtual screening and molecular docking Studies
Provedor de dados: 17
Autores: Pallapotu Navya; I Vani Priyadarshini; Amineni Umamaheswari.
The inhibitors of cyclophilin A (CyPA) have drawn a great deal of attention due to their promising potential as small-molecule therapeutics for the treatment of cardiovascular diseases. This ultimately prompts to explore structural geometries of these inhibitors to obtain insights on next generation CyPA inhibitors through rational drug designing. Herein, 2D similarity search for the seven CyPA inhibitors was performed using Ligand.Info database. Small subsets of 2800 molecules from one million compounds were predicted to have activity against cardiovascular drug target CyPA. The binding strength of 2800 ligands with CyPA was assessed through molecular docking analysis using Schr&amp;#xf6;dinger software 2011. The CyPA co-crystal structure and ligand...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6529/version/1

Gene Curation Software at the Rat Genome Database (RGD)
Provedor de dados: 17
Autores: Stanley J. F. Laulederkind; Mary  Shimoyama; Brad Taylor; Victoria  Petri; Timothy F. Lowry; G. Thomas Hayman; Shur-Jen Wang; Jennifer R. Smith; Rajni Nigam; Jeff De Pons; Weisong Liu; George Kowalski; Melinda R. Dwinell; Diane H. Munzenmaier; Howard J. Jacob.
At model organism databases data is curated for numerous biological categories using various ontologies and vocabularies.  The Rat Genome Database (RGD) uses four different ontologies to standardize annotation information for genes and their associations with disease, phenotypes, and pathways. For manual gene curation this is all done in a single user interface of a web-based annotation tool developed at RGD.  The same interface can be used for the curation of QTLs and strains. The development of the tool has been achieved through a collaboration of curators and software developers.  Features have been tailored to the needs of the curators to allow optimum efficiency of the data entry portion of the curation process.  Annotations using the Gene Ontology,...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5058/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/1

A set of ontologies to drive tools for the control of vector-borne diseases
Provedor de dados: 17
Autores: Pantelis Topalis; Emmanuel Dialynas; Elvira Mitraka; Elena Deliyanni; Inga Siden-Kiamos; Christos Louis.
We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3464/version/1

A Note on Measures of Single Timeseries Activity in Resting-State fMRI Studies
Provedor de dados: 17
Autores: Xi-Nian Zuo.
In statistics, signal processing and mathematical finance, a time series  is a sequence of data points, measured typically at successive times spaced at uniform time intervals. Here, I only focus on the discrete time series. The motivation of writing this methodology note is to clarify the relationship between the measures to quantify activity of an observed timeseries. Particularly, focus one several measures used in recently emerged field of resting-state fMRI studies. Although all these measures have been extensively developed in EEG or other timeseries studies, many researchers focusing on various applications in or new comers to this new field need to know existed measures and the relationships among these measures.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4379/version/1

Developing a Text Mining Prototype for the Comparative Toxicogenomics Database Biocuration Process
Provedor de dados: 17
Autores: Thomas C. Wiegers.
Understanding interactions between environmental chemicals and genes provides insights into the mechanisms of chemical action, disease susceptibility, therapeutic drug interactions, and toxicity. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org) is a web-based resource that integrates diverse information for the cross-species analysis of chemical, gene, and disease relationships.  Much of the data contained in CTD is manually gathered by biocurators; CTD integrates data curated manually from over 10,000 scientific documents.  CTD biocurators manually curate chemical-gene and chemical/gene-disease interactions from the scientific literature using controlled vocabularies.  Unfortunately, there are many more scientific documents available...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3142/version/1

A comparative analysis of 21 literature search engines
Provedor de dados: 17
Autores: Kshitish  K. Acharya; Greta Kasliwal; Haritha Haridas.
With increasing number of bibliographic software, scientists and health professionals either make a subjective choice of tool(s) that could suit their needs or face a challenge of analyzing multiple features of a plethora of search programs. There is an urgent need for a thorough comparative analysis of the available bio-literature scanning tools, from the user&amp;#x2019;s perspective. We report results of the first time semi-quantitative comparison of 21 programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. &amp;#xd;&amp;#xa;Some of the important...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2101/version/1

Signatures of spatial organizations &amp;#x2013; From the universe of proteins to the universe in general
Provedor de dados: 17
Autores: Aditya Mittal.
Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that,...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6038/version/1

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments
Provedor de dados: 17
Autores: Toshinori Endo; Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Kohji Hotta; Yutaka Satou; Lixy Yamada; Michio Ogasawara; Hiroki Takahashi; Ayako Nakajima; Mia Nakachi; Mamoru Nomura; Junko Yaguchi; Alu Konno; Sasakura Yasunori; Akiyasu C. Yoshizawa; Hisaaki Taniguchi; Chisato Yamasaki; Miho Sera; Tadashi Imanishi; Kazuo Inaba.
CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata.  Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans.  Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data.  The CIPRO database is aimed at not only collecting published data, but also presenting unique information,...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5435/version/1

GabiPD: GABI primary database - a plant integrative &amp;#x27;omics&amp;#x27; database
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Robert Wagner; Jost Neigenfind; Elke Weber; Svenja Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different &amp;#x27;omics&amp;#x27; fronts are incorporated in GabiPD (i.e., genomics,...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2221/version/1

In silico comparative study of epitopes predicted from different strains of genus parvovirus.
Provedor de dados: 17
Autores: Rahul  B. Chamute; Mahadev A. Jadhav; Anant Patil.
Parvoviruses are typically linear, non-segmented single-stranded DNA viruses, with an average genome size of 5000 nucleotides. Parvoviruses are some of the smallest viruses found in nature. Some have been found as small as 23 nm. Many types of mammalian species have a strain of parvovirus associated with them. Parvoviruses tend to be specific about the taxon of animal they will infect, but this is a somewhat flexible characteristic. Thus, all strains of parvovirus will affect dogs, wolves, and foxes, but only some of them will infect human. Parvovirus is treated with the help of vaccines but the traditional vaccine development process is very expensive and unsafe, with the help of insilico software tools and databases we can predict the epitopes of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5574/version/1

Hierarchical nanomechanics of collagen microfibrils
Provedor de dados: 17
Autores: Alfonso Gautieri; Simone  Vesentini; Alberto Redaelli; Markus J. Buehler.
Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to organisms and is thus the prime construction materials in biology. Collagen is also the dominating material in the extracellular matrix and its stiffness controls cell differentiation, growth and pathology. However, the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response remains unknown. By using x-ray diffraction data of a collagen fibril (Orgel et al., PNAS, 2006) here we present an experimentally validated model of the nanomechanics of a collagen microfibril that incorporates the full biochemical details of the amino acid sequence of constituting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4995/version/2

GO faster ChEBI with Reasonable Biochemistry
Provedor de dados: 17
Autores: Duncan Hull.
Chemical Entities of Biological Interest (ChEBI) [1] is a database and ontology that represents knowledge about more than 15,000 small molecules and their biochemistry. The database does not currently use description logic reasoning or OWL, but is investigating this possibility for better, cheaper and faster ontology development in the future. This poster describes four specific problems and solutions to reasoning in ChEBI: 1. Using necessary and sufficient conditions 2. identifying inconsistencies 3. Improving alignment with the the Gene Ontology (GO) 4. Reasoning with chemical structures.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2435/version/1

High-order chromatin architecture determines the landscape of chromosomal  alterations in cancer
Provedor de dados: 17
Autores: Geoffrey  Fudenberg; Gad Getz; Matthew Meyerson; Leonid Mirny.
The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the evidence for two major forces, spatial chromosome structure and purifying (or negative) selection, that shape the landscape of somatic copy-number alterations (SCNAs) in cancer. Using a maximum likelihood framework we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule (FG) model. This analysis provides evidence that the distribution of chromosomal alterations in cancer is spatially related to...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6356/version/1

Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth  Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon  Cockell; Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall&amp;#x2019;Olio; Chris Evelo.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered. Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see description from Joel Spolsky), a comparable site for programmers.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Users find the site valuable both for answers to questions they have and as a reference. Since the content can also be viewed without registration the site likely reaches a larger audience. For instance, BioStar questions are often referenced on Twitter and FriendFeed. This leads to the question of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6041/version/1

Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth
Provedor de dados: 17
Autores: I. C. Baianu.
Experimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7128/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/2

BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)
Provedor de dados: 17
Autores: Sridhar Hariharaputran.
The rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater biological insight than is possible with individual information sources. Furthermore, the rapidly growing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5164/version/1

Identification of Potent Leads for Human cAMP Dependent Protein Kinase Catalytic Subunit Alpha: A Strategic Application of Virtual Screening for Cancer Therapeutics
Provedor de dados: 17
Autores: Sandeep Swargam; Dibyabhaba Pradhan; Amineni  Umamaheswari.
The advancement in therapeutic applications focused on specific macromolecular compounds of deregulated cell signaling pathways bestowed novel approach to design the ligands as drug molecules against several life threatening diseases such as Cancer. In humans, protein kinase A is one of the important kinases those were involved in cell signaling mechanism. cAMP, G-proteins and ATP molecules were required for activation of protein kinase A (PKA), upon activation, PKA catalytic subunits (PRKACA,PRKACB and PRKACG) undergoes many cellular functions like cell proliferations, cell cycle regulation, and survival of cells through acting on many substrates. Overexpression of extracellular cAMP dependent protein kinase A catalytic subunits (PRKACA) causes severe...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4903/version/1

_In silico_ microRNA identification from  paprika (_Capsicum annuum_) ESTs
Provedor de dados: 17
Autores: T. M. Manila; A. Riju; K. Lakshmi Priya Darshini; A. Chandrasekar; S. J. Eapen.
A total of 33,311 Expressed Sequence Tags (EST) of paprika were mined from the GenBank EST database. The redundancy of the EST sequences was removed using CAP3 and it resulted 4,541 contigs 8,539 singletons as nonredundant data sets. The microRNAs were predicted using the program miRNAfinder. This program predicted a total of 85 miRNAs miRNAs. Another study was carried out to find the homologes miRNA using blast based tool named &amp;#x201c;miRseeK&amp;#x2019; A total of 13 miRNAs with significant similarity with the plant miRNAs were obtained from paprika ESTs. The targets of the predicted miRNAs were found using the program miRU2. Findings suggest that most miRNAs play an important role in plant development, signal transduction, protein degradation and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3737/version/1

Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
Provedor de dados: 17
Autores: David Tollervey; Jonathan Houseley.
Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST) databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems, involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4203/version/1

SGN Database: From QTLs to Genomes
Provedor de dados: 17
Autores: Isaak  Y. Tecle; Naama Menda; Robert Buels; Lukas Mueller.
Quantitative trait loci (QTL) analysis is used to dissect the genetic basis underlying polygenic traits. Several public databases have been storing and making QTL data available to research communities. To our knowledge, current QTL databases rely on manual curation where curators read literature and extract relevant QTL information to store in databases. Evidently, this approach is expensive in terms of expert manpower and time use and limits the type of data that can be curated. At the Solanaceae Genomics Network (SGN) (&amp;#x22;http://sgn.cornell.edu&amp;#x22;:http://sgn.cornell.edu), we have developed a database to store raw phenotype and genotype data from QTL studies, perform, on the fly, QTL analysis using R/QTL statistical software...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3160/version/1

Protein Ontology and Community Curation
Provedor de dados: 17
Autores: Cecilia Arighi.
The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways,...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3169/version/1

OntoCAT - a simpler way to access ontology resources
Provedor de dados: 17
Autores: Tomasz Adamusiak; Tony Burdett; K Joeri van der Velde; Niran Abeygunawardena; Despoina Antonakaki; Helen Parkinson; Morris Swertz.
OntoCAT is an open source package developed to simplify the task of querying heterogeneous ontology resources. It supports local ontologies in OBO and OWL format as well as public repositories NCBO BioPortal and EBI Ontology Lookup Service (OLS). It is available from &amp;#x22;http://ontocat.sourceforge.net&amp;#x22;:http://ontocat.sourceforge.net
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4666/version/1

In search of the right literature search engine(s)
Provedor de dados: 17
Autores: Akhilesh K. Bajpai; Sravanthi Davuluri; Haritha Haridas; Greta Kasliwal; Deepti H; Sreelakshmi KS; Darshan S. Chandrashekar; Pranami Bora; Mohammed Farouk; Neelima Chitturi; Samudyata V; ArunNehru KP; Kshitish K. Acharya.
*Background*&amp;#xd;&amp;#xa;Collecting scientific publications related to a specific topic is crucial for different phases of research, health care and &amp;#x2018;effective text mining&amp;#x2019;. Available bio-literature search engines vary in their ability to scan different sections of articles, for the user-provided search terms and/or phrases. Since a thorough scientific analysis of all major bibliographic tools has not been done, their selection has often remained subjective. We have considered most of the existing bio-literature search engines (http://www.shodhaka.com/startbioinfo/LitSearch.html) and performed an extensive analysis of 18 literature search engines, over a period of about 3 years. Eight different topics were taken and about 50...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/2101/version/3

Update: MIRIAM Registry and SBO
Provedor de dados: 17
Autores: Nick Juty.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We also describe current status and planned improvements to this system, as well as providing an update on the Systems Biology ontology since the last COMBINE meeting in Edinburgh (2010). &amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6405/version/1

Combining systems biology and pharmacokinetics - drug cardiotoxicity assessment
Provedor de dados: 17
Autores: Sebastian Polak.
Cardiotoxicity assessment is a compulsory element of the drug development process required by drug agencies including the FDA and EMA. The risk of fatal ventricular arrhythmia triggered by drugs is the rationale for such requirements. Over the last two decades prolongation of QT interval has been responsible for the withdrawal of several drugs from the market and extensive black box labeling restrictions. Although there are a number of mechanisms by which drugs may lead to QT prolongation, inhibition of the potassium channels encoded by the hERG gene has been a cause in many cases. Thus, it is not surprising that interaction with the hERG channel has become a major pharmacological safety concern. It can be reliably assessed with use of in silico realized...
Tipo: Presentation
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5900/version/1

Viral organization of human proteins
Provedor de dados: 17
Autores: Stefan Wuchty.
A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes....
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2041/version/1

Challenges in Whole-Genome Annotation of Pyrosequenced Fungal Genomes
Provedor de dados: 17
Autores: Alan Kuo; Igor Grigoriev.
Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454 sequenced fungal genome that is larger than a yeast (&amp;#x3e;30 Mbp). The pezizomycotine (filamentous ascomycote) _Aspergillus carbonarius_ belongs to the _Aspergillus_...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3191/version/1

Phylontal: Using Phylogenies to Align Phenotype Ontologies
Provedor de dados: 17
Autores: Peter Midford.
Phylontal is a simple approach to generating alignments of ontologies or constructs based on controlled vocabularies that correspond to tips on a phylogeny.  The method requires only a downpass (tips to root) and thus constructing alternative alignments from multiple or uncertain phylogenies may be relatively inexpensive.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4628/version/1

Human Transcript Database Search Showed Existence Of Extremely Short Introns
Provedor de dados: 17
Autores: Makoto Shimada; Noriko Haraguchi; Akila Mayeda.
Since pre-mRNA splicing is processed by a spliceosome that is a huge complex consists of RNAs and as many as 200 proteins, it is considered that minimum intron size is limited by molecular size of the spliceosome.  To understand splicing mechanism, we investigate human intron size distribution using annotated transcriptome database, H-InvDB.  Distribution of obtained intron length shows that there is a mode at 83 nt in length with 4049 transcripts and number of introns decreases drastically in shorter than 65 nt, where numbers of transcripts in each locus also decrease.  However, some introns less than 65 nt are observed, both shows high Codon Adaptation Index (CAI) and also observed orthologous transcripts in other mammals.  These suggests that there is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5115/version/1

Dissecting the Biological Motherboard (Systems Biology and Beyond)
Provedor de dados: 17
Autores: Abhay Krishna; Ajit Narayanan.
Genome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take environment-genome interactions into account.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Machine learning approaches are now increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are increasingly...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2003/version/1

SBML Team facilities &amp;#x26; software
Provedor de dados: 17
Autores: Frank T. Bergmann; Sarah M. Keating.
This presentation provides a brief overview of the new SBML online validator and the updates in the SBML Tool Matrix. This presentation ends with an update on the new version of the SBML Toolbox.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6401/version/1

Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it&amp;#x2019;s going to take is kind of depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/1

Report on the status of SBGN ER and proposed extensions
Provedor de dados: 17
Autores: Nicolas Le Novere.
The Systems Biology Graphical Notation (SBGN) is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology. SBGN is made up of  three orthogonal languages, representing different visions of biological systems. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted. In this presentation I recapitulated why SBGN was developed, and discuss the current state of the Entity Relationships language. I then describe the coming evolutions and the pending issues.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4963/version/1

ODIN: An Advanced Interface for the Curation of Biomedical Literature
Provedor de dados: 17
Autores: Fabio Rinaldi; Simon Clematide; Gerold Schneider; Martin Romacker; Therese Vachon.
We present *ODIN* (Ontogene Document INspector): a system for interactive curation of biomedical&amp;#xd;&amp;#xa;literature, developed within the scope of the &amp;#x22;*SASEBio* project&amp;#x22;:http://www.ontogene.org/projects/sasebio/ (Semi-Automated Semantic Enrichment of the Biomedical Literature), as a collaboration between the &amp;#x22;OntoGene group&amp;#x22;:http://www.ontogene.org/ at the University of Zurich and the NITAS/TMS group of Novartis Pharma AG. The purpose of the system is to allow a human annotator/curator to leverage upon the results of an advanced text mining system in order to enhance the speed and effectiveness of the annotation process. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The OntoGene system takes as input a document (e.g a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5169/version/1

Nuclear Medicine and Early Discovery of Disease
Provedor de dados: 17
Autores: I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major consequences for the society.&amp;#xd;&amp;#xa;Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) CAT/CT and Nuclear Magnetic Resonance Imaging (NMRI/MRI). These nuclear medicine techniques are discussed together with their clinical and research applications to early diagnosis of Alzheimer&amp;#x27;s Disease (AD) and cancers. Novel approaches to early detection and modeling of AD and cancers are then...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6196/version/1

Grofit: Fitting biological growth curves
Provedor de dados: 17
Autores: Matthias Kahm; Guido Hasenbrink; Hella Lichtenberg-Frate; Jost Ludwig; Maik Kschischo.
Growth experiments are routinely used to analyze basic properties of a given organism or cellular model. Similarly, within the TRANSLUCENT project the characterization of cellular growth and particularly under conditions of high extra cellular potassium or sodium is an important task. Any growth analysis should ideally reveal a relationship between the concentration of a compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such approaches. Within the software package, specifically tailored regression and bootstrapping techniques are utilized to statistically...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4508/version/1

Balancing noise and plasticity in gene expression
Provedor de dados: 17
Autores: Djordje Bajic; Juan F. Poyatos.
Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6729/version/1

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Provedor de dados: 17
Autores: Peter Csermely; Robin Palotai; Ruth Nussinov.
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (&amp;#x2018;discrete breathers&amp;#x2019;) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4422/version/1

Identification of Unique proteins of Candida albicans as Antifungal Drug Targets
Provedor de dados: 17
Autores: Himanshu Tripathi; Abha  Meena; Feroz  Khan; Suaib  Luqman.
There are growing examples of drug resistance in the fungal pathogens to evade antifungal drugs by developing mutation in the key targeted enzymes and high expression of drug transporter genes including ABC transporters and MFS transporters. This led to the urgent need to identify novel (unique or essential to fungus) targets that can be used in development of potential antifungal drugs. We have used a comparative genomics approach to find out novel targets in opportunistic fungus, Candida albicans responsible for severe infection in immunocompromised humans. To identify novel targets we have analyzed available total 14,633 protein sequences (proteome) of C. albicans [SC5314] retrieved through RefSeq, an experimentally curated reference sequence database...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6619/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine-v.4.0
Provedor de dados: 17
Autores: I Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6273/version/1

A simple clustering of the BioModels database using semanticSBML
Provedor de dados: 17
Autores: Falko Krause; Wolfram Liebermeister.
The BioModels database contains biochemical network models in SBML format, in which the biochemical meaning of elements is specified by MIRIAM-compliant RDF annotations. We used these annotations to define a similarity measure for models, scoring the overlap of the biochemical systems described. Based on this score, we used two-way clustering to detect groups of similar models and groups of co-occuring model elements. To recognize and compare biochemical elements, we used routines from the software semanticSBML. A Python script extracts all MIRIAM annotations (regardless of their qualifiers) using the semanticSBML annotation classes. The result is a matrix in which the rows represent the models (e.g. BioModel 001), while the columns represent specific...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3444/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Mona M. Aly; Jeffery  Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar  Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/3

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on the connection...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/2

Rule Responder: A Rule-Based Semantic eScience Service Infrastructure
Provedor de dados: 17
Autores: Adrian Paschke; Zhili Zhao.
To a large degree information and services for chemical e-Science have become accessible -anytime, anywhere -but not necessarily useful. The Rule Responder eScience middleware is about providing information consumers with rule-based agents to transform existing information into relevant information of practical consequences, hence providing control to the end-users to express in a declarative rule-based way how to turn existing information into personally relevant information and how to react or make automated decisions on top of it.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5632/version/1

A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains coexpressed in normal samples in a tissue-specific manner
Provedor de dados: 17
Autores: Weiyi Cheng; Dimitris Anastassiou.
A recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3 and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12 (aka SDF1)....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6813/version/1

DDBJ Activities: Contribution to the Research in Information Biology
Provedor de dados: 17
Autores: Jun Mashima; Takehide Kosuge; Toshihisa Okido; Yuichi Kodama; Kazuho Ikeo; Hideaki Sugawara; Yoshio Tateno; Takashi Gojobori.
DDBJ (DNA Data Bank of Japan; &amp;#x22;http://www.ddbj.nig.ac.jp/&amp;#x22;:http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; &amp;#x22;http://www.insdc.org/&amp;#x22;:http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3211/version/1

VO: Vaccine Ontology
Provedor de dados: 17
Autores: Yongqun He; Lindsay Cowell; Alexander  D. Diehl; Harry  Mobley; Bjoern  Peters; Alan  Ruttenberg; Richard  H. Scheuermann; Ryan R. Brinkman; Melanie  Courtot; Chris Mungall; Zuoshuang  Xiang; Fang Chen; Thomas  Todd; Lesley  Colby; Howard  Rush; Trish  Whetzel; Mark  A. Musen; Brian  D. Athey; Gilbert  S. Omenn; Barry  Smith.
The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects of the vaccine domain, with an emphasis on classification of vaccines and vaccine components, and on host immune response to vaccines. VO can be used for a number of applications, e.g., ontology-based vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI).
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3553/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; transition, enabled a punctuated sequence of increasingly complex genetic codes. These evolved until the ancestor to the present narrow spectrum of nearly maximal codes became locked-in by path dependence.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4120/version/1

Prediction Of Cancer Possibility By Pattern Recognition And Statistical Study Of Expression Of Gene Level Of Cancer Cells
Provedor de dados: 17
Autores: Medhavi Mallick; Devang Odedra.
The activity of the p53 tumor-suppressor protein has a key role in controlling both cancer and aging: under activity encourages the growth of cancer, and over activity can accelerate the aging process. The p53 protein is a tumor suppressor encoded by a gene whose disruption is associated with approximately 50 to 55 percent of human cancers. The p53 protein acts as a checkpoint in the cell cycle, either preventing or initiating programmed cell death (Apoptosis). p53 regulating genes MDM2, PARP, Oncogenicras, and p21 etc play a crucial role in tumor suppression.
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5624/version/1

Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia  Salgado; Hilda Solano; Julio Collado-Vides.
Since its inception, RegulonDB (&amp;#x22;http://regulondb.ccg.unam.mx/&amp;#x22;:http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/version/1

Data mining of protein families using common peptides
Provedor de dados: 17
Autores: Assaf Gottlieb; Uri Weingart; David Horn.
Predicting the function of a protein from its sequence is typically addressed using sequence-similarity. Here we propose a motif-based approach, using supervised motif extraction from protein sequences belonging to one functional family. The resulting deterministic motifs form Common Peptides (CPs) that characterize this family, allow for data mining of its proteins and facilitate further partition of the family into clusters
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2189/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/1

Design and Implementation of the UniProt Website
Provedor de dados: 17
Autores: Eric Jain; Isabelle Phan; Severine Duvaud; Elisabeth Gasteiger; Nicole Redaschi; Maria J. Martin; Peter McGarvey; Amos Bairoch.
The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The &amp;#x22;www.uniprot.org&amp;#x22;:http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2611/version/1

Complex Systems Biology of Organisms
Provedor de dados: 17
Autores: I. C. Baianu.
Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine&amp;#x27;s logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7044/version/1

Affymetrix probes containing runs of contiguous guanines are not gene-specific
Provedor de dados: 17
Autores: Graham J. Upton; William B. Langdon; Andrew P. Harrison.
High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene&amp;#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&amp;#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1825/version/1

FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation
Provedor de dados: 17
Autores: David Urbina-G&amp;#xf3;mez; Flavia  Vischi Winck; Bernd M&amp;#xfc;ller-R&amp;#xf6;ber; Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n.
For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7035/version/1

Reactome: A database of biological pathways
Provedor de dados: 17
Autores: David Croft.
REACTOME is an open-source, open access, manually curated, peer-reviewed and highly reliable pathway database. A new website is currently in preparation, which includes tools for visualising pathway diagrams and analyzing user-supplied data in a pathway context.  Reactome provides facilities for exporting its content in BioPax and SBML formats.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5025/version/1

Analysis of DNA structure as a 2D random walk by complex wavelet transform
Provedor de dados: 17
Autores: Eugene B. Postnikov; Alexander Y. Loskutov; Sergey A. Larionov; Evgeny V. Ryadchenko; Roman V. Kiseliov.
We propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex plane. Namely, we consider the mapping of two irreducible A &amp;#x2212; T and G &amp;#x2212; C  sequences into a walk trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. &amp;#xd;&amp;#xa;    This function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based on the representation of the transform&amp;#x2019;s result as a solution of the specific Cauchy problem for the system of PDE. &amp;#xd;&amp;#xa;    As an example, we applied the described algorithm to a part of the telomer region of the 22 human chromosome and demonstated...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1461/version/1

A three-dimensional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/2

Solving the protein folding problems
Provedor de dados: 17
Autores: Robert P. Bywater.
The protein folding problem persists in being the major unsolved problem in biophysics and molecular biology. The most immediate obstacle to its solution is said to be the immense combinatorial difficulty of finding the global minimum energy structure, due to the galactic number of possible rotamer states for the polypeptide backbone and its sidechains, the so-called Levinthal paradox1. Much attention has been paid to the topography of the free energy surface that the folding polypeptide has to negotiate in order to find this minimum and the notion of a funnel-shaped topography has been proposed2. While this has achieved wide acceptance, providing insight into the possible shape of the free energy surface, it still does not solve the problem. In this work...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4730/version/1

Development of GCP Ontology for Sharing Crop Information
Provedor de dados: 17
Autores: Rosemary Shrestha; Ramil Mauleon; Reinhard Simon; Jayashree  Balaji; Stephanie  Channeli&amp;#xe8;re; Adriana  Alercia; Martin Senger; Kevin Manansala; Thomas Metz; Guy  Davenport; Richard Bruskiewich; Graham McLaren; Elizabeth Arnaud.
The Generation Challenge Programme (GCP &amp;#x2013; &amp;#x22;http://www.generationcp.org&amp;#x22;:http://www.generationcp.org) is a globally distributed crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. GCP adopted the development paradigm of a &amp;#x2018;model-driven architecture&amp;#x2019; to achieve the interoperability and integration of diverse GCP data types that are available through distributed data sources and consumed by end-user data analysis tools. Its objective is to ensure semantic compatibility across the Consortium that will lead to the creation of robust global public goods from GCP research results....
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3087/version/1

ChEBI, an Open-access Chemistry Resource for the Life Sciences:  Facilities for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis.
ChEBI (Chemical Entities of Biological Interest) is a database of &amp;#x2018;small&amp;#x2019; molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5091/version/1

Wikis as platforms for scholarly publishing
Provedor de dados: 17
Autores: Daniel Mietchen.
While scholarly publishing has traditionally focused on stand-alone articles describing how a specific act of research advanced knowledge in a particular area for once, wikis and similar collaborative online environments provide the technical means to focus on contextually interlinked concepts instead and to update them continuously as new research results come in. Some platforms based totally or in part on these principles have already been put to practical tests whose relevance for Open Access publishing are discussed here, paying special attention to implementations of the review process. The presentation was given &amp;#x22;on-wiki&amp;#x22;:http://en.citizendium.org/wiki/User:Daniel_Mietchen/Talks/COASP_2010/Start .
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4880/version/1

WormBase - Nematode Biology and Genomes
Provedor de dados: 17
Autores: Paul Davis; WormBase Consortium.
WormBase is the major public online database resource for the _Caenorhabditis_ research community. The database was developed primarily for the nematode _C. elegans_ but expanded to host genomes and biological data from other closely related nematode species including _C. briggsae_, _C. remanei_, _C. brenneri_, _C. japonica_ and _Pristionchus pacificus_. WormBase has developed tools to mine the data held within the database and compare the hosted species. Over the years we have developed a variety of curation pipelines which often begin in a &amp;#x22;first-pass&amp;#x22; literature curation step. This involves a brief overview of the literature before directing it to specialised data curators who extract all relevant information. Curators focus on...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3127/version/1

BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
Provedor de dados: 17
Autores: Patricia L. Whetzel; Nigam H. Shah; Natalya F. Noy; Benjamin Dai; Michael Dorf; Nicholas Griffith; Clement Jonquet; Cherie Youn; Adrien Coulet; Chris Callendar; Daniel L. Rubin; Barry Smith; Margaret-Anne Storey; Christopher G. Chute; Mark A. Musen.
BioPortal (&amp;#x22;http://bioportal.bioontology.org&amp;#x22;:http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Prot&amp;#xe9;g&amp;#xe9; frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3868/version/1

Update on libSBML status
Provedor de dados: 17
Autores: Sarah M. Keating.
Update on the current status of the stable 4.2.0 release and the developmental 5.0.0 release of libSBML; an API library for reading/writing and manipulating SBML.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4996/version/1

The Eukaryote Genome Annotation Platform at Genoscope
Provedor de dados: 17
Autores: Betina M. Porcel; Franck  Aniere; Sylvain Bonneval; Benjamin Noel; Jean-Marc Aury; Corinne Da Silva; Olivier Jaillon; France Denoeud; Claude Scarpelli; Jean Weissenbach; Patrick Wincker; Fran&amp;#xe7;ois Artiguenave.
The Genoscope annotation workflow for eukaryote genomes relies on evidence from ab initio gene models predictions combined with homology searches, using collections of expressed sequences - full length cDNAs, ESTs or massive-scale mRNA sequences from the same or closely related organisms &amp;#x2013; proteins or other genomic sequences. Global analysis of these drafts or complete sequences are then combining both approaches in the form of gene prediction data integration using GAZE, capable to identify a majority of the existing gene features. Although of very good quality, gene-modelling remains still tentative at the end of the process. Even though computational predictors are useful on large scale annotation for global genomics analysis, there is no...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3457/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/2

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/2

The Unfolded Protein Response and its potential role in Huntington&amp;#x27;s disease
Provedor de dados: 17
Autores: Ravi  K. R. Kalathur; Kamesh Ayasolla; Matthias E. Futschik.
Huntington&amp;#x27;s disease (HD) is a progressive, neurodegenerative disease with fatal outcome. Although the disease-causing gene (huntingtin) has been known for some time, the exact cause of neuronal cell death is still unknown. One potential mechanism contributing to the massive loss of neurons in the brain of HD patients might be the unfolded protein response (UPR), which is activated by accumulation of misfolded proteins in the endoplasmatic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, it is known that persistent ER stress and activated UPR can...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7145/version/1

BRIF Workshop Minutes
Provedor de dados: 17
Autores: Laurence Mabile.
This document is a detailed summary of the presentations and discussions from the BRIF (Bioresource Impact Factor) workshop, held in Toulouse on 17-18 january 2011.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5879/version/1

The Control Fallacy: Why OA Out-Innovates the Alternative
Provedor de dados: 17
Autores: John Wilbanks.
This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of &amp;#x22;end to end&amp;#x22; network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1808/version/1

Novel determinants describe chaperonin substrate proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state and prevent their aggregation. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level. Its substrate proteins in E. coli have been identified and characterized. However, a long standing and yet unresolved question in the field is: what makes a protein a chaperone substrate?&amp;#xd;&amp;#xa;Here we demonstrate with a bioinformatics-based approach that a simple set of criteria is sufficient to describe the GroEL substrate proteome to unprecedented accuracy. We define two novel parameters differentiating GroEL substrates from other cellular proteins: evolutionary rate and hydrophobicity. We demonstrate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/2

Parkinson&amp;#x2019;s disease is a TH17 dominant autoimmune disorder against accumulated alpha-synuclein
Provedor de dados: 17
Autores: Wanchung(Wanjiung) Hu.
Parkinson&amp;#x2019;s disease is a very common neurodegenerative disorder. Patients usually undergo destruction of substantia nigra to develop typical symptoms such as resting tremor, hypokinesia, and rigidity. However, the exact mechanism of Parkinson&amp;#x2019;s disease is still unknown, so it is called idiopathic Parkinsonism. According to my microarray analysis of peripheral blood leukocytes and substantia nigra brain tissue, I propose that Parkinson&amp;#x2019;s disease is actually a TH17 dominant autoimmune disease. The autoantigen is mainly alpha-synuclein. After knowing the exact disease pathophysiology, we can develop better drugs to prevent or control the detrimental disorder.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6176/version/1

Suitability of dysphonia measurements for telemonitoring of Parkinson&amp;#x2019;s disease
Provedor de dados: 17
Autores: Max A. Little; Patrick E. McSharry; Eric J. Hunter; Jennifer Spielman; Lorraine O. Ramig.
We present an assessment of the practical value of existing traditional and non-standard measures for discriminating healthy people from people with Parkinson?s disease (PD) by detecting dysphonia. We introduce a new measure of dysphonia, Pitch Period Entropy (PPE), which is robust to many uncontrollable confounding effects including noisy acoustic environments and normal, healthy variations in voice frequency. We collected sustained phonations from 31 people, 23 with PD. We then selected 10 highly uncorrelated measures, and an exhaustive search of all possible combinations of these measures finds four that in combination lead to overall correct classification performance of 91.4%, using a kernel support vector machine. In conclusion, we find that...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2298/version/1

An Ontology To Represent Knowledge On Animal Testing Alternatives
Provedor de dados: 17
Autores: Thomas W&amp;#xe4;chter; Ursula G. Sauer; Andreas Doms; Barbara Grune; Michael R. Alvers; Horst Spielmann; Michael Schroeder.
EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R (&amp;#x22;www.Go3R.org&amp;#x22;:http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3148/version/1

SBML Level 3 Package Proposal: Flux
Provedor de dados: 17
Autores: Frank Bergmann; Brett G. Olivier.
This document describes  an easy to implement  package for storing information related &amp;#xd;&amp;#xa;to flux balance analysis of  SBML  Level  3 models  (the  FBA  package). In addition,  &amp;#xd;&amp;#xa;we  provide  an  example  of  how  this package  may be  implemented and  used as  a SBML&amp;#xd;&amp;#xa;Level 2 annotation.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4236/version/1

H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Elassai M. Labib; E Ayoub; Mona M. Aly; A-SA Arafa; Marshall R. Monteville; Bruce R. Boynton; Jeffery Tjaden; Kenneth C. Earhart; Moustafa M. Mansour; Nasr M. ElSayed; A I. Nayei; A A. Abdelghani; Hala M. Essmat.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/553/version/2

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: Rodrick Wallace.
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction, and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of communication theory, that instantiates the punctuated dynamic relations of organisms with their embedding environments, including the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis, making application to both relatively rapid evolutionary punctuated equilibrium and to the conservation of ecological interactions across deep evolutionary time.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4496/version/2

Regulation and feedback of cholesterol metabolism
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Holly C. Gibbs; Wayne Hsieh; Mohammed Ba Abdullah; Mathieu Blanc; William J. Griffiths; Tom C. Freeman; Peter Ghazal.
Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. An integrative knowledge representation of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking. Here we provide using Systems Biology Graphical Notation the research synthesis of a process diagram integrating the regulatory and feedback systems for cholesterol synthesis.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6315/version/1

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: V. I. Prisecaru; I C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/2

DNA Sequence Evolution through Integral Value Transformations
Provedor de dados: 17
Autores: Sk Sarif Hassan; Pabitra Pal Choudhury; Ranita Guha; Shantanav Chakraborty; Arunava Goswami.
In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as  numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database. This...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5729/version/1

In silico Genetic Network Models for &amp;#xb;Pre-clinical Drug Prioritization
Provedor de dados: 17
Autores: Jianghui Xiong; Juan Liu; Simon Rayner; Ze Tian; Yinghui Li; Shanguang Chen.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Patient population heterogeneity and unpredictable physiology complicate pre-clinical cancer modeling efforts. We hypothesize that gene networks associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. Here we propose a novel in vivo genetic interaction which we call &amp;#x2018;synergistic outcome determination&amp;#x2019; (SOD), a concept similar to &amp;#x2018;Synthetic Lethality&amp;#x2019;. SOD is defined as the synergy of a gene pair with respect to cancer patients&amp;#x27; outcome, whose correlation with outcome is due to...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5343/version/1

MaizeGDB , maize genetics cooperation and the ~2500MB B73 genome generated tsunami
Provedor de dados: 17
Autores: Mary Schaeffer; Jack Gardiner; Elisabeth Harper; Carson Andorf; Darwin Campbell; Ethalinda Cannon; Taner Z. Sen; Carolyn Lawrence.
Advances in sequencing technology have made it possible to sequence the 2500 MB B73 maize genome, both cheaply and in a relatively short time. Nearly simultaneously, other sequencing-based data are on the leading edge of a data tsunami: sequenced differences (currently &amp;#x3e;300,000 SNP for  &amp;#x3e;1000 inbred lines and related species) and gene expression data.  The MaizeGDB team integrates access to these datasets after considerable cooperation among both data users and suppliers, and typically while the data are being generated. In this way, data suppliers have resources in place to format data ready for integration with MaizeGDB.  And, we learn what details, including links to other resources, are needed to support our user community and what...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5258/version/1

Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Provedor de dados: 17
Autores: Max A. Little; Nick S. Jones.
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L1-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4318/version/1

Integrating &amp;#xa0;text-&amp;#xad;mining&amp;#xa0;effort requires&amp;#x9;output standards
Provedor de dados: 17
Autores: Andra Waagmeester.
We recently released a plugin to Pathvisio to assist the curator with automatic integration of heterogeneous pathway knowledge. Pathway curation involves gathering this knowledge not only through discussions with peers, but also from biological databases and the scientific literature. Integrating this all into one pathway is challenging and to date still mainly a laborious manual process. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More and more biological databases provide webservices (ie. REST or SOAP). The main objective of webservices is to provide an interface for other computer applications. Our plug-in uses these interfaces to gather binary relationships of a given pathway entity and present the relation in star shaped figures to the curator. The plug-in...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5850/version/1

A general model of continuous character evolution
Provedor de dados: 17
Autores: Carl Boettiger.
I present a general model for continuous character evolution, review some of the common challenges that emerge in such complex methods and review strategies for handling them.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6080/version/1

PrionOme: A database of prions and other sequences relevant to prion phenomena
Provedor de dados: 17
Autores: Djamel Harbi; Marimuthu Parthiban; Deena Gendoo; Sepehr Ehsani; Manish Kumar; Gerold Schmitt-Ulms; Ramanathan Sowdhamini; Paul M. Harrison.
Prions are units of propagation of an altered state of a protein or proteins. Prions can propagate from cell to cell, and from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We have compiled a database of &amp;#x3e;2000 prion-related sequences, called the PrionOme. The database comprises seven PrionOme classification categories: prionogenic...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6430/version/1

BFO/DOLCE Primitive Relation Comparison
Provedor de dados: 17
Autores: A. Patrice Seyed.
This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies, employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined, which sets a framework for developing a common upper ontology that utilizes the assets of both.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3481/version/1

Computational Studies Of Huntington Protein: Classification &amp;#x26; Binding Pattern Determination
Provedor de dados: 17
Autores: Nitin M. R. Chitranshi; Shipra M. S. Gupta.
Huntington&amp;#x27;s disease (HD) is a dominantly inherited neurodegenerative disorder characterized by progressive motor deficits, psychiatric deterioration, worsening chorea, cognitive impairment due to neuronal cell loss in the basal ganglia, cerebral cortex, and its fragments interactions with themselves and other biomolecules that results in aggregates , transcriptional repression , oxidative injury  and mitochondrial dysfunction . The repeat domain of Huntingtin interacting protein (HIP) 14 (PDB id 3eu9) is used to study the structure based drug design. We made the selection of 50 different small molecules which were screened out through various fixed parameters and applied descriptors to generate the model for molecules that shows the drug likeness...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5581/version/1

Elucidating Signal Transduction Modulatory Drug Target Network of Colon Cancer: A Network Biology Approach
Provedor de dados: 17
Autores: Deepak Ranjan Sethi; Sanjay Kundu; Ibnul Hassan; Biplab  Bhattacharjee; Jayadeepa R.M; Sushil Kumar  Middha.
Latest evaluation and validation of cancer drugs and their targets has demonstrated the lack and inadequate development of new and better drugs, based on available protocols. Even though the specificity of drug targets is a great challenge in the pharmaco-proteomics field of cancer biology, for eradicating such hurdles and paving the way for the drugs of future, a novel step has been envisaged here to study the relation between drug target network and the corresponding drug network using the advanced concepts of proteomics and network biology. The literature mining was done for the collection of receptors and the ligands. About 1000 natural compounds were collected and out of those 300 molecules showed anti-cancer activity against colon cancer. Ligand Vs...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4709/version/1

Systems Biology on Bio-Linux
Provedor de dados: 17
Autores: Mesude Bicak.
This presentation introduces the Bio-Linux Operating System which is a popular Computational Biology workstation with 500+ bioinformatics software. It then provides an overview of popular modelling approaches in systems biology, covering top-down, bottom-up and hybrid modelling. Finally it highlights the challenges being faced by systems biology modellers, agent-based modellers in particular, regarding standardisation efforts.
Tipo: Presentation
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6348/version/1

Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill
Provedor de dados: 17
Autores: William  R. Widger; Georgiy Golovko; Antonio F. Martinez; Efren V. Ballesteros; Jesse J. Howard; Zhenkang Xu; Utpal Pandya; Viacheslav Y. Fofanov; Mark Rojas; Christopher Bradburne; Ted Hadfield; Nels A. Olson; Joshua L. Santarpia; Yuriy Fofanov.
Estimates of 7x105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of the April 20th, 2010 Deep Water Horizon drilling rig explosion, leaving thousands of square miles of earth&amp;#x27;s surface covered in crude oil. Dispersants were used on large slicks and injected at the well head, resulting in oil being suspended throughout the water column. Starting in June 2010, oil reached hundreds of miles of Louisiana, Alabama, Mississippi, and Florida shoreline disturbing the ecological balance and economic stability of the region. While visible damages are evident in the wildlife populations and marine estuaries, the most significant affect may be on the most basic level of the ecosystems: the bacterial and plankton...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5733/version/1

Universal fractal scaling of self-organized networks
Provedor de dados: 17
Autores: Paul J. Laurienti; Karen E. Joyce; Qawi K. Telesford; Jonathan H. Burdette; Satoru Hayasaka.
There is an abundance of literature on complex networks describing a variety of relationships among units in social, biological, and technological systems. Such networks, consisting of interconnected nodes, are often self-organized, naturally emerging without any overarching designs on topological structure yet enabling efficient interactions among nodes. Here we show that the number of nodes and the density of connections in such self-organized networks exhibit a power law relationship. We examined the size and connection density of 46 self-organizing networks of various biological, social, and technological origins, and found that the size-density relationship follows a fractal relationship spanning over 6 orders of magnitude. This finding indicates that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4894/version/1

Considerate Approaches to Achieving Sufficiency for ABC Model Selection
Provedor de dados: 17
Autores: Chris Barnes; Sarah Filippi; Michael  Stumpf; Tom  Thorne.
ABC methods have gained popularity in situations where traditional methods which involve explicit evaluation of likelihoods are either too cumbersome or fail outright. This, almost by definition means that for any interesting real-world scenario we have no or little recourse to sufficient statistics, which had previously been central to ABC approaches and their derivation. In the context of model selection this can have particularly undesirable consequences if we have to compress the data through the use of summary statistics. In this talk we discuss complementary approaches that allow us to address this problem in a principled manner, and outline the scenarios where ABC model selection is unproblematic. We will argue that many of the most interesting...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5952/version/1

Modeling, Simulation and Application of Bacterial Transduction in Genetic Algorithms
Provedor de dados: 17
Autores: Carlos Perales-Gravan; Javier de Vicente Buendia; Rafael Lahoz-Beltra.
At present, all methods in Evolutionary Computation are bioinspired in the fundamental principles of neo-Darwinism as well as on a vertical gene transfer. Thus, on a mechanism in which an organism receives genetic material from its ancestor. Horizontal, lateral or cross-population gene transfer is any process in which an organism transfers a genetic segment to another one that is not its offspring. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganism (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring a possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting...
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3732/version/1

Studies on Regioselective Binding Mode of Steroid Molecules in Homology Modeled Cytochrome P450-2C11
Provedor de dados: 17
Autores: Hamed I. Ali; Morio Yamada; Hukihisa Fujita; Eiichi Akaho.
In this study, we investigated the regioselective binding mode of steroid molecules and structure requirements for steroid molecules for 16[alpha]-hydroxylation by Cytochrome P450-2C11. Docking study by using the homology Cytochrome P450-2C11 indicated that 16[alpha]-hydroxylation is favored with steroidal molecules possessing the following components, 1) a bent A-B ring configuration (5[beta]-reduced), 2) C-3[alpha]-hydroxyl group, 3) C-17[beta]-acetyl group, and 4) methyl group at both the C-18 and C-19. These respective steroid components requirements such as A-B ring configuration and functional groups at C-3 and C-17 were defined as the inhibitory contribution factor. Overall results by rat CYP2C11 revealed that steroidal structure requirements...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3541/version/1

SED-ML: Nested Simulation Proposal
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a second version of the proposal for nested simulation experiments for SED-ML (http://sed-ml.org). The proposal has been updated to include the feedback received in the meantime and has been enhanced by examples. A full implementation is available with libSedML (http://libsedml.sf.net) and the SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/)
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/4257/version/2

Standardization in UniProtKB/Swiss-Prot
Provedor de dados: 17
Autores: Serenella Ferro Rojas; Anne Morgat; UniProt Consortium.
Within the UniProt consortium, the UniProtKB/Swiss-Prot knowledge base provides the international community with a stable, comprehensive, fully classified, richly and accurately annotated protein sequence database that is fully operable with other databases. Annotation relates to function(s) of the protein (their catalytic activity and the corresponding metabolic pathway(s) in which the protein may be involved), their cellular location, their interactions with other cellular components, etc. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;It is challenging to unify the way we annotate proteins, to ensure consistency and to describe data unambiguously. It is also highly valuable both for querying the database and for analyzing high-throughput data (expression data for...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3214/version/1

Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems
Provedor de dados: 17
Autores: Bradly J. Alicea.
In this paper, a method for decoupling the neuromuscular function of a set of limbs from the role morphology plays in regulating the performance of an activity is introduced. This method is based on two previous methods: the rescaled range analysis specific to time series data, and the use of scaling laws. A review of the literature suggests that limb geometry can either facilitate or constrain performance as measured experimentally. Whether limb geometry is facilitatory or acts as a constraint depends on the size differential between arm morphology and the underlying muscle. &amp;#x22;Changes in size and shape&amp;#x22; are theoretically extrapolations of morphological geometry to other members of a population or species, to other species, or to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2845/version/1

Density functional theory calculation of interaction between bisphosphate and farnesyl pyrophosphate synthase
Provedor de dados: 17
Autores: Kazuki Ohno; Kenichi Mori; Yohsuke Hagiwara; Masaya Orita; Makoto Takeuchi.
Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Pagets disease of the bone. To date, a number of BPs-namely alendronate, risedronate, and minodronate-have been launched to market. Nitrogen-BPs (N-BPs) act by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and N-BPs have been identified. Understanding the physical basis of the binding between proteins and small molecules is an important goal in both medicinal chemistry and structural biology. Here, we conducted density functional theory calculations for BPs and their surrounding residues and were able to successfully reproduce experimental results qualitatively. In addition, we found that both...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4867/version/1

Some thoughts about the future of SBML
Provedor de dados: 17
Autores: Nicolas Le Novere.
SBML was designed in 2000, merely 2 years after the first official specification of XML. 11 years afterward, the current structure of the language is largely unchanged. Since then, its user base evolved much, as did the whole field of modeling in biology. &amp;#xd;&amp;#xa;If one wants SBML to evolve in the next decade, it is time to start discussing the basics now. The presentation covers a series of fundamental issues such as SBML coverage, unity of the language, use of elements and attributes etc.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6387/version/1

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfoded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/1

Plant Transcription Factors @ uni-potsdam.de
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Ingo Dreyer; Slobodan Ruzicic; Bernd Mueller-Roeber.
We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae _Chlamydomonas reinhardtii_, _Ostreococcus tauri_ and the vascular plants _Oryza sativa_ and _Arabidopsis thaliana_.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/243/version/1

Angiogenesis and Vasculogenesis at 7-Day of Reperfused Acute Myocardial Infarction
Provedor de dados: 17
Autores: Sheng  Kang; Yue-jin Yang; Qing-zhi Wang; Yue L. I. Li; Yi Tian; Yu-tong Cheng; Wei-feng Shen.
Objectives &amp;#xd;&amp;#xa;This study is to investigate the angiogenesis and vasculogenesis at the first week of reperfused acute myocardial infarction (AMI).&amp;#xd;&amp;#xa;Methods &amp;#xd;&amp;#xa;16 of mini-swines (20 to 30 Kg) were randomly assigned to the sham-operated group and the AMI group. The acute myocardial infarction and reperfusion model was created and the pig tail catheter was performed to monitor hemodynamics before left anterior descending coronary artery (LAD) occlusion, 90 min of LAD occlusion and 120 min of LAD reperfusion. Pathologic myocardial tissue was collected at 7-day of LAD reperfusion and further assessed by immunochemistry, dual immunochemistry, in-situ hybridization, real-time quantitative polymerase chain reaction and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2066/version/1

11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2
Provedor de dados: 17
Autores: Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish.  Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively.  Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs.  Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known.  An opportunity to understand their evolution is...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4649/version/1

Is it Prostate Cancer ?
Provedor de dados: 17
Autores: Hans-Heinrich Gl&amp;#xe4;ttli; Juergen Durner; Hans-J&amp;#xfc;rg Gerber.
Given a set of PSA values, we answer the question: &amp;#x201c;Is its information content typical for the existence of a prostate cancer, or not?&amp;#x201d; Our findings support PSA screening.
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4556/version/1

Workshop report: 1st INCF Workshop on Large-scale Modeling of the Nervous System
Provedor de dados: 17
Autores: Mikael Djurfeldt; Anders Lansner.
The goal of this workshop was to survey current demands, ongoing activities, and plans relating to development of tools for scalable neural network simulation. Areas covered included software components for preprocessing/model setup, as well&amp;#xd;&amp;#xa;as for storage, analysis, and visualization of results. Participants discussed the need for coordinated action in the field with regard to model, method and tool development. The reports a description of the state-of-art in the field as well as recommendations for actions to facilitate infrastructure developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/262/version/1

_M. tuberculosis_ interactome analysis unravels potential pathways to drug resistance
Provedor de dados: 17
Autores: Karthik Raman; Nagasuma Chandra.
Drug resistance is a major problem for combating tuberculosis. Lack of understanding of how resistance emerges in bacteria upon drug treatment limits our ability to counter resistance. By analysis of the _Mycobacterium tuberculosis_ interactome network, along with drug-induced expression data from literature, we show possible pathways for the emergence of drug resistance. To a curated set of resistance related proteins, we have identified sets of high propensity paths from different drug targets. Many top paths were upregulated upon exposure to anti-tubercular drugs. Different targets appear to have different propensities for the four resistance mechanisms. Knowledge of important proteins in such pathways enables identification of appropriate...
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1674/version/1

BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems biology standards
Provedor de dados: 17
Autores: Andrei Zinovyev.
BiNoM is a Cytoscape plugin which allows to read, analyze and convert biological networks represented in various systems biology standards.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5120/version/1

Translational Oncogenomics and Human Cancer Interactome Networks:
Provedor de dados: 17
Autores: I. C. Baianu.
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6190/version/1

Targeted Assembly of Short Sequence Reads
Provedor de dados: 17
Autores: Rene L. Warren; Robert A. Holt.
As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety.  Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5524/version/1

bioDBcore: overview of the checklist and steps towards implementation
Provedor de dados: 17
Autores: Pascale Gaudet (Pascale.Gaudet@isb-sib.ch); Philippe Rocca-Serra (proccaserra@googlemail.com).
Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this &amp;#x201c;one-stop shop&amp;#x201d; for those seeking information about the standards and data sharing policies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This presentation illustrates the rational for BioDBcore(P Gaudet) and the progresses for its implementation (P Rocca-Serra),...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6167/version/1

ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data
Provedor de dados: 17
Autores: Hossein Khiabanian; Pieter  Van Vlierberghe; Teresa Palomero; Adolfo  A. Ferrando; Raul Rabadan.
Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants using partially mapped reads in nextgen sequencing data. We also report ParMap&amp;#x2019;s successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4145/version/1

Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax
Provedor de dados: 17
Autores: Daniel Z. Bar.
The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes.  This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5690/version/1

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts
Provedor de dados: 17
Autores: Oliver Stegle; Philipp Drewe; Regina Bohnert; Karsten Borgwardt; Gunnar R&amp;#xe4;tsch.
As a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a &amp;#x27;gene structure sensitive&amp;#x27; Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4437/version/1

Dynamic is-a Hierarchy Generation from a Clinical Medical Ontology
Provedor de dados: 17
Autores: Hiroko Kou; Jun Zhou; Mamoru Ohta; Kouji Kozaki; Ken Imai; Riichiro Mizoguchi; Kazuhiko Ohe.
This article discusses an ontology-handling technology to provide on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physicians might have. It is one of the important benefits of our medical ontology which is developed as a Japanese national project. This technology tackles with the multi-perspective issues of medical knowledge.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3502/version/1

Prediction of specific virus outbreaks made from the increased concentration of a new class of virus genomic peptides, replikins.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Advance warning of pathogen outbreaks has not been possible heretofore. A new class of genomic peptides associated with rapid replication was discovered and named replikins. Software was designed to analyze replikins quantitatively. Replikin concentration changes were measured annually prior to, and &amp;#x201c;real time&amp;#x201d; every few days during, the 2009 H1N1 influenza pandemic. Replikins were seen by both linear sequence representation and three-dimensional X-ray diffraction, and found to expand on the virus hemagglutinin surface prior to and during the H1N1 pandemic.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A highly significant increased concentration of virus replikins was found a) retrospectively in three pandemics from 1918 to 1999 (14,227...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6279/version/1

ProDGe: investigating protein-protein interactions at the domain level
Provedor de dados: 17
Autores: Finja B&amp;#xfc;chel; Clemens Wrzodek; Florian Mittag; Andreas Dr&amp;#xe4;ger; Adrian Schr&amp;#xf6;der; Andreas Zell.
An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java^TM^ program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6188/version/1

NamesforLife Semantic Resolution Services for the Life Sciences
Provedor de dados: 17
Autores: Charles T. Parker; Dorothea K. Taylor; Kara Mannor; Sarah Wigley; Nicole Osier; Catherine Lyons; George M. Garrity.
A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5137/version/1

Transcriptomic analysis implicates ribosomal and energy metabolic pathways in antiepileptic drug action in a Drosophila model
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Mechanisms of long term action of antiepileptic drugs (AEDs), used in treating epilepsy and many other neurological and psychiatric disorders, are poorly understood. Recently, a novel Drosophila transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ), a chemoconvulsant commonly used to model epileptogenesis and test AEDs in rodents, has been described. In this model, two of the five AEDs tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Here, we describe transcriptomic effect of the AEDs in the fly model. Singular treatment with ETH, GBP and VGB in general caused downregulation of genes....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3396/version/1

The true story behind the annotation of a pathway
Provedor de dados: 17
Autores: Giovanni Marco G. M. Dall&amp;#x27;Olio; Hafid H. Laayouni.
On 2010 we worked on the annotation of the N-Glycosylation pathway in the Reactome database. During this process, we found some unclear points and errors in other databases, and we reported and helped fix them. After we finished, we realized that the work of reporting errors to a database is basically not acknowledged by the scientific community: this is unfortunate because if only this process would be a bit more recognized and transparent, we could have better data in the databases and a more active community. Moreover, the fact that many databases tend to keep error reporting private creates great issues to the reproducibility of a work.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Another way to look at this talk is: if you dedicate 6 months of your PhD thesis...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5561/version/2

Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game
Provedor de dados: 17
Autores: David Basanta; Jacob G. Scott; Mayer N. Fishman; Gustavo E. Ayala; Simon W. Hayward; Alexander R. A. Anderson.
BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6385/version/1

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)
Provedor de dados: 17
Autores: Xiaolong Wang; Yu  Fu; Yue  Zhao; Qi  Wang; Chandra Sekhar  Pedamallu; Shuang-yong  Xu; Yingbo  Niu; Jingjie  Hu.
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6730/version/1

Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds
Provedor de dados: 17
Autores: Shi Huang.
Molecular analysis of collagen sequences from an 80 million year old hadrosaur _B. canadensis_ and a 68 million year old dinosaur _T. rex_ suggest strongly that _B. canadensis_ is an outgroup to a clade containing _T. rex_ and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3255/version/1

ChemAxiom &amp;#x2013; An Ontological Framework for Chemistry in Science
Provedor de dados: 17
Autores: Nico Adams; Edward O. Cannon; Peter Murray-Rust.
We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective typing of resources, the identification of ambiguity and supports chemical text mining.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3714/version/1

On ARS-interacting multifunctional protein p18
Provedor de dados: 17
Autores: Viktor Deineko.
Nine aminoacyl-tRNA synthetases with three auxiliary components are forming a multisynthetase complex which is essential component of protein biosynthesis machinery. The smallest auxiliary component p18 takes part in biosynthesis channeling. It is also a regulator of p53 and has tumor suppressing function. Particular structure of this protein is still unknown. Here methods of structural bioinformatics were applied to generate a model of p18 spatial structure suitable for further research. The structure was created using homology modeling. DNA-binding residues of p18 were also derived both from raw sequence and from three-dimensional structure model.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1593/version/1

Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it&amp;#x2019;s going to take is kind of depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/2

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Qiime &amp;#x2013; a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;  &amp;#xd;&amp;#xa;B) UCHIME &amp;#x2013; a tool for rapid identification of chimeric 16S sequence fragments; &amp;#xd;&amp;#xa;C) Mothur &amp;#x2013; a C++-based software package for 16S analysis;&amp;#xd;&amp;#xa;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/2

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6115/version/2

Bioinformatics Approach for Functional Glycomics
Provedor de dados: 17
Autores: James C. Paulson.
Presentation in the Human Glycomics Proteomics Disease Initiative (HGPI) session.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/15/version/1

Community Outreach through Genomics Education Partnership
Provedor de dados: 17
Autores: Ramana Madupu; Anne G. Rosenwald; A. Malcolm Campbell; Satish C. Bhalla; Granger Sutton.
The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID&amp;#x2019;s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience.  Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3149/version/1

Validation of a Multivariate Serum Profile for Epithelial Ovarian Cancer Using a Prospective Multi-Site Collection
Provedor de dados: 17
Autores: Partha Seshaiah; Greg P. Bertenshaw; Tzong-Hao Chen; Katharine J. Bergstrom; Jinghua Zhao; James P. Mapes; Laurie L. Stephen; Suraj Amonkar; Michael E. McCollum; Brigitte E. Miller; Lynda D. Roman; Beth Y. Karlan; Eva Chalas; Paul A. DiSilvestro; James F. Barter; James W. Orr; Glenn E. Bigsby; Robert W. Holloway; Ronald D. Alvarez; Ping F. Yip; Brian C. Mansfield.
In previous studies we described the use of a retrospective collection of ovarian cancer and benign disease samples, in combination with a large set of multiplexed immunoassays and a multivariate pattern recognition algorithm, to develop an 11-biomarker classification profile that is predictive for the presence of epithelial ovarian cancer.  In this study, customized, Luminex-based multiplexed immunoassay kits were GMP-manufactured and the classification profile was refined from 11 to 8 biomarkers (CA-125, epidermal growth factor receptor, CA 19-9, C-reactive protein, tenascin C, apolipoprotein AI, apolipoprotein CIII, and myoglobin).  The customized kits and the 8-biomarker profile were then validated in a double-blinded manner using prospective samples...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4667/version/1

Annotation of SBML Models Through Rule-Based Semantic Integration
Provedor de dados: 17
Autores: Allyson L. Lister; Phillip Lord; Matthew  Pocock; Anil Wipat.
*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3286/version/1

The Human Microbiome and Recurrent Abdominal Pain in Children
Provedor de dados: 17
Autores: James Versalovic; Robert J. Shulman; Kevin Riehle; Delphine M. Saulnier; Toni-Ann Mistretta; Maria A. Diaz; Sabeen Raza; Debasmita Mandal; Xiang Qin; Susan Lynch; Joseph Petrosino; Richard Gibbs.
This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS).  Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain.  3. Perform functional gut metagenomics by evaluation of whole...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5228/version/1

Extending Astrobiology: Consciousness and Culture
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5286/version/2

Analysis of N-Glycosylation Sites in HIV glycoprotein 160
Provedor de dados: 17
Autores: Rajendra Mandage.
HIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system, which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that there are...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5571/version/1

Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an approach for identifying such &amp;#x201c;erroneous mappings&amp;#x201d; using Distributed Description Logics. Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings, and provide preliminary results...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3455/version/1

QSAR studies on Withanolide analogs for anticancer activity
Provedor de dados: 17
Autores: Dharmendra Kumar  Yadav; Feroz  Khan; Rajender S.  Sangwan.
Withanolides are a group of pharmacologically active compounds present in most prodigal amounts in roots and leaves of Withania somnifera (Indian ginseng), one of the most important medicinal plants of Indian systems of medicine. Withanolides are basically steroidal lactones (highly oxygenated C-28 phytochemicals) and similar to ginsenosides activity. Some of the withanolides that have been reported possess immunomodulatory, and anticancer activities. In the present investigation, a quantitative structure activity relationship (QSAR) model based on forward stepwise multiple linear regression (MLR) has been developed against the MCF7, MCF7/BUS, and SK-Br-3 human solid tumor breast cancer cell lines. Relationship correlation coefficient (r2) and cross...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6617/version/1

Evolution as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a &amp;#x27;language&amp;#x27; model in which genes, gene expression, and environment are represented as interacting information sources. The larger, composite, source that characterizes the high probability evolutionary paths then becomes, in a real sense, a language that speaks itself. The approach represents a significant extension of nonequilibrium condensed matter formalism in which the asymptotic limit theorems of information theory beat back the mathematical thicket a full step, providing necessary, but not sufficient, conditions for punctuated evolutionary transitions that can themselves be expressed as highly...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5339/version/1

Logical Operation Based Literature Association with Genes and its application, PosMed.
Provedor de dados: 17
Autores: Yuko Makita; Rinki Bhatia; Mrinalini Deshpande; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Yuko Yoshida; Norio Kobayashi; Testuro Toyoda.
PosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising documental neurons (or &amp;#x27;documentrons&amp;#x27;) that represent each document contained in databases such as MEDLINE and OMIM (Yoshida, _et al_. 2009, Makita, _et al_. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic keywords to the genes through connections representing gene&amp;#x2013;gene interactions other biological relationships, such as metabolite&amp;#x2013;gene, mutant mouse&amp;#x2013;gene, drug&amp;#x2013;gene, disease&amp;#x2013;gene, and protein&amp;#x2013;protein interactions, ortholog data, and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5071/version/1

Studying Biocuration Workflows
Provedor de dados: 17
Autores: Gully A. P. C. Burns; Martin Krallinger; Kevin Cohen; Cathy Wu; Lynette Hirschman.
As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. At present, more work is needed to perform this task.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3249/version/1

Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Provedor de dados: 17
Autores: Alexander Garnett; Heather A. Piwowar; Edie M. Rasmussen; Judy Illes.
Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process.  In this paper, we describe a system to help with this task, given an example set of  PubMed articles to retrieve and a corresponding set of articles to exclude.  The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold.  From this information and their knowledge of the domain, users can formulate a query and evaluate its performance.  We apply...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4270/version/1

BrainGrab: Capturing Curator Expertise as Reusable Annotation Rules
Provedor de dados: 17
Autores: Daniel H. Haft; Malay K. Basu; Roland A. Richter.
Experienced biocurators can outperform automated systems on specific genes once they determine which pieces of evidence should drive annotation, and which annotations should be spread. The annotation logic may weigh both homology evidence (BLAST matches or HMM hits) and non-homology evidence (neighboring genes, metabolic context, taxonomic group). Unfortunately, the expertise developed to annotate each gene is short-lived, and is mostly lost if the logic driving the annotation is not captured. We report the development of BrainGrab, an interface added to the MANATEE manual annotation tool for prokaryotic genomes. The curator can specify evidence scenarios that should always lead to equivalent annotation for similar genes in similar contexts, and thus...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3313/version/1

Biodiversity informatics: the challenge of linking data and the role of shared identifiers
Provedor de dados: 17
Autores: Roderic Page.
A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1760/version/1

Plant Metabolic Pathways in MetaCyc and SolCyc
Provedor de dados: 17
Autores: Anuradha Pujar; Ron Caspi; Naama Menda; Isaak Tecle; Peter Karp; Lukas Mueller.
MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3192/version/1

Delayed-Type hypersensitivity to latex: Computational prediction of MHC class II epitopes on latex allergens
Provedor de dados: 17
Autores: Bell R. Eapen.
Delayed type hypersensitivity to natural rubber latex is rare compared to IgE mediated immediate reactions. Binding of allergens to MHC Class II is a crucial step in the presentation of antigens to CD4+ T Cells responsible for delayed reactions. Computational prediction of MHC class II epitopes on thirteen known latex allergens using SMM-align method revealed strong binding with several alleles. This shows that latex allergens are capable of initiating delayed type hypersensitivity in susceptible individuals.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2931/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/1

Development of a Decision Support System (DSS) for an integrated test system towards the effective and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine  H&amp;#xf6;flich; Andreas  M&amp;#xfc;ller; J&amp;#xf6;rg  Schmidtke; Kerstin  Schmidt; Inge  Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to implement environmental effects e.g. on non-targets or the variability of transgene expression.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/2

The use of Web Ontology Language (OWL) to Combine Extant Controlled Vocabularies in Biodiversity Informatics Appears Redundant
Provedor de dados: 17
Autores: Roger D. Hyam.
Implementation of PESI requires data to be combined from multiple source databases. Some of the shared fields in the source databases used different controlled vocabularies of terms. OWL DL was investigated as a mechanism to build an extensible, shared ontology of species occurrence terms that permitted the source database to continue using and extending their own vocabularies whilst formally mapping to a more generic shared vocabulary. The merits of this approach were explored and it was concluded that the building of such a complex mapping ontology probably wasn&amp;#x27;t worthwhile. The level of semantic complexity involved outweighed the costs of simply imposing a flat list of well defined terms onto data suppliers. The main problem with exiting...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5168/version/1

Insilico based designing of short peptide and ligands for calcineurin receptor
Provedor de dados: 17
Autores: Vishwamhabr V. Bhandare; T. G. Jagtap; M. M. Pillai; P. S. Patil.
Calcineurin is a target protein for Cyclosporin A (CsA) an immunosuppressive drug which prevents transplant rejection. CsA has complex structure of 11 amino acids, a cyclic structure with uncommon amino acids, and can&amp;#x2019;t be chemically synthesized. CsA can be synthesized commercially by using fermentation. One report shows chemical synthesis of CsA with partial success (Jason and Diver, 2002). In view of this it is proposed to model a peptide and ligand as an alternate for CsA with the same function and can be chemically synthesized. The target for Cyclosporin is Cyclophilin which forms a ternary complex with calcineurin (CN). An in silico study concludes that all four peptides (1 wild + 3 mutant) were found to bind in the catalytic site of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6072/version/1

Frequency-dependent selection predicts patterns of radiations and biodiversity
Provedor de dados: 17
Autores: Carlos Melian; David Alonso; Diego Vazquez; James Regetz; Stefano Allesina.
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking niche-filling processes, whereas constant rates have been attributed to non-adaptive processes such as sexual selection, mutation, and dispersal. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the speciation rate is driven by frequency dependent selection. We used a frequency-dependent and DNA sequence-based model of populations and genetic-distance-based speciation, in the absence of adaptation to ecological niches. We tested the...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3752/version/1

What are the ethical and social responsibilities of scientists?
Provedor de dados: 17
Autores: Philip Campbell.
Presented as part of the session titled &amp;#x22;Sharing scientific data: who benefits?&amp;#x22; at ESOF (The Euroscience Open Forum) 2008.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Session abstract: Digital datasets&amp;#x2014;text-based, numeric, audio, video or image-based&amp;#x2014;form the output of all scientific disciplines. How are these data being made available for sharing? What quality control mechanisms are in place? What kinds of naming conventions, tags, and metadata are in use and how effective are they at helping to manage open data? Who is storing, archiving and curating open data and at which levels? And how is the production and sharing of open data assessed: what processes are in place for crediting scientists for making their raw data...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2176/version/1

Evolution signatures in genome network properties
Provedor de dados: 17
Autores: Rita de Almeida; Leonardo Brunnet; Jos&amp;#xe9; Luiz Rybarczyk-Filho; Ricardo Ferreira; Jose Claudio Moreira; Mauro Castro; Rodrigo Dalmolin.
Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6653/version/1

The Neonatal Microbiome and Necrotizing Enterocolitis.
Provedor de dados: 17
Autores: Phillip I. Tarr; Barbara Warner; Erica Sodergren; William Shannon; Aaron Hamvas; Vincent Magrini; George Weinstock.
Necrotizing enterocolitis (NEC) is a devastating disorder that affects approximately 10% of premature infants. Its mortality remains high (15-30%), and its cause remains unknown. About 80% of cases occur within 35 days of birth among hospitalized newborns of low birth weight. Probiotics diminish the incidence and severity of NEC, and NEC does not occur antepartum. NEC affects a readily identifiable at-risk group, has a tightly defined interval before its onset, occurs in an organ system that is intimately associated with a microbial population in flux, has a plausible association with the intestinal microbiota, and cohorts at risk have rarely been studied in large numbers, or prospectively. This disorder, therefore, provides a unique opportunity to explore...
Tipo: Marker Paper / Data Plan
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5285/version/1

A Study of the Mechanism of Action of Zervamicin IIB Peptide Antibiotic by Molecular Dynamics Simulation
Provedor de dados: 17
Autores: Konstantin Shaitan; Olga V. Levtsova; Vladimir Makarov; Mikhail P. Kirpichnikov.
We model mechanism of action of a channel-forming peptide antibiotic, zervamicin IIB, by molecular dynamics (MD) simulation. Interaction of this peptide with neutral and negatively charged lipid bilayers is investigated. It is found that charge of membrane surface influences the orientation of zervamicin IIB molecule, that may in turn effect its permeation into the membrane. On this basis we propose modifications to ZrvIIB structure that may increase its affinity towards the prokaryotic cellular membrane. Zervamicin IIB transmembrane channels are modeled as bundles consisting of 4, 5 and 6 individual peptide monomers. Our results suggest that four monomers don&amp;#x2019;t form a stable water-filled ion channel. Thus the channel with the least number of...
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3624/version/1

Towards a model of non-equilibrium binding of a metal ion in a biological system
Provedor de dados: 17
Autores: James Beardmore; Christopher Exley.
We have used a systems biology approach to address the hitherto insoluble problem of the quantitative analysis of non-equilibrium binding of aqueous metal ions by competitive ligands in heterogeneous media. To-date, the relative proportions of different metal complexes in aqueous media have only been modelled at chemical equilibrium and there are no quantitative analyses of the approach to equilibrium1. While these models have improved our understanding of how metals are used in biological systems they cannot account for the influence of kinetic factors in metal binding, transport and fate2. Here we have modelled the binding of aluminium in blood serum by the iron transport protein transferrin (Tf) as it is widely accepted that the biological fate of this...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2025/version/1

A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Provedor de dados: 17
Autores: Jin Gu.
Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4038/version/1

Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation
Provedor de dados: 17
Autores: I C. Baianu.
Novel, two-photon NIR excitation fluorescence correlation microspectroscopy tests and preliminary results were presented in this article with submicron resolution for concentrated suspensions of functional cells and chloroplast membranes. Related developments of these technique involve applications of Fluorescence Cross-Correlation Spectroscopy (FCCS) detection to monitoring: &amp;#xd;&amp;#xa;DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and HIV-HBV testing. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7116/version/1

Cancer Clinical Trials Optimization and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7046/version/1

SBGN-ED - a tool for editing, validating, and translating of SBGN maps
Provedor de dados: 17
Autores: Tobias Czauderna; Christian Klukas; Astrid Junker; Falk Schreiber.
The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We present methods for these tasks, the tool SBGN-ED, and an application example. SBGN-ED allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG and MetaCrop databases into SBGN, and to export SBGN maps into several file and...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4973/version/1

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Provedor de dados: 17
Autores: Leming D. Shi; Wendell D. Jones; Roderick V. Jensen; Stephen C. Harris; Roger G. Perkins; Federico M. Goodsaid; Lei Guo; Lisa J. Croner; Cecilie Boysen; Hong Fang; Shashi Amur; Wenjun Bao; Catalin C. Barbacioru; Vincent Bertholet; Xiaoxi Megan Cao; Tzu-Ming Chu; Patrick J. Collins; Xiao-hui Fan; Felix W. Frueh; James C. Fuscoe; Xu Guo; Jing Han; Damir Herman; Huixiao Hong; Ernest S. Kawasaki; Quan-Zhen Li; Yuling Luo; Yunqing Ma; Nan Mei; Ron L. Peterson; Raj K. Puri; Feng Qian; Richard Shippy; Zhenqiang Su; Yongming Andrew Sun; Hongmei Sun; Brett Thorn; Yaron Turpaz; Charles Wang; Sue-Jane Wang; Janet A. Warrington; James C. Willey; Jie Wu; Qian Xie; Liang Zhang; Lu Zhang; Sheng Zhong; Russell D. Wolfinger; Weida Tong.
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts.  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values.  We recommend the use of FC...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/306/version/2

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniel Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/version/1

Malaria Diagnosis and the Plasmodium Life Cycle: the BFO Perspective
Provedor de dados: 17
Autores: Werner Ceusters; Barry Smith.
Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We here address a challenge to this realist approach...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/3960/version/2

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
Provedor de dados: 17
Autores: Adam A. Margolin; Teresa Palomero; Pavel Sumazin; Andrea Califano; Adolfo Ferrando; Gustavo A. Stolovitzky.
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Biochemically validated analysis in human T-cells reveals that three transcription factor oncogenes, NOTCH1, MYC, and HES1, bind one order of magnitude more promoters than previously thought. Gene expression profiling upon NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, establishing a closer link between occupancy and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1364/version/1

The role of Havana and communities in the manual curation of unfinished  vertebrate genomes
Provedor de dados: 17
Autores: Denise R. Carvalho-Silva; Chao-Kung Chen; Adam Frankish; James Gilbert; Leo Gordon; Toby Hunt; Mustapha Larbaoui; Jane E. Loveland; Jonathan Mudge; Harminder Sehra; Catherine Snow; Charlie Steward; Marie Marthe Suner; Mark Thomas; Laurens Wilming; Jennifer Harrow.
Manual annotation&amp;#x202d; (&amp;#x202c;the&amp;#x202d; &amp;#x22;&amp;#x202c;museum&amp;#x202d;&amp;#x22; &amp;#x202c;model of annotation&amp;#x202d;) &amp;#x202c;relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.&amp;#x202d; This&amp;#x202c; is both costly and time consuming and therefore is used only for model organisms with sufficient funding.&amp;#x202d; &amp;#x202c;Smaller research communities often have to rely on other models of annotation,&amp;#x202d; &amp;#x202c;mainly automated annotation&amp;#x202d; (&amp;#x202c;the&amp;#x202d; &amp;#x22;&amp;#x202c;factory&amp;#x202d;&amp;#x22; &amp;#x202c;model,&amp;#x202d; &amp;#x202c;e.g.&amp;#x202d;...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3102/version/1

Waist Circumference predicting Cardiovascular Disease in Korean Men and Women
Provedor de dados: 17
Autores: Sun Ha Jee; Sat Byul Park.
Objective: Obesity and cardiovascular disease (CVD) are closely related and have become increasingly prevalent in Korea. Asians are more prone to obesity-related co-morbidities than Caucasians, even at lower body mass index (BMI) and/or smaller waist circumference (WC) values. Nevertheless, little is known regarding the association of WC with the risk of CVD in non-Caucasian populations. The authors conducted a prospective cohort study of WC and the risk of CVD in the Korean Heart Study.Methods: We examined the association of WC to CVD incidence among 53,026 Korean adults (30,152 men, 22,874 women) with no history of CVD and/or cancer. During a mean follow-up of 8.6 years, 2,722 incident cases of atherosclerotic cardiovascular disease (ASCVD) including...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4609/version/1

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions
Provedor de dados: 17
Autores: Luiz A. Bovolenta; Marcio L. Acencio; Ney Lemke.
Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).&amp;#xd;&amp;#xa;Description: The HTRIdb is an open-access database of experimentally validated...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6995/version/1

Development of a Decision Support System (DSS) for an integrated test system towards the effective and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine  H&amp;#xf6;flich; Andreas  M&amp;#xfc;ller; J&amp;#xf6;rg  Schmidtke; Kerstin  Schmidt; Inge  Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to implement environmental effects e.g. on non-targets or the variability of transgene expression.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/1

In silico identification of potential inhibitors for human aurora kinase b
Provedor de dados: 17
Autores: Mahesh Babu G; Pradeep N.; Dibyabhaba  Pradhan; Manne  MuniKumar; Amineni  Umamaheswari.
Cell cycle progression through mitosis and meiosis involves regulation by serine/threonine kinases from the aurora family. Aurora kinase b (Aurkb) is mainly involved in the proper segregation of chromosomes during mitosis as well as meiosis. However, over expression of Aurkb leads to the unequal distribution of genetic information creating aneuploid cells, a hallmark of cancer. Thus, Aurkb can be used as an effective molecular target for computer-aided drug discovery against cancer. Existing Aurkb inhibitors are less efficient, hence an in silico work was carried out to identify novel potent inhibitors. Three published inhibitors azd1152, zm447439 and  N-(4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy) quinazolin- 4-yl] amino} phenyl) benzamide were subjected to...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5458/version/1

The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem
Provedor de dados: 17
Autores: Todd Vision.
Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4595/version/1

BridgeDb: standardized access to gene, protein and metabolite identifier mapping services
Provedor de dados: 17
Autores: Martijn P. van Iersel; Alexander R. Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R. Conklin; Chris T. A. Evelo.
Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5023/version/1

Bio2RDF: Convert, Provide And Reuse.
Provedor de dados: 17
Autores: Marc-Alexandre Nolin; Jacques Corbeil; Luc Lamontagne; Michel Dumontier.
The Bio2RDF project uses open-source Semantic Web technologies to provide interlinked life science data in order to maximize productivity and facilitate biological knowledge discovery. Using both syntactic and semantic data integration techniques, Bio2RDF puts into practice a simple methodology to generate and&amp;#xd;&amp;#xa;seamlessly integrate machine-interpretable data that can be powerfully interrogated with SPARQL-based queries to answer sophisticated questions.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;At its core, database records are converted into a set of statements or so-called triples that are captured together as a named graph annotated with provenance. The records and the entities they are about are provided with a Uniform Resource Identifier...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5060/version/1

Protein Data Integration through Ontologies
Provedor de dados: 17
Autores: Amandeep S. Sidhu.
In this paper, we consider the challenges of information integration in proteomics from the prospective of researchers using information technology as an integral part of their discovery process. Specifically, data integration, meta-data specification, data provenance and data quality are discussed here. Here we review existing protein data integration methods and propose the use of common vocabulary for protein data integration using ontologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4062/version/1

SNPxGE2: a database for human 3-way SNP-expression associations
Provedor de dados: 17
Autores: Yupeng Wang; Sandeep J. Joseph; Xinyu Liu; Michael Kelly; Romdhane Rekaya.
Recently, gene co-expression relationships have been found to be often conditional and dynamic. Besides, many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE2 database contains the computationally predicted human 3-way SNP-expression associations, that is, the differential co-expression between 2 genes is associated with a genotype/SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 701,202 SNPs and 15,000 gene expression profiles. Two models of 3-way SNP-expression associations were considered: gap/substitution and on/off. The implementation was carried out...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5704/version/1

A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel  Ega&amp;#xf1;a Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies  has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies&amp;#x27; Cell Type Ontology, is included as an illustration.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3478/version/1

The BioGRID Interaction Database
Provedor de dados: 17
Autores: Michael S. Livstone; Bobby-Joe Breitkreutz; Chris Stark; Lorrie Boucher; Andrew Chatr-Aryamontri; Rose Oughtred; Julie Nixon; Teresa Reguly; Jennifer Rust; Andrew Winter; Kara Dolinski; Mike Tyers.
The goal of the Biological General Repository for Interaction Datasets (BioGRID) (http://www.thebiogrid.org) is to archive and freely disseminate collections of genetic and protein interactions from major model organisms. BioGRID currently houses over 335,000 interactions curated from high-throughput datasets and individual focused studies found in the primary literature, as derived from some 23,000 publications. Complete coverage of the entire literature for both the budding yeast _Saccharomyces cerevisiae_ and the fission yeast _Schizosaccharomyces pombe_ has been achieved, resulting in the curation of over 246,000 interactions, and efforts to expand curation across multiple species are underway. Through collaborations with the Gene Ontology (GO)...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5627/version/1

Embedding machine-readable proteins interactions data in scientific articles for easy access and retrieval
Provedor de dados: 17
Autores: Paolo Tieri; Alberto Termanini; Piero Fariselli; Claudio Franceschi.
Extraction of protein-protein interactions data from scientific literature remains a hard, time- and resource-consuming task. This task would be greatly simplified by embedding in the source, i.e. research articles, a standardized, synthetic, machine-readable codification for protein-protein interactions data description, to make the identification and the retrieval of such very valuable information easier, faster, and more reliable than now.&amp;#xd;&amp;#xa;We shortly discuss how this information can be easily encoded and embedded in research papers with the collaboration of authors and scientific publishers, and propose an online demonstrative tool that shows how to help and allow authors for the easy and fast conversion of such valuable biological data...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2337/version/1

Agenda of the  &amp;#x22;BioSharing workshop -  Bringing catalogues of bio-resource and standards together&amp;#x22;
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Pascale Gaudet.
This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were twofold:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;1. Ensure that BioSharing (www.biosharing.org), a catalogue of minimal information checklists, terminologies and exchange formats (hereafter called standards) and policies, complements and links to existing catalogues of tools and databases, and also to publications and related material;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;2. Outline the technical implementations of the bioDBcore checklist (www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to ensure (bi-directional) linking to the BioSharing catalogue....
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6145/version/1

BioSharing Overview
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Dawn Field; Annapaola Santarsiero; Eamonn  Maguire; Philippe Rocca-Serra; Chris Taylor; Lee Harland; The BioSharing  Communities.
Download this poster providing an overview of the BioSharing effort.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5936/version/1

Computational methods in cancer gene networking
Provedor de dados: 17
Autores: Edwin Wang.
In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as &amp;#x201c;next generation&amp;#x201d; genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but &amp;#x2018;real signals&amp;#x2019; or biological insights, molecular mechanisms and biological principles...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2737/version/1

Visualising a scienti&amp;#xfb01;c article
Provedor de dados: 17
Autores: Roderic Page.
This paper describes my entry in the Elsevier Grand Challenge &amp;#x22;Knowledge Enhancement in the Life Sciences&amp;#x22; contest.  The entry takes a collection of fulltext issues of _Molecular Phylogenetics and Evolution_ as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a &amp;#x22;web&amp;#x22; of objects linked by typed relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2579/version/1

Can ABC be Used for Model Selection?
Provedor de dados: 17
Autores: Xavier  Didelot; Rich  Everitt; Adam  Johansen; Dan  Lawson.
Over the past ten years, Approximate Bayesian Computation (ABC) has become hugely popular to estimate the parameters of a model when the likelihood function cannot be computed in a reasonable amount of time. ABC can in principle be used also to perform Bayesian model comparison, but this raises the  question of which summary statistic should be used for such applications. Here we present a general method for constructing a summary statistic that is sufficient for the model choice problem. We apply this construction to models from the exponential family. Unfortunately, in more complex models, our construct often results in statistics with too high dimensionality to use in ABC. We therefore discuss the possibility of applying ABC with non-sufficient...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5955/version/1

Effective Phylogenetic Compression with TreeZip
Provedor de dados: 17
Autores: Suzanne J. Matthews; SeungJin Sul; Tiffani L. Williams.
Phylogenetic trees are family trees that represent the relationships between a group of organisms, or taxa. The most popular techniques for reconstructing phylogenetic trees intelligently navigate an exponentially-sized tree space by solving NP-hard optimization problems that that best hypothesize the evolutionary history for a given set of taxa. Instead of reconstructing a single tree, these heuristics often return tens to hundreds of thousands of trees that represent equally-plausible hypotheses for how the taxa of interest evolved from a common ancestor. As biologists attempt to reconstruct increasingly larger phylogenies, these tree collections only continue to grow in size. To combat the cost of storage and to facilitate the transfer of these large...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4613/version/1

MEMOFinder: combining _de_ _novo_ motif prediction methods with a database of known motifs
Provedor de dados: 17
Autores: Bartek Wilczynski; Milosz  Darzynkiewicz; Jerzy  Tiuryn.
*Background:* Methods for finding overrepresented sequence motifs are useful in several key areas of computational biology. They aim at detecting very weak signals responsible for biological processes requiring robust sequence identification like transcription-factor binding to DNA or docking sites in proteins. Currently, general performance of the model-based motif-finding methods is unsatisfactory; however, different methods are successful in different cases. This leads to the practical problem of combining results of different motif-finding tools, taking into account current knowledge collected in motif databases.&amp;#xd;&amp;#xa;*Results:* We propose a new complete service allowing researchers to submit their sequences for analysis by four different...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2289/version/2

semanticSBML 2.0 - A Collection of Online Services for SBML Models
Provedor de dados: 17
Autores: Falko Krause; Timo Lubitz; Marvin Schulz; Edda Klipp.
semanticSBML 2.0 is a collection of online services for the processing of biochemical networks in the SBML (Systems Biology Markup Language) document format. It allows users to edit SBO (Systems Biology Ontology) and RDF based MIRIAM (Minimum Information Required in the Annotation of Models) annotations, check for semantic validity, compare and merge SBML documents, and to create submodels. Given an annotated SBML document similar SBML documents can be retrieved from the BioModels Database via a ranked similarity search. Further  features of semanticSBML 2.0 include  graph visualization of SBML documents, parameter balancing, creation of SBML documents using shorthand SBML, and an interface to the BioModels Database that allows the comparison of document...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5402/version/1

Interoperability With Moby 1.0 - It&amp;#x27;s Better Than Sharing Your Toothbrush!
Provedor de dados: 17
Autores: Mark Wilkinson.
The BioMoby project was initiated in 2001 from within the model organism database community.  It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach.  Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry API, and supporting Perl and Java code-bases.  Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow.  Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1486/version/1

Normalization and Matching of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Jasmin &amp;#x160;ari&amp;#x107;; Henriette Engelken; Meik Bittkowski; Ulrike Wittig; Wolfgang M&amp;#xfc;ller; Isabel Rojas.
The identification of a chemical compound solely based on its name requires comprehensive chemical knowledge and often extensive searches in chemical databases. However, it is crucial for the integration of biochemical data extracted from the literature, since many publications exclusively describe a compound by its name. We have developed an application which matches synonymic names of chemical compounds and thereby facilitates the bundling of corresponding data referring to the same compound.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The tool that we have developed is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Matching of synonymous names is achieved by comparison of the normalized...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3322/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; transition, enabled a punctuated sequence of increasingly complex genetic codes and protein translators under mechanisms similar to the Serial Endosymbiosis effecting the Eukaryotic transition. These evolved until the ancestor to the present narrow spectrum of nearly maximally robust codes became locked-in by path dependence.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/2

Simcluster: clustering enumeration gene expression data on the simplex space
Provedor de dados: 17
Autores: Ricardo Z. N. V&amp;#xea;ncio; Leonardo A. B. Varuzza; Carlos Pereira; Helena Brentani; Ilya Shmulevich.
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST &amp;#x22;digital northern&amp;#x22;, are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/202/version/1

Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Provedor de dados: 17
Autores: I. C. Baianu.
Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for &amp;#x27;skeletal models&amp;#x27;, graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7075/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Navonil De Sarkar; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/2

Universal Features in the Genome-level Evolution of Protein Domains
Provedor de dados: 17
Autores: Marco Cosentino Lagomarsino; Alessandro L. Sellerio; Philip D. Heijning; Bruno Bassetti.
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity.  Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only.  We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data.  Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1376/version/2

Food Physical Chemistry and Biophysical Chemistry
Provedor de dados: 17
Autores: I.C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/1

ABC for ancestral inference
Provedor de dados: 17
Autores: Richard  Wilkinson; Simon  Tavare.
ABC for ancestral inference
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5963/version/1

A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints
Provedor de dados: 17
Autores: Tingting Qin; Lam Tsoi; Andrew Lawson; Jim Zheng.
We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us to distinguish biological relevant gene&amp;#x2014;gene connections in the network.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3511/version/1

Deciphering the phylogenetic history of neuroserpin orthologs  across metazoans by analysis of synteny and rare genomic characters
Provedor de dados: 17
Autores: Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.&amp;#xd;&amp;#xa;The objective of this study was to elucidate the phylogenetic kinships of serpins involved in...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2496/version/1

EvolveAGene 3: A DNA coding sequence evolution simulation program
Provedor de dados: 17
Autores: Barry G. Hall.
EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches.  Variation includes base substitutions, insertions and deletions.  Output includes a log file,  the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1230/version/1

Novel approaches, including systems biology, to HIV vaccine research and development: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Bali  Pulendran; Rino Rappuoli; Alan Aderem; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a two-day workshop on August 10-11 2009, at the Fred Hutchison Cancer Research Center offices in Seattle, WA, to discuss the application of novel approaches,including systems biology, to HIV vaccine research and development. The goals of this Working Group were to identify key scientific issues and opportunities that have emerged since the Enterprise Scientific Strategic Plan1 was published in 2005, and to make recommendations to Enterprise stakeholders.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4798/version/2

Tales From the Code Front:  Translating Modularity
Provedor de dados: 17
Autores: Lucian P. Smith.
In translating modular Antimony models to and from CellML, two differences appeared:  CellML&amp;#x27;s &amp;#x27;black box&amp;#x27; approach vs. Antimony&amp;#x27;s &amp;#x27;model composition&amp;#x27; approach, and CellML&amp;#x27;s math-based encoding vs. Antimony&amp;#x27;s object and rule-based encoding.  The latter turned out to have a much larger impact on the translation than anticipated.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5132/version/1

Grid technology for collaborative ontology development
Provedor de dados: 17
Autores: Stuart Aitken; Kemian Dang; Jonathan Bard.
In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on stand-alone editors running on users&amp;#x2019; desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and Prot&amp;#xe9;g&amp;#xe9;) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3186/version/1

INCF Workshops on Needs for Training in Neuroinformatics: Extended and Short Course Provision
Provedor de dados: 17
Autores: David Willshaw.
The second and third _INCF Workshops on Training in Neuroinformatics_ were organized by the INCF National Node of the UK. In these workshops, the issues arising in providing extended courses, such as a full time Masters, or short courses, of a few days or a few weeks, were discussed. There was a focus on how the INCF could facilitate training in these types of courses. In this report, the recommendations from all three Training workshops are brought together.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5599/version/1

FreePub: Collecting and Organizing Scienti&amp;#xc;c Material Using Mindmaps
Provedor de dados: 17
Autores: Theodore Dalamagas; Tryfon Farmakakis; Manolis Maragkakis; Artemis Hatzigeorgiou G. Hatzigeorgiou.
This paper presents a creativity support tool, called FreePub,to collect and organize scientifi&amp;#xc;c material using mindmaps. Mindmaps are visual, graph-based representations of concepts, ideas, notes, tasks, etc. They generally take a hierarchical or tree branch format, with ideas branching into their subsections. FreePub supports creativity cycles. A user starts such a cycle by setting up her domain of interest using mindmaps. Then, she can browse mindmaps and launch search tasks to gather relevant publications from several data sources. FreePub, besides publications, identifies helpful supporting material (e.g., blog posts, presentations). All retrieved information from FreePub can be imported and organized in mindmaps. FreePub has been fully...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5432/version/1

EvoIO: Community-driven standards for sustainable interoperability
Provedor de dados: 17
Autores: Arlin Stoltzfus; Karen Cranston; Hilmar Lapp; Sheldon McKay; Enrico Pontelli; Rutger Vos; Nico Cellinese.
Interoperability is the property that allows systems to work together independent of who created them, or how or for what purpose they were implemented. It is crucial for aggregating data from different online resources and for integrating different kinds of data. Interoperability is based on effective standards that become and remain broadly adopted. We argue that to develop and apply such standards for evolutionary and biodiversity data sustainably, we need a community-driven, open, and participatory approach. With the goal to build such an approach, the EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities.  EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4588/version/1

Bringing Text Miners and Biologists Closer Together
Provedor de dados: 17
Autores: An&amp;#xe1;lia Louren&amp;#xe7;o; S&amp;#xf3;nia Carneiro; Rafael Carreira; Miguel Rocha; Isabel Rocha; Eug&amp;#xe9;nio C. Ferreira.
The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do, whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3188/version/1

Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia  Salgado; Hilda Solano; Julio Collado-Vides.
Since its inception, RegulonDB (&amp;#x22;http://regulondb.ccg.unam.mx/&amp;#x22;:http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/version/2

TreeBASE2: Rise of the Machines
Provedor de dados: 17
Autores: Rutger A. Vos; Hilmar Lapp; William H. Piel; Val Tannen.
TreeBASE is a public repository of peer-reviewed phylogenetic knowledge. Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4600/version/1

Research Objects: Towards Exchange and Reuse of Digital Knowledge
Provedor de dados: 17
Autores: Sean Bechhofer; David De Roure; Matthew Gamble; Carole Goble; Iain Buchan.
What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  In this paper we discuss the notion of _research objects_, semantically rich aggregations of resources, that can possess some scientific intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4626/version/1

12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era
Provedor de dados: 17
Autores: Rafa&amp;#x142; W&amp;#xf3;ycicki; Justyna Witkowicz; Magdalena Pawe&amp;#x142;kowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pl&amp;#x105;der; Anna Seroczy&amp;#x144;ska; Mieczys&amp;#x142;aw &amp;#x15a;miech; Katarzyna Niemirowicz-Szczytt; Stanis&amp;#x142;aw Karpi&amp;#x144;ski; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. &amp;#xd;&amp;#xa;We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15&amp;#x2019;196 contigs of 197 Mbp length and N50 27&amp;#x2019;086 bp and 4&amp;#x2019;157 scaffolds of 224 Mbp length...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5466/version/1

Networking Phylogeny for Indo-European and Austronesian Languages
Provedor de dados: 17
Autores: Philippe Blanchard; Filippo Petroni; Maurizio Serva; Dimitri Volchenkov.
Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the &amp;#x2018;express train&amp;#x2019; model of Austronesian expansion from South-East Asia, with...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3156/version/1

Using TreeBASE from R
Provedor de dados: 17
Autores: Carl Boettiger.
I introduce an R package allowing programmatic access to the phylogenetic data in the TreeBASE archive and highlight why this is important.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6851/version/1

Phylogeny of conserved adenines in linkers of Group-I introns
Provedor de dados: 17
Autores: Natarajan Ganesan; Chandrasekhar Kesavan.
We have analyzed the linkers in group-I introns, a characteristic region that is crucial to the folding and splicing process of the folded RNA, in seventy sequences spreading across r-RNA, t-RNA and organelle genes from various organisms including algae, fungi and protozoa. The study revealed a high degree of consensus of specific adenine residues in J3/4, J6/7 and J8/7 stems of the linker regions that were required to stabilize the local orientation, either as single residue or by forming unusual base pairs along with divalent metal ions. Conservation of these residues in the Group-I intron linkers suggests their significant contribution to the folded structure whose bonding and geometry recruit metal ions to interact in stabilizing the folded nature of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2909/version/1

A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin  Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/1

Precise Atomic Structures of two Important Molecules in Biochemistry:
Provedor de dados: 17
Autores: Raji Heyrovska; Saraswathi Narayan; Lakshmi Atchison.
This work celebrates the &amp;#x201c;International Year of Chemistry &amp;#x2013; 2011&amp;#x201d;, by providing &amp;#x201c;for the first time&amp;#x201d;, the structures at the atomic level of two important molecules, namely, ascorbic acid and aspirin. Ascorbic acid, also known as vitamin C, was discovered as a cure for scurvy which claimed many human lives and hence got its name. It is also supposed to be an antioxidant and to prevent flu. Aspirin is synthesized from salicylic acid and is widely used as a remedy for flu and has other medical uses such as saving the lives of cardiac patients as an anticoagulant of blood. The biochemistry and chemistry of both these compounds have been evolving for nearly a century ever since their discoveries. Here, the...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5966/version/1

Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical Morphology
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; B. S. Dayasagar; Shantanav Chakraborty; Ranita  Guha; Arunava Goswami.
Fractals and Mathematical Morphology are immensely used to study many problems in different branches of science and technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human, Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can be exposed through intricate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5674/version/1

Pharmacophore Modeling and Binding Analysis for targeting Mycobacterium tuberculosis MurC ligase
Provedor de dados: 17
Autores: Yogesh N; Jignesh P; Vivek K; C Gopi Mohan.
Despite the availability of effective chemotherapy and the moderately protective vaccine, new anti-Tuberculosis agents are urgently needed to decrease the global incidence of Tuberculosis (TB). The resumption of TB, mainly caused by the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains and HIV epidemics, led to an increased need to understand the molecular mechanisms of drug action and drug resistance, which should provide significant insight into the development of newer compounds.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Based on this ground, computational studies of Mtb-MurC enzyme inhibition were carried out to find out novel lead molecules against the same.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4163/version/1

Docking-based virtual screening for the exploration of potential antagonists for human IGFBP6
Provedor de dados: 17
Autores: Bhuvanagiri Sravani; Dibyabhaba Pradhan; Amineni  Umamaheswari.
Design of potential drug-like candidates for cardiovascular therapy is of interest in recent years. Elevated level of IGFBP-6 leads to perilous diseases like atherosclerosis, high output cardiac failure and myocardial infarction. The current IGFBP-6 inhibitors available in clinical practice are not having satisfactory anti-cardiovascular effects, leaving room for further improvement. Therefore, with an aim to propose a potent inhibitor to arrest the cardiovascular disease caused by IGFBP-6, tools of computer-aided drug designing were used for virtual screening from small molecule databases. Accordingly, IGFBP-6 tertiary structure was solved through nuclear magnetic resonance techniques retrieved from the protein data bank. Fifteen IGFBP-6 inhibitors were...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6525/version/1

Statistical analysis of protein molecules
Provedor de dados: 17
Autores: Kushal Shah.
In this paper, entropy and auto-correlation values of main chain dihedral angles of 22,356 protein molecules are calculated and found to lie within a well-specified range for most proteins. Also, the entropy values obey a Gaussian distribution, which indicates that entropy plays a crucial role in evolution and conservation of protein tertiary structures. A comparison of the auto-correlation values of the dihedral angles of the entire protein molecule with those of the alpha helices and beta sheets indicates that random coils play an important role in determining the tertiary structure of protein molecules.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6298/version/1

H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts
Provedor de dados: 17
Autores: Chisato Yamasaki; Katsuhiko Murakami; Jun-ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB; &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3251/version/1

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain
Provedor de dados: 17
Autores: Michael Hawrylycz; Jyl Boline; Albert Burger; Tsutomu Hashikawa; G. Allan Johnson; Maryann Martone; Lydia Ng; Jonathan Nissanov; Luis Puelles; Seth Ruffins; Fons Verbeek; Ilya Zaslavsky.
The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/4000/version/1

The Cognitive Atlas: Employing Interaction Design Processes to Facilitate Collaborative Ontology Creation
Provedor de dados: 17
Autores: Eric Miller; Christian Seppa; Aniket Kittur; Fred W. Sabb; Russell A. Poldrack.
The Cognitive Atlas is a collaborative knowledge-building project that aims to develop an ontology that characterizes the current conceptual framework among researchers in cognitive science and neuroscience. The project objectives from the beginning focused on usability, simplicity, and utility for end users. Support for Semantic Web technologies was also a priority in order to support interoperability with other neuroscience projects and knowledge bases. Current off-the-shelf semantic web or semantic wiki technologies, however, do not often lend themselves to simple user interaction designs for non-technical researchers and practitioners; the abstract nature and complexity of these systems acts as point of friction for user interaction, inhibiting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4532/version/1

Ligand Based Virtual Screening to Design Novel Human MEK1 Protein Inhibitors for Potential Development of Drugs Against Melanoma
Provedor de dados: 17
Autores: Vijayasree Potluri; Dibyabhaba  Pradhan; Amineni Umamaheswari.
The Ras-dependent Raf/MEK/ERK signaling pathway is a major regulator of cell proliferation and survival. Hyper activation of the pathway is frequently observed in human malignancies as a result of aberrant activation of receptor tyrosine kinases or mutations in RAF (V600E).  MEK1 is dual-specificity tyrosine/threonine protein kinases found in the pathway. The RAF  mutation (present in 50% of melanomas) have been shown to be highly dependent on MEK1 activity and also MEK1 is the only acknowledged activator of ERK, making them attractive targets for therapeutic intervention. In view of its importance, identification of potent inhibitor against MEK1 may be valuable to design effective drugs against melanoma. Inhibitors for human MEK1 reported till dates have...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4901/version/1

_Drosophila_ and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome
Provedor de dados: 17
Autores: Abhay Sharma.
Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ&amp;#x2019;s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a _Drosophila_ model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ&amp;#x2019;s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4330/version/1

Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
Provedor de dados: 17
Autores: Andrey Ptitsyn; Jeffrey Gimble.
*Background*&amp;#xd;&amp;#xa;It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results*&amp;#xd;&amp;#xa;We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/858/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/2

Tendril, adhesive disc and super adhesive effect of climbing plant
Provedor de dados: 17
Autores: Wenli Deng.
Understanding the super adhesion mechanism of biological system is of great scientific interest and a prerequisite for bioinspired design of adhesive systems. To investigate the versatile climbing plant requires the development of new methods. Here I present strategies to fully study the super adhesive effect of climbing plant _Parthenocissus tricuspidata_ by the first time measuring the mass and the attached area of single adhesive disc, by further determining the microscopic structure and the adhesive strength of single adhesive disc and by finally elucidating the adhesion mechanism in cellular and molecular level using the classical theories and the proposed new hypothesis and model. I have measured that a single mature adhesive disc has an average mass...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1513/version/1

OneStop:JWS Online&amp;#x27;s access point to SBML,SBGN and MIRIAM compliant annotation
Provedor de dados: 17
Autores: Franco B. Du Preez; Stuart Owen; Katherine Wolstencroft; Olga Krebs; Wolfgang M&amp;#xfc;ller; Carole Goble; Jacky L. Snoep.
We have developed an online model constructor and validator called OneStop, which is compliant with SBGN, SBML and MIRIAM standards. Key features of OneStop are: 1) a human readable input form (in addition to SBML upload and saving); 2) live visualization (SBGN graphics) of the reaction network during the construction phase; and 3) online access from any machine with a compatible browser. Sophisticated error feedback simplifies the debugging process during model construction significantly and guides the efforts of new users in a step by step fashion. OneStop is seamlessly integrated with the JWS Online model repository and simulator and also facilitates the importation of models from the BioModels database. In addition, OneStop is part of the SysMO-SEEK...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6349/version/1

The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
Provedor de dados: 17
Autores: D.B.R.K. Gupta Udatha; Irene  Kouskoumvekaki; Lisbeth Olsson; Gianni  Panagiotou.
One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4762/version/1

Gene and Pathway-Based Analysis: Second Wave of Genome-wide Association Studies
Provedor de dados: 17
Autores: Gang Peng; Li Luo; H1oicheong Siu; Yun Zhu; Pengfei Hu; Shengjun Hong; Jinying Zhao; Xiaodong Zhou; John D. Reveille; Li Jin; Christopher I. Amos; Momiao Xiong.
Despite great success of GWAS in identification of common genetic variants associated with complex diseases, the current GWAS have focused on single SNP analysis. However, single SNP analysis often identifies a number of the most significant SNPs that account for only a small proportion of the genetic variants and offers limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis for thirteen published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single SNP analysis, but also...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2068/version/1

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review
Provedor de dados: 17
Autores: Peter Csermely; Kuljeet Singh Sandhu; Eszter Hazai; Zsolt Hoksza; Huba J. M. Kiss; Federico Miozzo; Daniel V. Veres; Francesco Piazza; Ruth Nussinov.
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into &amp;#x2018;cumulus-type&amp;#x2019;, i.e., those similar to puffy (white) clouds, and &amp;#x2018;stratus-type&amp;#x2019;, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5608/version/1

Robust information from phylogenetic trees?
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics.  I present both these weaknesses and a more robust comparison by likelihood ratio.  I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4614/version/1

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
Provedor de dados: 17
Autores: Ralph Haygood; Olivier Fedrigo; Brian Hanson; Ken-Daigoro Yokoyama; Gregory Wray.
Surveys of protein-coding sequences for evidence of positive selection in humans and chimpanzees have flagged surprisingly few genes known to be involved in neural or nutritional processes, despite the pronounced differences between humans and chimpanzees in behavior, cognition, and diet. It may be that most such differences are due to changes in gene regulation rather than protein structure. Here, we present the first survey of promoter (5&amp;#x27;-flanking) regions, which are rich in _cis_-regulatory sequences, for signatures of positive selection in humans. Our results indicate that positive selection has targeted the regulation of many genes known to be involved in neural development and function, both in the brain and elsewhere in the nervous system,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/69/version/1

Analysis and visualisation of RDF resources in Ondex
Provedor de dados: 17
Autores: Catherine Canevet; Artem Lysenko; Andrea Splendiani; Matthew Pocock; Chris Rawlings.
An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1].  This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.&amp;#xd;&amp;#xa;Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5430/version/1

Genome Replikin Count Predicts Increased Infectivity/Lethality of Viruses
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
The genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in &amp;#x2018;resting&amp;#x2019; virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7144/version/1

The Role of Neuregulin 1 in Schizophrenia:  A Bioinformatics Approach
Provedor de dados: 17
Autores: Alvaro M. Dias; Vinicius V. M. C. Maracaja-Coutinho; Artur A. Q. L. Lopo.
*Context:* Notwithstanding the great number of studies on the etiology and pathophysiology of schizophrenia, both issues remain far from being fully understood. Schizophrenia seems to be related to several biochemical abnormalities, which point to a multi-factor etiology and pathophysiology, as well as to the perspective that several etiologically diverse disorders might coexist within this nosographic entity. On the other hand, identical twins reveal a high concordance for schizophrenia. From that standpoint, the perspective that structurally-related proteins may play an important and yet non-deterministic role seems attractive. Among these proteins, it is suggestive that Neuregulin 1 exerts a pivotal role. &amp;#xd;&amp;#xa;*Objective:* This paper aims...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3905/version/1

Huntington&amp;#x2019;s disease is a TH17 related autoimmune disorder against mutant Huntingtin coded by multiple CAG triplets
Provedor de dados: 17
Autores: Wanchung(Wanjiung) Hu.
Huntington&amp;#x2019;s disease is an inherited neurodegenerative disorder. It belongs to the polyQ accumulation disease with mutant Huntington protein. The mutant Huntington has expanded CAG triplet repeats which make it easy to accumulate. However, the exact mechanism causing Huntington&amp;#x2019;s disease pathophysiology is unknown. Here, I propose that Huntington&amp;#x2019;s disease is an autoimmune disease. During childhood, there are Treg cells from the thymus to prevent autoimmune reaction against mutant Huntington. When the patient grows older with thymus atrophy, the accumulated mutant Huntington triggers TH17 related inflammatory reaction via heat shock proteins and toll-like receptor activation. Then, TH17 related cytokines such as...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6129/version/1

A community of biocurators
Provedor de dados: 17
Autores: Pascale Gaudet.
Biocuration is a difficult mission: biological data is highly heterogeneous, and there are few areas where guidelines for data preservation and exchange exist. This has hampered the speed, quantity and diversity of data possible to capture. Hence, a major challenge for the biocuration community is to explore innovative ways to capture, represent and display information. It is also essential to increase the involvement of researchers, publishers and funding agencies in this process. I will discuss the work of the International Society for Biocuration to build a community of biocurators to achieve these goals.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5134/version/1

SBML Level 3 Package Proposal: Annotation
Provedor de dados: 17
Autores: Dagmar Waltemath; Neil Swainston; Allyson L. Lister; Frank Bergmann; Ron Henkel; Stefan Hoops; Michael Hucka; Nick Juty; Sarah Keating; Christian Knuepfer; Falko Krause; Camille Laibe; Wolfram Liebermeister; Catherine Lloyd; Goksel Misirli; Marvin Schulz; Morgan Taschuk; Nicolas Le Nov&amp;#xe8;re.
The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5610/version/1

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Provedor de dados: 17
Autores: Leming Shi; Wendell D. Jones; Roderick V. Jensen; Stephen C. Harris; Roger G. Perkins; Federico M. Goodsaid; Lei Guo; Lisa J. Croner; Cecilie Boysen; Hong Fang; Shashi Amur; Wenjun Bao; Catalin C. Barbacioru; Vincent Bertholet; Xiaoxi Megan Cao; Tzu-Ming Chu; Patrick J. Collins; Xiao-hui Fan; Felix W. Frueh; James C. Fuscoe; Xu Guo; Jing Han; Damir Herman; Huixiao Hong; Ernest S. Kawasaki; Quan-Zhen Li; Yuling Luo; Yunqing Ma; Nan Mei; Ron L. Peterson; Raj K. Puri; Feng Qian; Richard Shippy; Zhenqiang Su; Yongming Andrew Sun; Hongmei Sun; Brett Thorn; Yaron Turpaz; Charles Wang; Sue-Jane Wang; Janet A. Warrington; James C. Willey; Jie Wu; Qian Xie; Liang Zhang; Lu Zhang; Sheng Zhong; James J. Chen; Russell D. Wolfinger; Weida Tong.
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts.  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values.  We recommend the use of FC...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/306/version/1

Text Mining in Full Text Articles -- Methodical and Represenation Issues
Provedor de dados: 17
Autores: Roman Klinger; Robert Pesch; Theo Mevissen; Juliane Fluck.
In many cases, information from abstracts of biomedical publications is not sufficient for annotation of database entries. Therefore, text mining systems supporting curators of biodatabases should be able to process full text articles. Beside the technical problems arising from full text parsing, the representation of the annotated full text is an important issue. Journal articles are mostly electronically available in PDF or HTML format. Also with more easily manageable XML formats, readers would like to have a visualisation of annotations and semantic enrichment directly in the PDF or HTML. We summarize the technical problems arising from parsing of HTML and PDF journal full texts and show first results of visualisation in both formats.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3141/version/1

Open Biomedical Ontologies Applied to Prostate Cancer
Provedor de dados: 17
Autores: James A. Overton; Cesare Romagnoli; Rethy Chhem.
This paper surveys preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the Open Biomedical Ontologies (OBO) library have been used to annotate clinical reports about prostate cancer. First we discuss why we rejected several controlled vocabularies, including SNOMED, DICOM, and RadLex, preferring instead to use the OBO library. We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked to the ontology terms. This method allows us to discover which relevant terms exist in the OBO library, and which do not. The final section of this paper discusses these gaps in the...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3570/version/1

LexOWL: A Bridge from LexGrid to OWL
Provedor de dados: 17
Autores: Cui Tao; Jyotishman Pathak; Harold Solbrig; Christopher Chute.
The Lexical Grid project is an on-going community driven initiative that provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. In order to add more powerful functionalities to the existing infrastructure and align LexGrid more closely with various Semantic Web technologies, we introduce the LexOWL project for representing the ontologies modeled within the LexGrid environment in OWL (Web Ontology Language). The crux of this effort is to create a &amp;#x201c;bridge&amp;#x201d; that functionally connects the LexBIG (a LexGrid API) and the OWL API (an interface that implements OWL) seamlessly. In this paper, we discuss the key aspects of designing and...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3468/version/1

Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially &amp;#x2018;A/T&amp;#x2019;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3581/version/1

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the &amp;#x27;energy&amp;#x27; picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual &amp;#x27;developmental&amp;#x27; perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/2

The Vaginal Microbiome: Disease, Genetics and the Environment
Provedor de dados: 17
Autores: Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James  P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael  D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico A. Puma; Mark A. Reimers; Maria C. Rivera; Seth B. Roberts; Myrna G. Serrano; Nihar U. Sheth; Judy L. Silbert; Logan Voegtly; Elizabeth C. Prom-Wormley; Bin Xie; Timothy  P. York; Cynthia N. Cornelissen; Jerome L. Strauss; Lindon J. Eaves; Gregory A. Buck.
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5150/version/1

Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker; Charlie Chandsawangbhuwana.
*Background.*  The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood.  Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate.  Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.&amp;#xd;&amp;#xa;*Results.*  We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts.  We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus and human estrogen-related receptor...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1542/version/1

TATA binding protein binds to single stranded DNA: A new model for eukaryotic transcription
Provedor de dados: 17
Autores: Rostem J. Irani.
Although the players mediating the initiation of eukaryotic transcription appear to be known, the mechanism is not. In this paper we report findings on the interaction between the TATA box binding protein (TBP) and DNA, using a novel optical technology, that point to a potential plausible physical mechanism, and at the same time tie together a number of otherwise disparate observations. TBP plays a central and ubiquitous role in initiating eukaryotic transcription, binding to promoters with and without the canonical 5&amp;#x2019; TATA(A/T)A(A/T)(G/A) 3&amp;#x2019; motif1. It also tends to bind to double-stranded DNA promiscuously, and though affinity is lower, the number of binding opportunities is greater. TBP-DNA complexes have been characterized...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4139/version/1

Integrative Approach - New Level Knowledge of Functions: Opportunities and Prospects
Provedor de dados: 17
Autores: Vladimir M. Pokrovskii.
In this article, the example of the mechanisms of heart rhythmogenesis in the intact organism is used to demonstrate the new capabilities provided by an integrative approach. It is shown that the rhythm is formed in the brain, transmitted to the heart in the form of signals along the vagus nerves and reproduces the heart. Evidence: the heart rhythm reproduces the natural efferent signals in the vagus nerves in the cardio-respiratory synchronism and in the intact organism sino-atrial node performs the functions of the latent pacemaker. Integration of the two hierarchical levels of rhythmogenesis (brain and intracardiac) provides the reliability and functional perfection of cardiac rhythm generation in the body. It is expedient to extend the presented...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6938/version/1

Evolvability of Chaperonin Substrate Proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state, and prevent their aggregation. Recently, an additional function was proposed for molecular chaperones: they serve as buffers (_capacitors_) for evolution by permitting their substrate proteins to mutate and at the same time still allowing them to fold productively.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Using pairwise alignments of _E. coli_ genes with genes from other gamma-proteobacteria, we showed that the described buffering effect cannot be observed among substrate proteins of GroEL, an essential chaperone in _E. coli_. Instead, we find that GroEL substrate proteins evolve less than other soluble _E. coli_ proteins. We analyzed several specific structural and...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/1

Sharing Detailed Research Data Is Associated with Increased Citation Rate
Provedor de dados: 17
Autores: Heather A. Piwowar.
Presentation based on the publication here:&amp;#xd;&amp;#xa;Piwowar HA, Day RS, Fridsma DB (2007) Sharing Detailed Research Data Is Associated with Increased Citation Rate. PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/361/version/1

PathExpand: Extending biological pathways using molecular interaction networks
Provedor de dados: 17
Autores: Enrico Glaab; Anais Baudot; Natalio Krasnogor; Alfonso Valencia.
We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyze their enrichment in cancer mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes.
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5639/version/1

A Framework for BioCuration Workflows (part II)
Provedor de dados: 17
Autores: Martin Krallinger.
This is the second part of the talk &amp;#x2018;A Framework for BioCuration Workflows&amp;#x2019;, given by Martin Krallinger from the Spanish National Cancer Research Centre at the &amp;#x27;Text Mining for the BioCuration Workflow&amp;#x27; workshop. The first part was held by Gully APC Burns (USC Information Sciences Institute, USA). This presentation covered some of the main general tasks often shared by existing literature biocuration workflows: Identification of relevant articles, identification and normalization of the actual bio-entities, the extraction of the annotation event and the identification of some evidential support (e.g. experimental evidence). Some of the important aspects, bottlenecks and potential text mining approaches were briefly...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3126/version/1

Searching for better flu surveillance? A brief communication arising from Ginsberg et al. Nature 457, 1012-1014 (2009)
Provedor de dados: 17
Autores: Donald R. Olson; Atar Baer; Michael  A. Coletta; Lana  Deyneka; Ryan  Gentry; Amy  Ising; Erin  L. Murray; Marc  Paladini; Justin  Pendarvis; Karl  Soetebier; Kevin J. Konty; Jill  Schulmann; Jeffrey  Engel; Julia  Gunn; Robert  T. Rolfs; Farzad  Mostashari.
Through retrospectively analyzing billions of internet search queries, Ginsberg et al. identified a collection of specific searches that track the course of influenza-like illness (ILI) reported by the US Centers for Disease Control and Prevention (CDC). Prospective monitoring during 2007-2008 found high correlation between Google estimates and CDC-reported ILI, with next-day timeliness compared to the 1-2 week delay reported in traditional CDC ILI surveillance. The assertion by Ginsberg et al., however, that internet search term estimates enable public health officials to respond better to seasonal and pandemic influenza does not take into account the current practice of public health, or the state of the art in electronic disease surveillance.
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3493/version/1

Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision
Provedor de dados: 17
Autores: Masa Tsuchiya; Vincent Piras; Masaru Tomita; Alessandro Giuliani; Kumar Selvarajoo.
Cells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors.  However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4401/version/1

Future Outlook for Databases from the Perspective of Bioresources Databases
Provedor de dados: 17
Autores: Yukiko Yamazaki.
Databases, like journals, are now an essential component of our research activities. However, the maintenance of databases and the timely, accurate, and complete incorporation into them of the wealth of data being created daily through scientific activities represent a difficult problem.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;I have been working on bioresources databases and come to appreciate the need for closer links between journals and databases to improve the scientific value of databases. For example, it is frequently difficult to identify experimental materials from articles in journals. In experimental science, it is vital that one scientist&amp;#x2019;s experiments are readily reproducible by others; this requires an environment that provides other...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5068/version/1

A Quantitative Approach to Investigating the Hypothesis of Prokaryotic Intron Loss
Provedor de dados: 17
Autores: Robert M. Sinclair.
Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate splicing in environments harboring...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5770/version/1

The &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) specification
Provedor de dados: 17
Autores: Pelin  Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette  Johnston; Guy Cochrane; Robert  Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine  A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn  Maguire; Barbara A. Meth&amp;#xe9;; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; J&amp;#xf6;rg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aym&amp;#xe9; Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Gl&amp;#xf6;ckner.
We present the Genomic Standards Consortium&amp;#x2019;s (GSC) &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5252/version/2

Creatine kinase in energy metabolic signaling in muscle
Provedor de dados: 17
Autores: Olav Kongas; Johannes H. G. M. van Beek.
There has been much debate on the mechanism of regulation of mitochondrial ATP synthesis to balance ATP consumption during changing cardiac workloads. A key role of creatine kinase (CK) isoenzymes in this regulation of oxidative phosphorylation and in intracellular energy transport had been proposed, but has in the mean time been disputed for many years. It was hypothesized that high-energy phosphoryl groups are obligatorily transferred via CK; this is termed the phosphocreatine shuttle. The other important role ascribed to the CK system is its ability to buffer ADP concentration in cytosol near sites of ATP hydrolysis. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Almost all of the experiments to determine the role of CK had been done in the steady state, but...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1317/version/1

Implementation of SBML Level 3 Support within iBioSim
Provedor de dados: 17
Autores: Chris J. Myers.
This presentation gives details about our experiences when adding SBML Level 3 support to our iBioSim tool.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4988/version/1

Evolution of malaria virulence in cross-generation transmission through selective immune pressure
Provedor de dados: 17
Autores: David E. Gurarie.
Theoretical arguments and some mathematical models of host-parasite coevolution (e.g. [1- 6]) suggest host immunity as the driving source for the evolution of parasite virulence. Imperfect vaccines in particular, can play the role and recent work [7] sets to test these ideas experimentally, using the mouse malaria model, Plasmodium chabaudi. To this end the authors evolve parasite lines in immunized and nonimmunized (&amp;#x201c;na&amp;#xef;ve&amp;#x201d;) mice using serial passage of infected blood samples. They find parasite lines evolved in immunized mice become more virulent than those evolved in naive mice. Furthermore, this feature persisted even when the evolved strains were transmitted through mosquitoes. &amp;#xd;&amp;#xa;Here we develop a...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/203/version/1

Comparative methods in R hackathon
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Michael Alfaro; Charles Bell; Benjamin Bolker; Marguerite Butler; Peter Cowan; Damien de Vienne; Richard Desper; Joseph Felsenstein; Luke Harmon; Christoph Heibl; Andrew Hipp; Gene Hunt; Thibaut Jombart; Steve Kembel; Hilmar Lapp; Scott Loarie; Wayne Maddison; Peter Midford; David Orme; Emmanuel Paradis; Sam Price; Dan Rabosky; Brian Sidlauskas; Stacey Smith; Dave Swofford; Todd Vision; Peter Waddell; Amy Zanne; Derrick Zwickl.
The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2126/version/1

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST [1] &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates [1]; &amp;#xd;&amp;#xa;B) BLASTX and BLASTN [2] for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats [3] and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/1

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: shankaracharya shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/1

Ontology (Science)
Provedor de dados: 17
Autores: Barry Smith.
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type &amp;#x2013; the Gene Ontology (GO) being the most conspicuous example &amp;#x2013; are a _part of science_. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2027/version/1

Identification and Evolution of Transcription Factors in Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
Background. &amp;#xd;&amp;#xa;Many transcriptional regulatory proteins have been identified and classified into several families on the basis of sequence similarity (Fukami, 2003), these families usually regulate important biological processes, such as development and responses to external stimuli. Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases (Latchman, 2004); in addition to TFs, other Transcriptional regulators (TRs) participate in transcriptional modulation by e.g., chromatin remodeling. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of Transcription...
Tipo: Presentation
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6400/version/1

LifeWatch &amp;#x2013; A European e-Science and observatory infrastructure supporting access and use of biodiversity and ecosystem data
Provedor de dados: 17
Autores: Mark Frenzel; Stefan Klotz; Alex Hardisty; Olaf Banki.
There are many promising earth and biodiversity-monitoring projects underway across the globe, but they often operate in information islands, unable easily to share data with others. This is not convenient: It is a barrier to scientists collaborating on complex, cross-disciplinary projects which is an essential nature of biodiversity research. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;LifeWatch (www.lifewatch.eu) is an ESFRI (European Strategy Forum on Research Infrastructures) initiative which has just entered its construction phase. It is aiming at new ways of collaboration, in an open-access research environment to solve complex societal and scientific questions on biodiversity and ecosystems. It installs a range of new services and tools to help the...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5843/version/1

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher  J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/2

Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
Provedor de dados: 17
Autores: Nicolo Fusi; Oliver Stegle; Neil Lawrence.
Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown environmental influences.  These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an&amp;#xd;&amp;#xa;eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5995/version/1

Dibutyltin Disrupts Glucocorticoid Receptor Function and Impairs Glucocorticoid-induced Suppression of Cytokine Production
Provedor de dados: 17
Autores: Christel Gumy; Charlie Chandsawangbhuwana; Anna A. Dzyakanchuk; Denise V. Kratschmar; Michael E. Baker; Alex Odermatt.
_Background_. Organotins are highly toxic and widely distributed environmental chemicals. Dibutyltin (DBT) is used as stabilizer in the production of polyvinyl chloride plastics, and it is also the major metabolite formed from tributyltin (TBT) _in vivo_. DBT is immunotoxic, however, the responsible targets remain to be defined. Due to the importance of glucocorticoids in immune-modulation, we investigated whether DBT could interfere with glucocorticoid receptor (GR) function.&amp;#xd;&amp;#xa;_Methodology_. We used HEK-293 cells transiently transfected with human GR as well as rat H4IIE hepatoma cells and native human macrophages and human THP-1 macrophages expressing endogenous receptor to study organotin effects on GR function. Docking of organotins was...
Tipo: Manuscript
Palavras-chave: Immunology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2312/version/1

An evaluation of taxonomic name finding &amp;#x26; next steps in Biodiversity Heritage Library (BHL) developments
Provedor de dados: 17
Autores: Chris Freeland.
The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name...
Tipo: Presentation
Palavras-chave: Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3372/version/1

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
INTRODUCTION&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;MR techniques have delivered images of brains from a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007), which also hampers a deeper understanding of the mechanisms behind structural alterations in neurodevelopmental disorders (Kochunov et al., 2010).  One of the reasons for this is the lack of computational tools suitable for morphometrci comparisons across multiple species. In this work, we aim to characterize this gap, taking primates as an...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/2

An Olfactory Receptor Pseudogene whose Function emerged in Humans
Provedor de dados: 17
Autores: Peter Lai; Gautam Bahl; Maryse Gremigni; Valery  Matarazzo; Olivier Clot-Faybesse; Catherine Ronin; Chiquito J. Crasto.
Human olfactory receptor, hOR17-210, is identified as a pseudogene in the human genome. Experimental data has shown however, that the gene product of cloned hOR17-210 cDNA was able to bind an odorant-binding protein and is narrowly tuned for excitation by cyclic ketones. Supported by experimental results, we used the bioinformatics methods of sequence analysis, computational protein modeling and docking, to show that functionality in this receptor is retained due to sequence-structure features not previously observed in mammalian ORs. This receptor does not possess the first two transmembrane helical domains (of seven typically seen in GPCRs). It however, possesses an additional TM that has not been observed in other human olfactory receptors. By...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1290/version/1

Automatic protein clustering as a basis of automatic annotation
Provedor de dados: 17
Autores: Naoki Sato.
Development of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP searches.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Here I propose a potentially automatic method of annotation that exploits automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs using &amp;#x2018;entropy-optimized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5086/version/1

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong Sang Low; Christopher J. O. Baker; Alex Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3542/version/1

Analysis of Cancer Omics Data In A Semantic Web Framework
Provedor de dados: 17
Autores: Matthew Holford; James P. McCusker; Kei Cheung; Michael Krauthammer.
Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancel cell&amp;#x27;s molecular state and its response to anti-cancer therapy.  To study the problem, we have previously focused on data warehousing technologies and statistical data integration.  In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology.  A key new component presented here is a SPARQL endpoint to our existing data warehouse.  This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO).  We show how such variegated quantitative and functional data can be integrated and...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5391/version/1

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/2

Chromosomal mutational algebra: a new algebra to manipulate chromosomal mutation
Provedor de dados: 17
Autores: Dipankar Mazumdar.
This study leads to a new algebra. An algebra is defined on the common mechanisms of chromosomal mutation. The algebra (_S^[PSI](C)_^, ~*~, &amp;#x27;, [DELTA], _D_) is constructed for a given _C_ and [PSI]. This algebra represents the most common chromosomal mutational mechanisms. This can lead to a new way to manipulate chromosomal mutation with higher structures of abstract mathematics. The first proposal of the algebra was reported in Mazumdar _et al._, 2007.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3874/version/1

Open Notebook Science - Falcipain-2 Preliminary Results
Provedor de dados: 17
Autores: Jean-Claude Bradley; Philip Rosenthal; Rajarshi Guha; Khalid Mirza; Jiri Gut.
This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Screencast available at:...
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2216/version/1

Tutorial: Query Federation with SWObjects
Provedor de dados: 17
Autores: Eric Prud&amp;#x27;hommeaux; Helena Deus; M. Scott Marshall.
Query federation is a way to make use of distributed data sources on the Web, including many SPARQL endpoints as well as relational databases. SWObjects makes use of mapping rules represented as SPARQL Constructs to dynamically rewrite the terms and predicates of a SPARQL query into corresponding terms in another vocabulary and connect the resulting query with the appropriate service for answering the query. SWObjects can also rewrite SPARQL queries in SQL, effectively including relational databases alongside SPARQL endpoints in a linked data federation. The author of SWObjects, Eric Prud&amp;#x27;hommeaux, is the W3C staff contact for the W3C Health Care and Life Sciences Interest Group (HCLS IG) and will give the tutorial via a teleconference connection,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5538/version/1

Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
Provedor de dados: 17
Autores: Satya N. V. Arjunan; Masaru Tomita.
The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3526/version/1

A novel Drosophila transcriptomic and behavioral model detects potassium chloride with therapeutic potential
Provedor de dados: 17
Autores: Farhan Mohammad; Priyanka Singh; Abhay Sharma.
In a newly described _Drosophila_ model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the chronic PTZ model. Both...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3429/version/1

An Ontology for Designing Models of Epidemics
Provedor de dados: 17
Autores: Geoffrey Frank; William Wheaton; Vesselina Bakalov; Phillip Cooley; Diane Wagener.
Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics.&amp;#xd;&amp;#xa;An ontology has been developed for MIDAS to support the collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious disease ontology) that define the scope of its models and supporting documentation.&amp;#xd;&amp;#xa;The ontology is used to aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the MIDAS repository...
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3555/version/1

IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and alleles
Provedor de dados: 17
Autores: Fatena Bellahcene; Ge&amp;#x301;raldine Folch; Joumana Jabado-Michaloud; Chantal Ginestoux; Patrice Duroux; Ve&amp;#x301;ronique Giudicelli; Marie-Paule Lefranc.
The immunoglobulin (IG) and T cell receptor (TR) major loci span about 6 Megabases (Mb) of the human genome on chromosomes 2, 7, 14 and 22, and 9 Mb in mouse on chromosomes 6, 12, 13, 14 and 16. There are seven major loci: three IG loci (IGH, IGK, IGL) and four TR loci (TRA, TRB, TRG, TRD), with a distinct repartition of the variable (V), diversity (D), joining (J) and constant (C) genes. The human genome comprises a total number of 608-665 IG and TR genes (371-422 IG and 237-243 TR), depending on the haplotypes, per haploid genome ^1, 2^ of which 531-588 genes are located in the major loci (distributed in 369-418 V, 32 D, 105-109 J and 25-29 C genes). There are also 77 orphons (68 IG and 9 TR) including two processed IG genes, outside the major loci. The...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3158/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses- (v.3)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/3

Identifying Copy Number Variations based on Next Generation Sequencing Data by a Mixture of Poisson Model
Provedor de dados: 17
Autores: Karin Schwarzbauer; G&amp;#xfc;nter  Klambauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more popular due to cost effectiveness and their speed. NGS can be utilized to identify DNA structural variants, namely copy number variations (CNVs) which showed association with diseases like HIV, diabetes II, or cancer.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;There have been first approaches to detect CNVs in NGS data, where most of them detect a CNV by a  significant difference of read counts within neighboring windows at the chromosome. However these methods suffer from systematical variations of the underlying read count distributions along the chromosome due to biological and technical noise. In contrast to these global methods, we locally...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4716/version/1

Data integration in myGrid with Taverna
Provedor de dados: 17
Autores: Duncan Hull.
Many areas of life sciences research involve integrating terabytes of heterogeneous, &amp;#xd;&amp;#xa;distributed and autonomous data available on the Web. The myGrid project has addressed &amp;#xd;&amp;#xa;these challenging problems by developing and applying novel grid and semantic web &amp;#xd;&amp;#xa;services technology to life science data integration, particularly genome annotation and &amp;#xd;&amp;#xa;microarray analysis. This presentation outlines the past, present and future of the Taverna workflow system.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/331/version/1

Determination of Soybean Oil, Protein and Amino Acid Residues in Soybean Seeds by High Resolution Nuclear Magnetic Resonance (NMRS) and Near Infrared (NIRS)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina Costescu; P R. Lozano; Valentin Prisecaru; Randall   L. Nelson.
A detailed account is presented of our high resolution nuclear magnetic resonance (HR-NMR) and near infrared (NIR) calibration models, methodologies and validation procedures, together with a large number of composition analyses for soybean seeds. NIR calibrations were developed based on both HR-NMR and analytical chemistry reference data for oil and twelve amino acid residues in mature soybeans and soybean embryos. This is our first report of HR-NMR determinations of amino acid profiles of proteins from whole soybean seeds, without protein extraction from the seed.  It was found that the best results for both oil and protein calibrations were obtained with a Partial Least Squares Regression (PLS-1) analysis of our extensive NIR spectral data, acquired...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7053/version/1

Specification of spatial relationships in directed graphs of cell signaling networks
Provedor de dados: 17
Autores: Azi Lipshtat; Susana R. Neves; Ravi Iyengar.
Graph theory provides a useful and powerful tool for the analysis of cellular signaling networks. Intracellular components such as cytoplasmic signaling proteins, transcription factors and genes are connected by links, representing various types of chemical interactions that result in functional consequences. However, these graphs lack important information regarding the spatial distribution of cellular components. The ability of two cellular components to interact depends not only on their mutual chemical affinity but also on co-localization to the same subcellular region.  Localization of components is often used as a regulatory mechanism to achieve specific effects in response to different receptor signals.  Here we describe an approach for...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2038/version/1

The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Analysis
Provedor de dados: 17
Autores: Jacques  Ravel; Larry J. Forney.
The vaginal microbiota play an important protective role in maintaining the health of women. Disruption of the mutualistic relationship that exists between bacterial communities in the vagina and their hosts can lead to bacterial vaginosis (BV), a condition in which lactic acid producing bacteria are supplanted by a diverse array of strictly anaerobic bacteria. BV has been shown to be an independent risk factor for adverse outcomes including preterm delivery and low infant birth weight, acquisition of sexually transmitted infections and HIV, and development of pelvic inflammatory disease. National surveys indicate the prevalence of BV among U.S. women is 29.2%, and yet, despite considerable effort, the etiology of BV remains unknown. Moreover, there are no...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5062/version/1

Annotation-based meta-analysis of microarray experiments
Provedor de dados: 17
Autores: Jie Zheng; Junmin Liu; Elisabetta Manduchi; Christian J. Stoeckert, Jr.
We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3569/version/1

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein &amp;#x27;molten globule&amp;#x27;. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty&amp;#x27;s (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry&amp;#x27;, that is, insulated from water fluctuations. We show that patterns of `dry&amp;#x27; residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom&amp;#x27;s depth inside an interface. We...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/version/1

Workspaces, exposures, and multiscale modelling
Provedor de dados: 17
Autores: David P. Nickerson.
Here I present technical details on the software package PMR2, which is the software running the CellML and Physiome Project model repositories. In particular, the use of mercurial repositories to define workspaces for collaborative model development, creating modular hierarchies of embedded workspaces, and defining exposures as a means to provide permanent links to specific revisions of model workspaces. I also briefly mention the use of OpenCMISS to link CellML models into large scale, spatially distributed field modeling and simulation.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4969/version/1

Subtyping of Dengue Viruses using Return Time Distribution based Appproach
Provedor de dados: 17
Autores: Pandurang Kolekar; Mohan Kale; Urmila Kulkarni-Kale.
Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind &amp;#x26; severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5590/version/1

Networking Phylogeny for Indo-European and Austronesian Languages
Provedor de dados: 17
Autores: Philippe Blanchard; Filippo Petroni; Maurizio Serva; Dimitri Volchenkov.
Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the &amp;#x2018;express train&amp;#x2019; model of Austronesian expansion from South-East Asia, with...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3156/version/2

Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils
Provedor de dados: 17
Autores: Andrea Nova; Sinan Keten; Nicola Pugno; Alberto Redaelli; Markus  J. Buehler.
Spider silk is one of the strongest, most extensible and toughest biological materials known, exceeding the properties of many engineered materials including steel.  Silks feature a hierarchical architecture where highly organized, densely H-bonded beta-sheet nanocrystals are arranged within a semi-amorphous protein matrix consisting of 31-helices and beta-turn protein structures. By using a bottom-up molecular-based mesoscale model that bridges the scales from Angstroms to hundreds of nanometers, here we show that the specific combination of a crystalline phase and a semi-amorphous matrix is crucial for the unique properties of silks. Specifically, our results reveal that the superior mechanical properties of spider silk can be explained solely by...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4336/version/1

Creating a Translational Medicine Ontology
Provedor de dados: 17
Autores: Christine Denney; Colin Batchelor; Olivier Bodenreider; Sam Cheng; John Hart; John Hill; John Madden; Mark Musen; Elgar Pichler; Matthias Samwald; Sa&amp;#x301;ndor Szalma; Lynn Schriml; David Sedlock; Larisa Soldatova; Koji Sonoda; David Statham; Holger Stenzhorn; Patricia L. Whetzel; Elizabeth Wu; Susie Stephens.
*Abstract*&amp;#xd;&amp;#xa;We, participants in the Translational Medicine Ontology activity of the World Wide Web Consortium&amp;#x2019;s Health Care and Life Sciences Interest Group (&amp;#x22;http://esw.w3.org/topic/HCLSIG&amp;#x22;:http://esw.w3.org/topic/HCLSIG) and members of the National Center for Biomedical Ontology (&amp;#x22;http://bioontology.org/&amp;#x22;:http://bioontology.org/), are developing a high-level, patient-centric ontology for translational medicine which will draw on existing domain ontologies and allow the integration of data throughout the drug development process.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The pharmaceutical industry has historically focused on the development of novel blockbuster drugs....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3686/version/1

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited
Provedor de dados: 17
Autores: Stephen D. Turner.
This manuscript provides software and a tutorial for creating manhattan plots and QQ plots for genome-wide association studies using the R statistical computing environment.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6070/version/1

The What, Why and How of openness in science
Provedor de dados: 17
Autores: Konrad U. Foerstner; Lars J. Jensen.
We give a short introduction to open science followed by an overview of Creative Commons and open source licenses.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1655/version/1

Online Human Health Risk Assessment &amp;#x26; Management: An in-silico approach
Provedor de dados: 17
Autores: Lavkush Dwivedi.
Dreamed quality of life can be achieved by good health and further restored and maintained by the identification of health-related issues and their effective management. Human health risk assessment &amp;#x26; management (HHRAM) approaches are applied for doing so. As internet is now increasingly being used by citizens as a major source of health information, the HHRAM approach was developed in the present study which could predict and manage online the health risks associated with any possible health hazard present in an Indian scenario. The approach is communicated to the entire population through the developed website www.healthrisk.co.in.&amp;#xd;&amp;#xa;The study was completed in three phases (1) Preparation of online health risk assessment...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5357/version/1

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers
Provedor de dados: 17
Autores: Shi Huang.
Interpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results.  This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution.  The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction.  Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny.  A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time.  This &amp;#x2018;slow clock&amp;#x2019; method showed that humans are...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3794/version/1

A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3447/version/1

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness
Provedor de dados: 17
Autores: Melanie Dulong de Rosnay.
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitates innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2083/version/1

A new phylogenetic comparative method: detecting niches and transitions with continuous characters
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples of these weaknesses using a classic data set on Anoles lizards.  I describe a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4615/version/1

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4967/version/1

Implementation Methods for Estimating Haplotypes with Grid Computing Technology
Provedor de dados: 17
Autores: Zafri Muhammad; Sanjaya KC; Phua Kia Kien.
Introduction: PHASE is a software for haplotype reconstruction and recombination rate estimation from population data and implements the methods for estimating haplotypes from population genotype data. This software require enormous computing power due to the complexity algorithms used. Recent advancement in grid computing and multi-core processing technology has resulted in the creating of virtual supercomputers (that are capable of massive parallel computations).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Method: PHASE version 2.0 was downloaded from PHASE&amp;#x2019;s homepage (http://stephenslab.uchicago.edu/software.html), and installed on 10 Apple iMac computers (20 CPUs) running Mac OS 10.5 using Apple&amp;#x2122; Xserve as a controller. A PHP web-based...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4168/version/1

Bacterial Capnine Blocks Transcription of Human Antimicrobial Peptides
Provedor de dados: 17
Autores: Trevor G. Marshall.
The US CDC believes that 65% of all infections in developed countries may be caused by pathogens in biofilms. Electron Microscopy has shown that these bacterial communities can evade phagocytosis, and persist in the cytoplasm of monocytes, macrophages, lymphocytes and neutrophils. Three decades ago, Wirostko _et al._ found such intraphagocytic communities in Crohn&amp;#x2019;s disease, Juvenile Rheumatoid Arthritis and Sarcoidosis. However, the mechanism(s) by which such persistent bacteria could evade the immune system have remained elusive. Recently, 16S RNA from species of gliding bacteria never thought to be able to survive _in vivo_, have been found in surgically removed biofilms. This study set out to identify whether the genomes of these gliding...
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/164/version/1

Community curation on WikiPathways: How we assist knowledge collection
Provedor de dados: 17
Autores: Chris Evelo.
Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal mechanism,...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3115/version/1

Keynote: A renaissance for the point mutation: from legacy data to semantic web service
Provedor de dados: 17
Autores: Christopher J. O. Baker.
Experiments that construct or discover protein point-mutations and investigate their functional consequences represent one of the cornerstones of biomedical investigation. And yet, despite the importance of these annotations, the interpretation and reuse of knowledge about their impacts remains a formidable task. This is due to a number of reasons including (i) the publishing of salient mutation impact descriptions in unstructured text, (ii) the existence of numerous boutique databases of mutation information which can have many years of latency, and (iii) errors within manually populated mutation databases. In recent years the mining of mutations from scientific documents has emerged as a promising research theme resulting in automated methods for...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5443/version/1

Docking studies to explore novel inhibitors against human beta-site APP cleaving enzyme (BACE-1) involved in Alzheimer&amp;#x2019;s disease
Provedor de dados: 17
Autores: S Anjum Mobeen; Manne  Munikumar; Amineni Umamaheswari.
Alzheimer&amp;#x2019;s disease (AD) is one of the most prominent neurodegenerative disorders, particularly in elder persons over 65 age. It is characterized by progressive cognitive deterioration together with declining activities. Amyloid precursor protein (APP) cleaves at A-beta (A&amp;#x3b2;) peptide by rate limiting factor of Beta-site APP cleaving enzyme (BACE-1) in amyloidogenic pathway. Elevated level of BACE-1 leads to the accumulation of an insoluble form of A&amp;#x3b2; peptides (Senile Plaques), an important hallmark in the pathogenesis of Alzheimer disease. Five published inhibitors of BACE-1, thiazolidinediones, rosiglitazone, pioglitazone, Sc7 and tartaric acid are available with poor pharmacological properties and intolerable side effects....
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6964/version/1

Cancer invasion associated gene expression signature is present in differentially expressed genes in the reprogramming of fibroblasts into stem cells
Provedor de dados: 17
Autores: Wei-yi Cheng; Hoon Kim; Jessica Kandel; Dimitris Anastassiou.
Tumors become invasive by penetrating adjacent connective tissue, but the underlying biological mechanisms remain obscure. We recently identified a precise gene expression signature of fibroblastic origin associated with cancer invasion, the first step of the metastatic cascade. The signature contains many coordinately overexpressed genes, prominent among which are COL11A1, THBS2 and INHBA. Here we show that there is a striking similarity between the set of expressed genes in this metastasis-associated fibroblastic (MAF) signature and the set of genes that are downregulated when fibroblasts are reprogrammed to induced pluripotent stem cells (iPSCs). Because it is known that fibroblast reprogramming involves a mesenchymal epithelial transition (MET), the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5924/version/1

SSR - Identification from EST
Provedor de dados: 17
Autores: Aikkal Riju.
Tutorial of Identification of SSR from EST resources using online Tools
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3908/version/1

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
Not applicable
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/58/version/1

Intra- and inter-individual genetic differences in gene expression
Provedor de dados: 17
Autores: Mark J. Cowley; Chris J. Cotsapas; Rohan B. H. Williams; Eva K. F. Chan; Jeremy N. Pulvers; Michael Y. Liu; Oscar J. Luo; David J. Nott; Peter F. R. Little.
Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1799/version/1

GabiPD: The GABI Primary Database - a plant integrative &amp;#x2018;omics&amp;#x2019; database
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Jost Neigenfind; Robert Wagner; Rico Basekow; Elke Weber; Bernd  Mueller-Roeber; Svenja Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different &amp;#x2018;omics&amp;#x2019; fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2210/version/1

Ecoinformatics: where are we, where do we want to go, and how to reach there.
Provedor de dados: 17
Autores: Abhay Krishna.
Compared to other natural sciences ecological sciences has always been about seeing the bigger picture. The realization that local actions can have global impact has been the hallmark of ecological research. This integrative view is getting more and more accepted now with the recognition that whole is definitely more then sum of its parts. Advancement in computer sciences has now made it possible to comprehend the complexity arising from an integrative approach. This has given rise to a field interfacing computer science and ecological sciences called Ecoinformatics. The other popular parallel and more mature field is bioinformatics or computational biology. The presentation will take the audience on an Ecoinformatics tour touching on present status of...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2018/version/1

Copyrights and digitizing the systematic literature: the horror... the horror...
Provedor de dados: 17
Autores: N. Dean Pentcheff.
It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world. It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. &amp;#x22;Fair Use&amp;#x22; guidelines, we can.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4644/version/1

Performance of the Charniak-Lease parser on biological text using different training corpora
Provedor de dados: 17
Autores: Alison V. Callahan; Michel Dumontier.
POS tagging is used as the first step in many NLP workflows, although the accuracy of tag assignment frequently goes unchecked. We hypothesize that changing the training corpora for a parser will affect its POS tagging of a target corpus. To this end we train the Charniak-Lease parser on the WSJ corpus and two biomedical corpora and evaluate its output to MedPost, a POS tagger with a reported 97% accuracy on biomedical text. Our findings indicate that using biomedical training corpora significantly improves performance, but that minor differences in the biomedical training corpora have a significant effect on the correctness of POS tagging. Specifically, the tagging of hyphenated words and verbs was affected. This work suggests that the choice of training...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2310/version/1

Mining the Largest Quasi-clique in Human Protein Interactome
Provedor de dados: 17
Autores: Sanghamitra Bandyopadhyay; Malay Bhattacharyya.
A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem of finding quasicliques that are almost complete subgraphs of a graph. In sparse and very large scale-free networks, the problem of finding the largest quasi-clique becomes hard to manage with the existing approaches. Here, we propose a heuristic algorithm in this paper for locating the largest quasi-clique from the human protein-protein interaction networks. The results show promise in computational biology research by the exploration of significant protein modules.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7125/version/1

A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel M&amp;#xf6;ller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and (c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a terminology on radiology
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/1

Analysis of Genetic Interaction Maps Reveals Functional Pleiotropy
Provedor de dados: 17
Autores: Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak.
Epistatic or genetic interactions, representing the effects of mutations on the phenotypes caused by other mutations, can be very helpful for uncovering functional relationships between genes. Recently, the Epistasis Miniarray Profile (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. As part of this approach, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles.  Here we present an original biclustering algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2182/version/1

Hyperinsulinemia and insulin resistance : What comes first ?
Provedor de dados: 17
Autores: Pramod  P. Patil; Milind M. Watve.
Background&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;1)&amp;#x9;Classical explanation :&amp;#xd;&amp;#xa;Classical explanation of diabetic pathophysiology states that obesity induced insulin resistance develops first and is followed by compensatory hyperinsulinnemia. Further  insulin resistance leads to prolonged, increased secretary demand on  beta cells  leading to subsequent secondary beta cell failure, giving rise  to hyperglycaemia and diabetes^2^.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;2)&amp;#x9; Neurobehavioral origin hypothesis :&amp;#xd;&amp;#xa;The  Neurobehavioral origin hypothesis suggests that insulin resistance mediates a shift from muscle dependent (soldier) to brain dependent (diplomat) strategies of making a livelihood.  If nutrient limitation...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5416/version/1

Comments and Suggestions for Improvement of the  Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Alexander Wait Zaranek; Tom Clegg; Ward  Vandewege; Joseph V. Thakuria.
This document is a comment on the X PRIZE validation protocol written by Kedes et al. (2011).  We propose several modifications which we think will improve the fairness and transparency of the contest while keeping the cost of the validation process under control.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5766/version/1

Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Provedor de dados: 17
Autores: Alexander Garnett; Heather A. Piwowar; Edie M. Rasmussen; Judy Illes.
Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process.  In this paper, we describe a system to help with this task, given an example set of  PubMed articles to retrieve and a corresponding set of articles to exclude.  The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold.  From this information and their knowledge of the domain, users can formulate a query and evaluate its performance.  We apply...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4270/version/2

The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins
Provedor de dados: 17
Autores: Francesca Diella; Allegra Via; Claudia Chica; Katja Luck; Catherin M. Gould; Toby J. Gibson.
Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein&amp;#x2013;protein interaction.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3152/version/1

Segmenting DNA sequence into words based on statistical language model
Provedor de dados: 17
Autores: Wang Liang.
This paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA &amp;#x201c;words&amp;#x201d; is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised &amp;#x2018;probability approach to word segmentation&amp;#x2019; method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6939/version/1

Mining Co-expression Graphs: Applications to MicroRNA Regulation and Disease Analysis
Provedor de dados: 17
Autores: Malay Bhattacharyya.
MicroRNAs (miRNAs) are known to translationally repress or post-transcriptionally regulate mRNAs and are responsible for many diseases. We are preparing a comprehensive framework of co-expression analysis to figure out co-expression, differential co-expression and co-expression dynamics within multiple phenotypes in expression profiles. The purpose is to elucidate the disease association of miRNAs via co-regulatory pattern analysis.
Tipo: Presentation
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7119/version/1

Mechanistic mechanisms of competition and biodiversity
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The nature of competition and biodiversity are open basic questions since Darwin. To investigate mechanisms of interspecific competition and their contribution in biodiversity as closely as possible we offer a white-box modelling method based on physically interpreted ecological axioms. These models are implemented as deterministic individual-based cellular automata and able to give a direct physico-mechanistic insight into studied phenomena. Competition of two trophically identical but fitness different species, competing for one limiting resource in one stable uniform habitat (which is closed for immigration, emigration, predation, herbivory and parasitism) has been investigated in conditions, which are the most unfavourable for their coexistence. The...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7105/version/1

Integrating Text Mining into the MGI Biocuration Workflow
Provedor de dados: 17
Autores: Karen G. Dowell; Monica S. McAndrews-Hill; David P. Hill; Harold J. Drabkin; Judith A. Blake.
A major challenge for the development of resources for functional and comparative genomics is the extraction of data from the biomedical literature.  Although text retrieval and extraction for biological data is an active research field, few applications have been integrated into production literature curation systems such as those of the model organism databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In September 2008, Mouse Genome Informatics (MGI) at The Jackson Lab initiated a search for dictionary-based text mining tools that we could integrate into our curation workflow.  MGI has rigorous document triage and annotation procedures designed to identify articles about mouse genome biology and determine whether those articles should be curated.  We...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3262/version/1

Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration
Provedor de dados: 17
Autores: Karin Radrich; Yoshimasa Tsuruoka; Paul Dobson; Albert Gevorgyan; Neil Swainston; Jean-Marc Schwartz.
The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3309/version/1

LibSBGN: current status and future plans
Provedor de dados: 17
Autores: Alice C. Villeger.
LibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.&amp;#xd;&amp;#xa;These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).&amp;#xd;&amp;#xa;The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.&amp;#xd;&amp;#xa;Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5304/version/1

Extending the Foundational Model of Anatomy with Automatically Acquired Spatial Relations
Provedor de dados: 17
Autores: Manuel M&amp;#xf6;ller; Christian  Folz; Michael Sintek; Sascha Seifert; Pinar Wennerberg.
Formal ontologies have made significant impact in bioscience over the last ten years. Among them, the Foundational Model of Anatomy Ontology (FMA) is the most comprehensive model for the spatio-structural representation of human anatomy. In the research project MEDICO we use the FMA as our main source of background knowledge about human anatomy. Our ultimate goals are to use spatial knowledge from the FMA (1) to improve automatic parsing algorithms for 3D volume data sets generated by Computed Tomography and Magnetic Resonance Imaging and (2) to generate semantic annotations using the concepts from the FMA to allow semantic search on medical image repositories. We argue that in this context more spatial relation instances are needed than those currently...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3471/version/1

Screening of actinobacteria for antimicrobial activities by a modified &amp;#x22;Cross-Streak&amp;#x22; method
Provedor de dados: 17
Autores: Nandkumar Kamat; Sonashia Velho-Pereira.
New molecule discovery from natural sources, such as that of actinobacteria, has proved to be an interesting area in antibiotic research, as most of these antibiotics are difficult to synthesize. Out of 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a &amp;#x2018;modified cross streak method.&amp;#x27; The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. 53%, 13% and 10% of tested actinobacterial strains belonging to Streptomyces, Micromonospora and Actinomadura genera, respectively, showed the ability of producing antimicrobial...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Immunology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6765/version/1

A new approach to generating research-quality data through citizen science: The USA National Phenology Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Lisa Benton; Theresa M. Crimmins; Mark Losleben; Andrew D. Richardson; Alyssa Rosemartin; Mark D. Schwartz; Kathryn A. Thomas; Jake F. Weltzin; Bruce E. Wilson.
Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our understanding of species&amp;#x2019; phenologies and how these phenologies are responding to recent, rapid climate change. Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level, naturally inspire human curiosity&amp;#x2014; thus providing an excellent opportunity to engage citizen scientists. The USA National Phenology Network has recently initiated a national effort to encourage people at different levels of...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3695/version/1

Ontology for Biomedical Investigations
Provedor de dados: 17
Autores: Bjoern Peters; The OBI Consortium.
The goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives, experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3623/version/1

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models.  The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/58/version/2

The Role of Bio-Ontologies in Data-Driven Research: A Philosophical Perspective
Provedor de dados: 17
Autores: Sabina Leonelli.
This project aims to reach a philosophical understanding of the role played by theory in the practices of data dissemination and re-use that characterise data-driven research. Bio-ontologies have the potential to play the epistemic role of theories in this context, insofar as they (1) express the knowledge underlying data-driven research and (2) guide such research towards future discoveries.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3646/version/1

Systems Pharmacology
Provedor de dados: 17
Autores: Ravi Iyengar.
The slides are from a presentation given by Professor Ravi Iyengar from Mount Sinai School of Medicine at the Drug Forum Meeting #9 that took place in Washington, DC on February 20-21, 2008. The slides describe two projects: one that was published last year, and the other unpublished. These projects used network analysis to explore the relationships between FDA approved drugs and a human protein-protein interaction network.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1749/version/1

Nucleotide repeats in mitochondrial genome determine human lifespan
Provedor de dados: 17
Autores: Konstantin Popadin; Georgii Bazykin.
Direct nucleotide repeats can facilitate deletions of segments of mitochondrial genome1, leading to a wide range of neuromuscular disorders1,2 as well as aging2,3 in humans. We hypothesized that the number of the direct perfect repeats in human mitochondrial genomes influences longevity through the formation of harmful mtDNA deletions in the somatic cells. The analysis of the complete mitochondrial genomes of 762 unrelated Japanese individuals4-6 reveals a negative correlation between the abundance of the direct perfect repeats and the expected longevity. This association is largely due to the disruption of the common repeat (8470,13447) by a point mutation 8473C which occurred at the origin of the D4a haplogroup characterized by extreme longevity in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2399/version/1

Standardising bioresource acknowledgement in papers
Provedor de dados: 17
Autores: Dr Robert Hewitt.
This presentation describes the speakers experience of gathering performance indicator data, for biobank assessment.  Problems encountered in collecting data on the number of publications resulting from supported studies are described.  These include difficulty in obtaining a complete record of all the resulting publications and also frequent misnaming of the biobank in the acknowledgment section of papers.  The presentation also includes a discussion of approaches to providing credit to all the contributors in the biobanking effort.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5607/version/1

Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
Provedor de dados: 17
Autores: Jonas Almeida; Helena Deus; Wolfgang Maass.
Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5537/version/1

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Qiime &amp;#x2013; a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;  &amp;#xd;&amp;#xa;B) UCHIME &amp;#x2013; a tool for rapid identification of chimeric 16S sequence fragments; &amp;#xd;&amp;#xa;C) Mothur &amp;#x2013; a C++-based software package for 16S analysis;&amp;#xd;&amp;#xa;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/1

MUSIC - Multisimulation Coordinator: Request For Comments
Provedor de dados: 17
Autores: &amp;#xd6;rjan Ekeberg; Mikael Djurfeldt.
MUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. MUSIC provides mechanisms to transfer massive amounts of event information and continuous values from one parallel application to another. Special care has been taken to ensure that existing simulators can be adapted to MUSIC. In particular, MUSIC handles data transfer between applications that use different time steps and different data allocation strategies. This RFC - Request For Comments - document invites comments on the proposed design and prototype specifications. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1830/version/1

Pyrosequencing/Sanger Plant Genome Assembly (Limitations, Problems And Solutions) - On The Way To Cucumber (Cucumis sativus L. cv. Borszczagowski) Draft Genome Sequence Publishing
Provedor de dados: 17
Autores: Rafal Woycicki; Zbigniew Przybecki.
Genome sequencing give us an opportunity to broaden the range and improve the quality of omics studies. New sequencing technologies make it possible to achieve the sequencing reads fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.&amp;#xd;&amp;#xa;We focus here on the wide range of approaches undertaken to assemble the draft cucumber (Cucumis sativus L. cv. Borszczagowski) genome done by using 12x coverage of pyrosequencing Titanium chemistry shotgun paired and unpaired reads combined with Sanger reads.
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4630/version/1

Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Provedor de dados: 17
Autores: Zengyou He; Chao Yang; Can Yang; Robert Z Qi; Jason Po-Ming Tam; Weichuan Yu.
*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques.  Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2268/version/1

2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/1

Review of Immunoinformatic approaches to in-silico B-cell epitope prediction
Provedor de dados: 17
Autores: Rick Reitmaier.
In this paper, the current state of in-silico, B-cell epitope prediction is discussed.   Recommendations for improving some of the approaches encountered are outlined, along with the presentation of an entirely novel technique, which uses molecular mechanics for epitope classification, evaluation and prediction.
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/353/version/1

The Simulation Experiment  Description Markup Language - Update
Provedor de dados: 17
Autores: Frank T. Bergmann.
This presentation gives a brief overview of the Simulation Experiment Description Markup Language L1V1 as well as an introduction to LibSedML (http://libsedml.sf.net) a library for reading and writing SED-ML documents.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5589/version/1

Sisseton Wahpeton College Student Internship &amp;#x2013; Learning About Water Quality Assessment, Geospatial Technologies, Landuse Classification and Statistical Analysis
Provedor de dados: 17
Autores: Brendon  Barker; Destinee  Eastman; Steven  Farmer, Jr.
Three student interns from Sisseton Wahpeton College and their advisor Karla Witt worked with researchers from South Dakota State University to explore the hypothesis that satellite imagery could be used as a tool to evaluate water quality in lakes on the Sisseton Wahpeton Reservation. Interns constructed their own Secchi disks and used them to measure transparency in lakes and mark the locations with a global positioning system (GPS) on days when satellite imagery was available. A geographic information system (GIS) was used to relate field measurements to satellite images. The students also conducted monthly water quality sampling on Pickerel, Enemy Swim and Clear Lakes to determine current trophic state. Existing land use maps for Pickerel Lake were...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5340/version/1

Large-scale imaging of brain network activity from &amp;#x3e;10,000 neocortical cells
Provedor de dados: 17
Autores: Shigehiro Namiki; Norio Matsuki; Yuji  Ikegaya.
Large-scale recording from populations of neurons is a promising strategy in the study of complex brain function. Here we introduce a simple optical technique that simultaneously probes the calcium activity of ~10,000 cells at the single cell resolution _in vitro_. We employed a combination of a low-magnification objective lens and an electron-multiplying charge-coupled device megapixel camera to achieve large-view-field and high-resolution imaging.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2893/version/1

SBGN-ED &amp;#x2013; working with the Systems Biology Graphical Notation
Provedor de dados: 17
Autores: Tobias Czauderna; Falk Schreiber.
The Systems Biology Graphical Notation - SBGN [1] provides a standard for the visual representation of biochemical and cellular processes. SBGN aims to improve information exchange and to support the collaborative creation of large maps based on individual modules. The language contains three views of biological processes covering different levels of detail:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(1) Process Description (PD): this sublanguage provides a detailed presentation of the temporal dependencies of biological  interactions in a network;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(2) Entity Relationship (ER): this sublanguage displays the relationships in which a given entity can participate in a network; and&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(3) Activity Flow...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6445/version/1

Ontology-driven International Maize Information System (IMIS) for Phenotypic and Genotypic Data Exchange
Provedor de dados: 17
Autores: Rosemary Shrestha; Hector Sanchez; Claudio Ayala; Peter Wenzl; Elizabeth Arnaud.
The Consultative Group on International Agricultural Research (CGIAR; http://www.cgiar.org/) centres have developed the International Crop Information System (ICIS; http://www.icis.cgiar.org) for the management and integration of global information on genetic resources, and germplasm improvement for any crop. The Maize breeding programs at CIMMYT (http://beta.cimmyt.org/) have different software tools to manage phenotypic, genotypic, and environmental information for their experiments generated worldwide. These tools have the capacity of collecting information in the field, wet lab, and store it into different relational databases. The IMIS (http://imis.cimmyt.org/confluence/display/IMIS/Crop+Finder) is an implementation of the ICIS, which is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5029/version/1

Fractal geometry of nature (bone) may inspire medical devices shape
Provedor de dados: 17
Autores: Salvatore Longoni; Matteo Sartori.
Medical devices, as orthopaedics prostheses and dental implants, have been designed over years on the strength of mechanical, clinical and biological indications. This sequence is the commonly accepted cognitive and research process: adapting the device to the surrounding environment (host tissue). Inverting this traditional logical approach, we started from bone microarchitecture analysis. Here we show that a unique geometric rule seems to underlie different morphologic and functional aspects of human jaw bone tissue: fractal properties of white trabeculae in low quality bone are similar to fractal properties of black spaces in high quality bone and vice versa. These data inspired the fractal bone quality classification and they were the starting point...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4512/version/1

BioModels Database: Next generation model repository
Provedor de dados: 17
Autores: Camille Laibe; Michael Hoehl.
Public announce that the software system running BioModels Database (&amp;#x22;http://www.ebi.ac.uk/biomodels/&amp;#x22;:http://www.ebi.ac.uk/biomodels/) will evolve from open source to a community developed project.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5127/version/1

Advancing transcriptome platforms
Provedor de dados: 17
Autores: Shuobo Shi.
During the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination of the transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based platform. Importantly, these next-generation technologies revolutionize assessing the entire transcriptome via the recent RNA-Seq technology.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5894/version/1

Homology modeling and in silico screening of inhibitors for human CD5 antigen-like protein involved in cardiovascular disease
Provedor de dados: 17
Autores: Varala Sravani; S Rajitha Reddy; Amineni Umamaheswari.
CD5L (CD5 antigen -like) is a secreted glycoprotein that belongs to the SRCR (scavenger receptor cysteine rich) group B family of proteins that regulate leukocyte function. Over expression of human CD5L leads to Kawasaki disease and atherosclerosis. In the quest of designing novel inhibitors against CD5L, homology models for the protein were predicted based on crystal structures of 1BY2, 2OYA and 2OY3 as multiple templates using Modeller 9v9. The CD5L homology models were selected using GA341 score, DOPE score, PROCHECK and ProSA to select the best model. The selected CD5L model was analyzed using CASTp to locate the largest ligand binding pocket. Five known inhibitors of human CD5L were searched for structural analogs from Ligand.Info Meta database. The...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6586/version/1

SARS-CoV Regulates Immune Function-Related Gene Expressions in Human Monocytic Cells
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu; Yu-Ting Yen; Sher Singh; Chuan-Liang Kao; Betty A. Wu-Hsieh.
Background: Severe Acute Respiratory Syndrome (SARS) is characterized by acute respiratory distress (ARDS) and pulmonary fibrosis, and the monocyte/macrophage is the key player in the pathogenesis of SARS.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Methods: In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV) infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection and the gene expression was profiled by oligonucleotide-based microarray. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: Analysis of immune-related gene expression profiles showed that 24 h after SARS-CoV infection, (i)...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5908/version/1

Expression cartography of human tissues using self organizing maps
Provedor de dados: 17
Autores: Henry Wirth; Hans Binder.
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.&amp;#xd;&amp;#xa;Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5825/version/1

A unified mechanistic model of niche, neutrality and violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10% difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%)....
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7089/version/1

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation
Provedor de dados: 17
Autores: Satya N. V. Arjunan; Masaru Tomita.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3845/version/1

SBGN Activity Flow Update
Provedor de dados: 17
Autores: Huaiyu Mi.
SBGN Activity Flow specification was released in September 2009.  In this talk, a brief review is provided on the specification, and a number of issues raised by the community are discussed.  Particular focus was on the issue of graphical representation of entity decoration of a biological activity.  A number of proposals from the community are discussed in detail.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5680/version/1

Present and future of proteomics data curation at the PRIDE database
Provedor de dados: 17
Autores: Juan Antonio Vizcaino; Henning Hermjakob; Lennart Martens.
Significant progress has been made in improving the accessibility and utility of the large amounts of generated high-throughput proteomics data by the introduction of publicly available proteomics repositories. One such repository is PRIDE (the &amp;#x2018;PRoteomics IDEntifications&amp;#x2019; database, &amp;#x22;http://www.ebi.ac.uk/pride&amp;#x22;:http://www.ebi.ac.uk/pride). PRIDE stores mass spectrometry related data, including peptide and protein identifications, mass spectra and valuable additional metadata.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;At present, data curation in PRIDE is limited to data submission support. The format in which all submissions need to take place is PRIDE XML. Mass spectrometry derived data is very heterogeneous in terms of...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3222/version/1

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniela Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Background: Every protein has a variable atomic and energetic cost to the cell based on the synthesis of its constituent amino acids. Quantifying the cost of amino acid synthesis is challenging, however natural selection is expected to favour the use of proteins whose constituents are cheaper to produce in terms of energetic and atomic cost.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We develop a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models, and directly investigate the effects of the cost of amino acid synthesis on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We used our two new and six previously reported measures of amino acid cost in conjunction with codon...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/version/2

Voluntary universal testing and treatment is unlikely to lead to HIV elimination: a modeling analysis
Provedor de dados: 17
Autores: Bradley  G. Wagner; Sally Blower.
Recently Granich et al. at the World Health Organization (WHO) concluded, using mathematical modeling, that HIV epidemics could be eliminated within a decade. They assumed all individuals would be tested annually and every infected individual (regardless of stage of infection) would be put on treatment. Based on this modeling study the WHO is considering using universal testing and treatment as an HIV elimination strategy. Here we examine the study by Granich et al. and assess its validity. We present new analyses of their model by varying assumptions and parameter values. We find that under certain very optimistic assumptions HIV elimination would be (theoretically) possible, but it would take at least 70 years. To obtain this result we assumed ~65% of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3917/version/1

Human ovarian reserve from conception to the menopause
Provedor de dados: 17
Autores: William H. B. Wallace; Thomas W. Kelsey.
Current understanding is that the human ovary contains a fixed number of several million non-growing follicles (NGF), established by five months of gestational age, that declines with increasing age to the menopause when approximately 1,000 NGF remain at an average age of 50-51 years. With approximately 450 ovulatory monthly cycles in the normal human reproductive lifespan, this progressive decline in NGF numbers is attributed to follicle death by apoptosis. Individual histological studies have quantified NGF numbers over limited age ranges. However, no model describing the rate of establishment and decline of the NGF population from conception to menopause has been previously reported. Here we describe the best fitting model of the age-related NGF...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3179/version/1

UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and  computational linguists
Provedor de dados: 17
Autores: Bart  Mellebeek; Carlos Rodriguez-Penagos; Laura Ines Furlong.
As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3171/version/1

Schizophrenia is a TH2 dominant autoimmune disease possibly against acetylcholine receptors of CNS
Provedor de dados: 17
Autores: Wanchung(Wan-Jiung) Hu.
Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6978/version/1

Integrative analysis of large-scale  biological data sets
Provedor de dados: 17
Autores: Enrico Glaab; Jonathan M. Garibaldi; Natalio Krasnogor.
We present two novel web-applications for microarray and gene/protein set analysis, ArrayMining.net and TopoGSA. These bioinformatics tools use integrative analysis methods, including ensemble and consensus machine learning techniques, as well as modular combinations of different analysis types, to extract new biological insights from experimental transcriptomics and proteomics data. They enable researchers to combine related algorithms and datasets to increase the robustness and accuracy of statistical analyses and exploit synergies of different computational methods, ranging from statistical learning to optimization and topological network analysis.
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5598/version/1

Internal ribosomal entry site lacks secondary structure
Provedor de dados: 17
Autores: Xuhua Xia.
The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1248/version/1

The TA-p73 functions as a Lung tumor suppressor by increasing the expression of miRNA, let-7
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
I have previously proposed that TA-p73-depenedent tumor suppressor pathway could inhibit the development of lung adenocarcinoma.  This hypothesis is strongly supported by a recent finding showing that TA-p73 specific knockout mice are prone to lung adenocarcinoma.  However, the p73-dependent tumor suppressor pathway remains ill defined.  It has been shown that let-7 cluster is highly expressed in normal lung.  Loss of let-7 expression: a) is common in Non-small cell lung carcinoma; and b) enhances lung tumor formation, indicating that it could function as a lung tumor suppressor.  Based on these facts, I hypothesized that let-7 could be a transcriptional target of p73.  To confirm this hypothesis, I have analyzed the let-7 cluster promoters using TRASFAC...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4252/version/1

Artificial Neural Network
Provedor de dados: 17
Autores: Smrita Singh.
In the postgenomic era, computational methods are being used in diverse areas like drug discovery, robotics, weather forecasting etc. Computational methods are incorporated with various programmes that are further instructed with complex algorithms based on different logistic approaches. Artificial neural network is one of them to be utilized in various molecular dynamics and simulation studies. Therefore, it is essential to understand the basic logic while programming in order to troubleshoot the computational methods.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6623/version/1

Detection of Metabolites by Proton Ex Vivo NMR, in Vivo MR Spectroscopy Peaks and Tissue Content Analysis: Biochemical-Magnetic Resonance Correlation: Preliminary Results
Provedor de dados: 17
Autores: Rakesh Sharma; Madan Rehani; Arun Agrawala.
*Aim*: Metabolite concentrations by in vivo magnetic resonance spectroscopy and ex vivo NMR spectroscopy were compared with excised normal human tissue relaxation times and tissue homogenate contents.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Hypothesis*: Biochemical analysis combined with NMR and MR spectroscopy defines better tissue analysis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Materials and Methods*: Metabolites were measured using peak area, amplitude and molecular weights of metabolites in the reference solutions. In normal brain and heart autopsy, muscle and liver biopsy tissue ex vivo NMR peaks and spin-lattice (T1) and spin-spin (T2) relaxation times, were compared with diseased tissue NMR data in meningioma brain, myocardial infarct heart,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4121/version/1

Unique features of Plasmids among different Citrobacter species
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The _Citrobacter_ plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The  _Citrobacter_ plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 _Citrobacter_ plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6836/version/1

Genome Replikin Count Predicts Increased Lethality of Resistant Tuberculosis
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
The genomic Replikin Count of all the sequences  on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7141/version/1

In-silico identification of potential antagonists for human Casein kinase II subunit alpha&amp;#x27; (CK2&amp;#x3b1;2)
Provedor de dados: 17
Autores: Kanipakam Hema; Harika  Meduru; Navya Pallapotu; Amineni Umamaheswari.
Human CK2&amp;#x3b1;2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal transduction. Over expression of CK2&amp;#x3b1;2 causes kidney cancer therefore, human CK2&amp;#x3b1;2 has been identified as a drug target for the development of potential antagonists against cancer therapy. The existing human CK2&amp;#x3b1;2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting. High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the present study to identify potential inhibitors of human CK2&amp;#x3b1;2. The co-crystal structure of human CK2&amp;#x3b1;2 was retrieved from the protein data bank. A...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6958/version/1

GO faster ChEBI with Reasonable Biochemistry
Provedor de dados: 17
Autores: Duncan Hull.
Chemical Entities of Biological Interest (ChEBI) is a database and ontology that represents biochemical knowledge about small molecules. Recent changes to the ontology have created new opportunities for automated reasoning with description logic, that have not previously been fully exploited in Chemistry. These changes open up the possibility of building an improved chemical semantic web, by making more use of necessary and sufficient conditions, allowing reasoning about chemical structure, highlighting ambiguous inconsistencies and improving alignment with the Gene Ontology (GO). This paper briefly discusses some of the problems with reasoning over the current version of ChEBI, to tackle these issues, and their potential solutions.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2329/version/1

The Genetic Signature of Perineuronal Oligodendrocytes
Provedor de dados: 17
Autores: Sara Szuchet; Joseph A. Nielsen; Gabor Lovas; Javier Martinez de Velasco; Dragan Maric; Lynn D. Hudson.
Oligodendrocytes in the central nervous system can be categorized as precursors, myelin-forming, and non-myelinating perineuronal cells. The function of perineuronal oligodendrocytes is unknown; it was proposed that following injury, they may remyelinate denuded axons. We investigated these cells&amp;#x27; potential. A combination of cell-specific tags, microarray technology and bioinformatics tools to identify gene expression differences between these subpopulations allowed us to capture the genetic signature of perineuronal oligodendrocytes. Here we report that perineuronal oligodendrocytes are configured for a dual role. As cells that embrace neuronal somata, they integrate a repertoire of transcripts designed to create their own code for communicating...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1821/version/1

The Evolution Ontology
Provedor de dados: 17
Autores: Adam M. Goldstein.
Existing ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts (e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include data curation, data mining, and literature curation, EO&amp;#x2019;s developers working on the latter two for works of Darwin and the Biodiversity Heritage Library.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3557/version/1

Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB)
Provedor de dados: 17
Autores: Rebecca E. Foulger; UniProt Consortium.
The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3153/version/1

PDBWiki
Provedor de dados: 17
Autores: Henning Stehr; Jose Duarte; Michael Lappe; Jong Bhak; Dan Bolser.
*Background:* The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. However, there is currently no consensus about how best to achieve this goal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings:* Here we present a community knowledge base for the annotation of biological molecular structures that addresses some of these issues. This Wiki-style database consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows users to attach categorised comments and discussions to the entries. The core data for each entry is shown as a summary and can be used for searching and navigation via categories. A user-editable list of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3123/version/1

An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Kouji Kozaki; Hiroko Kou; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on &amp;#x22;anatomical structure of organs&amp;#x22; and &amp;#x22;abnormal states in the human body&amp;#x22;. On the basis of the investigation, we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of relations.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3506/version/1

Population genomics of domestic and wild yeasts
Provedor de dados: 17
Autores: David M. Carter; Gianni Liti; Alan M. Moses; Leopold Parts; Stephen A. James; Robert P. Davey; Ian N. Roberts; Anders Blomberg; Jonas Warringer; Austin Burt; Vassiliki Koufopanou; Isheng J. Tsai; Casey M. Bergman; Douda Bensasson; Michael J. T. O&amp;#x27;Kelly; Alexander van Oudenaarden; David B. H. Barton; Elizabeth Bailes; Matthew Jones; Michael A. Quail; Ian Goodhead; Sarah Sims; Frances Smith; Richard Durbin; Edward Louis.
The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker&amp;#x27;s yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1988/version/1

SemanticSBML &amp;#x2013; state of affairs
Provedor de dados: 17
Autores: Wolfram Liebermeister; Falko Krause; Marvin Schulz; Timo Lubitz.
A number of new functions in the software tool semanticSBML make extensive use of MIRIAM-compliant annotations in SBML models. Semantic model search allows to obtain, from BioModels Database, a ranked list of models resembling a given query model or data set. Model clustering allows for exploring and visualising similarities among large numbers of SBML models. Parameter balancing uses collected kinetic constants - retrieved by using semantic annotations - to infer consistent sets of model parameters.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4987/version/1

Topological network alignment uncovers biological function and phylogeny
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Tijana Milenkovic; Vesna Memisevic; Wayne Hayes; Natasa Przulj.
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4089/version/1

Genome Network Project: An Integrated Genomic Platform
Provedor de dados: 17
Autores: Jose C. Clemente; So Nakagawa; Kazuho Ikeo; Takashi Gojobori.
With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform (&amp;#x22;http://genomenetwork.nig.ac.jp/&amp;#x22;:http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics. Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and _in vitro_ virus (IVV) methods. The Genome Network...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3180/version/1

Wikipedia as an encyclopaedia of life
Provedor de dados: 17
Autores: Roderic Page.
In his 2003 essay E O Wilson outlined his vision for an &amp;#x201c;encyclopaedia of life&amp;#x201d; comprising &amp;#x201c;an electronic page for each species of organism on Earth&amp;#x201d;, each page containing &amp;#x201c;the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.&amp;#x201d; Although the &amp;#x201c;quiet revolution&amp;#x201d; in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson&amp;#x27;s essay (e.g., &amp;#x22;http://ispecies.org&amp;#x22;:http://ispecies.org, &amp;#x22;http://www.eol.org&amp;#x22;:http://www.eol.org), we are still some way from the goal of having...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4242/version/1

Side effect profile prediction - Tackling Big Pharma&amp;#x27;s worst nightmare at an early stage
Provedor de dados: 17
Autores: Josef Scheiber.
This talk presents a method that predicts adverse side effects for molecules based on the chemical structure only. Also, targets for the compounds are predicted. Therefore it becomes possible to link a certain side effect to the interaction with a certain target through molecular space. Examples are given in the talk.
Tipo: Presentation
Palavras-chave: Chemistry; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1239/version/1

Variant calling comparison CASAVA1.8 and GATK
Provedor de dados: 17
Autores: Denis C. Bauer.
This work aims at addressing the question of whether the new CASAVA1.8, which boasts improvements such as local realignments of reads, is at par with the well accepted pipeline of BWA mapping, duplicate removal, local realignment, re-calibration and variant calling using GATK. We therefore compare the two methods on chromosome 21 of a Yoruba trio and compare the results to the genotype identified by the 1000 genomes project. &amp;#xd;&amp;#xa;We &amp;#xfb01;nd that the mapping performance is the same for CASAVA1.8 and the academic pipeline, resulting in a mean coverage of about 22. CASAVA1.8 and GATK both call about 70.000 SNPs per individual of which 80% overlap between CASAVA1.8, GATK and the 1000 genomes project. This stands in contrast to the indel...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6107/version/1

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Provedor de dados: 17
Autores: Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson.
This is the final specification for _Release 1_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More information about SBML and this specification is available online at...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4959/version/1

How do you choose your literature search tool(s)?
Provedor de dados: 17
Autores: Kshitish  K. Acharya; Greta Kasliwal; Haritha Haridas.
With increasing number of bio-literature search engines, scientists and health professionals either make a subjective choice of tool(s) or face a challenge of analyzing multiple features of a plethora of bibliographic software. There is an urgent need for a thorough comparative analysis of the available literature scanning tools, from the user&amp;#x2019;s perspective. We report results of the first time semi-quantitative comparison of 21 search programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. &amp;#xd;&amp;#xa;Some of the important findings are:...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2101/version/2

In silico designing of activator for human IGF2 protein for effective cardiovascular disease therapeutics
Provedor de dados: 17
Autores: M Sandhya rani; Manne  Munikumar; Amineni  Umamaheswari.
Insulin like growth factor-II (IGF2) is a member of IGF family, the main role of IGF2 is as a growth hormone during gestation or fetal development. Ischematic stroke, atherosclerosis and pathological cardiac hypertrophy are associated with low circulating levels of IGF2. 5-aza-2&amp;#x2019;-deoxycytidine increases the activity of IGF2, due to high toxicity of 5aza2&amp;#x2019;deoxycytidine, some silenced genes are also expressed that cause various cancer diseases. In the present study an in silico approach was used to design the potential activator for IGF2 without side effects to treat cardiovascular diseases. Ligand binding sites were predicted using CASTp for drug target. 361 ligand analogs for 5-aza-2&amp;#x2019;-deoxycytidine were identified through...
Tipo: Presentation
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6558/version/1

InterPro Curation: Integrating Predictive Protein Signatures Into Biological Hierarchies
Provedor de dados: 17
Autores: Sarah Burge.
InterPro is an integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. As InterPro curators, we are responsible for assimilating information from our member databases and communicating it to our end users in a way that adds value to each individual signature. We categorise signatures according to their type (for example, Family, Domain or Repeat) and annotate entries with links to other databases, abstracts and protein matches.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The InterPro database also identifies relationships between entries. For example, signatures at a general Family level are related to more specific subfamilies through a Parent/Child relationship. Families may also Contain...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5330/version/1

ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_
Provedor de dados: 17
Autores: Jan-Ole  Christian; Patrick May; Stefan Kempa; Dirk Walther.
*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.&amp;#xd;&amp;#xa;*Results* - In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently features about 270 metabolic pathways...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3108/version/1

A novel _Drosophila_ post-genomic CNS drug discovery model detects tetraethylammonium chloride with therapeutic potential
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad*; Abhay Sharma.
A _Drosophila_ behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was distinct from the other one...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3418/version/1

An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using mathematical biological approach
Provedor de dados: 17
Autores: Arunava Goswami; Sk Sarif Hassan; Pabitra  Pal Choudhury.
Protein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of (chain of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4891/version/1

Role of CellML and FieldML in VPH/Physiome Applications
Provedor de dados: 17
Autores: Peter J. Hunter.
Discusses the use of the VPH/Physiome markup languages in VPH applications.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5911/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/2

Memristance can explain Spike-Time-Dependent-Plasticity in Neural Synapses
Provedor de dados: 17
Autores: Bernab&amp;#xe9; Linares-Barranco; Teresa Serrano-Gotarredona.
Interdisciplinary research broadens the view of particular problems yielding fresh and possibly unexpected insights. This is the case of neuromorphic engineering where technology and neuroscience cross-fertilize each other. For example, consider on one side the recently discovered memristor, postulated in 1974, thanks to research in nanotechnology electronics. On the other side, consider the mechanism known as Spike-Time-Dependent-Plasticity (STDP) which describes a neuronal synaptic learning mechanism that outperforms the traditional Hebbian synaptic plasticity proposed in 1949. STDP was originally postulated as a computer learning algorithm, and is being used by the machine intelligence and computational neuroscience community. At the same time its...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3010/version/1

A call for disruptive innovation in science publishing with a new open data-sharing platform for the life sciences
Provedor de dados: 17
Autores: Donald  C. Cooper.
&amp;#x201c;A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used in business and technology literature to describe innovations that improve a product or service in ways that the market does not expect.&amp;#x201d; -Wikipedia&amp;#xd;&amp;#xa;On April 3rd, 2012 Nature Precedings, Nature Publishing Group&amp;#x2019;s experiment in free pre-print publishing was shut down and no longer accepts submissions. According to the Nature Precedings website it was created in 2007 as &amp;#x201c;a place for researchers to share documents, including presentations, posters, white...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7151/version/1

1st INCF Workshop on Genetic Animal Models for Brain Diseases
Provedor de dados: 17
Autores: Olaf Riess; Holm Graessner.
The INCF Secretariat organized a workshop to focus on the &amp;#x201c;role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases&amp;#x201d; in Stockholm, December 13&amp;#x2013;14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5909/version/1

Agenda of the &amp;#x201c;BioSharing workshop - Unifying Bio-Resources Descriptors&amp;#x201d;
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Pascale Gaudet; Dawn Field.
Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB, www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The focus on the workshop was a strawman uniform system for describing these bio-resources (www.biodbcore.org), in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement (www.biosharing.org/standards).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Location: ISMB/ECCB,...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6148/version/1

Genomic Replikin Count Predicts Increased Lethality of Malaria
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin Counts predict both the increase and the decrease of lethality of malaria
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7142/version/1

Rethinking Leucine Zipper &amp;#x2013; a ubiquitous signal transduction motif
Provedor de dados: 17
Autores: Yaroslav Nikolaev; Konstantin Pervushin.
In this essay we attempt to reconsider the concept of the &amp;#x201c;Leucine Zipper&amp;#x201d; (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended &amp;#x201c;Coiled Coil&amp;#x201d; motifs, on the functional level short and moderately stable &amp;#x201c;Leucine Zippers&amp;#x201d; might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended &amp;#x201c;Coiled Coils&amp;#x201d;. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3271/version/1

JSBML update
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez.
This presentation gives an overview about the major changes in JSBML since the release of version 0.8-b1, which will become part of the first release candidate.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6358/version/1

Dynamic Topology of Biological Networks
Provedor de dados: 17
Autores: Ravi Iyengar.
The mammalian cell can be represented as a large modular network that consists of a central signal network that interacts with and regulates multiple cellular machines that are responsible for phenotypic behavior.  We have used graph-theory approaches to analyze signal flow through a network representing the hippocampal neuron and find that signal-induced connectivity results in the formation of many regulatory motifs. Information flow through the central signaling network is initiated by extra-cellular signals such as hormones binding to their receptors. The flow of information through the signaling network results in the appearance of regulatory motifs such as feedback loops, feedforward and bifan motifs. Within the large cellular networks, these...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/24/version/1

Virtual screening to design drug molecules for human proto oncogene Fyn kinase
Provedor de dados: 17
Autores: Manne Mannekumar; Pasupuleti Sravana lakshmi; Ikkurthi  Vani Priyadarshini; Dibyabhaba Pradhan; Amineni Umamaheswari.
Human Fyn tyrosine kinase, a Src-family enzyme plays a pivotal role in the integrin mediated cell signaling pathway and is known to interact with several molecular signals including FAK and paxillin that accounts for morphogenic transformation leading to cancer. The present study was aimed to design a persuasive inhibitor for Fyn kinase. The crystal structure was optimized and energy minimized applying OPLS2001 force field in Maestro v9.0. The inhibitor binding site residues such as LEU-17, GLY-18, ASN-19, VAL-25, ALA-37, LYS-39, GLU-54, THR-82, GLU-83, TYR-84, MET-85, GLY-88, ALA-134, ASN-135, LEU-137, and ASP-148 were located from the Fyn kinase co-crystal structure with staurosporine. Three published inhibitors (staurosporine, Rosmarinic acid and...
Tipo: Presentation
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6108/version/1

Environmental modelling and Web 2.0 - using Connotea to share XML-represented information
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
Much academic information can be represented in a structured way and published on the web as XML documents.   Such information can then be displayed in a wide variety of ways, using different XSLT stylesheets.   &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This presentation presents MultiGuise, a Web application which allows any of several XML documents to be displayed using any of several stylesheets.   Both the documents and the stylesheets are bookmarked in Connotea, from where MultiGuise retrieves them using a special tag.   This approach means that anyone can add documents and stylesheets, simply by bookmarking them in Connotea.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The approach is illustrated primarily with environmental models represented in XML, but also with...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/18/version/1

Epitopes in ChEBI - A Collaboration with the IEDB
Provedor de dados: 17
Autores: Zara Josephs; Marcus Ennis; Steve Turner; Gareth Owen; Bjoern Peters; Randi Vita; Christoph Steinbeck.
*ChEBI background:* Chemical Entities of Biological Interest (ChEBI) is a curated database of small chemical entities important in biosystems. As well as a description of entities, it provides a semantically rich knowledge base; and an internal hierarchy that organises the entities by their molecular structure types and potential r&amp;#xf4;les.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*The ChEBI-IEDB collaboration:* The Immune Epitope and Analysis Resource (IEDB) is a project supported by contract from the National Institute of Allergy and Infectious Diseases (NIAID). Its goal is to make epitope-related data on infectious diseases and immune disorders freely available to researchers worldwide. In June 2009, ChEBI began working with the IEDB on a project aimed...
Tipo: Poster
Palavras-chave: Chemistry; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5094/version/1

Differences in the gene expression profile of human monocytic cells activated by high and low affinity Fc-gamma-receptors.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Renji Reghunathan; Alirio Jose Melendez; Peter Natesan Pushparaj.
Receptors for the constant (Fc) region of immunoglobulin G, play an important role in linking the humoral and cellular arms of immune response. Three different classes of receptors have been defined, Fc&amp;#x3b3;RI (CD64), Fc&amp;#x3b3;RII (CD 32), and Fc&amp;#x3b3;RIII (CD16). We have previously shown that in a human monocyte model (IFN&amp;#x3b3;-primed U937 cells), Fc&amp;#x3b3;RI and Fc&amp;#x3b3;RII stimulation trigger two very distinct intracellular signalling pathways. Here we show for the first time, the use of oligonucleotide microarrays to investigate the overall gene-expression profile of human monocytes triggered with Fc&amp;#x3b3;RI or Fc&amp;#x3b3;RII. Our data indicate that several interesting genes are differentially expressed in response...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1149/version/1

Integrating genomics, transcriptomics, proteomics, and metabolomics into environmental enzymology:  the next frontier or fool&amp;#x27;s gold?
Provedor de dados: 17
Autores: Matthew D. Wallenstein.
Extracellular enzymes are widely measured as indices of microbial activity, resource allocation, and substrate availability.  However, interpretation of enzyme activities is hampered by a limited understanding of controls on enzyme production, turnover, and in-situ activity.  In part, this is the consequence of methodological limitations, which require artificial substrates and are conducted under conditions that differ from in situ conditions.  Recently, new tools have emerged that have potential to provide new insights into microbial enzymology. Will these methods open a new frontier in enzymology research, or will they only result in the discovery of fool&amp;#x2019;s gold? I will highlight how genomic, transcriptomic, proteomic, and metabolomic tools...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6159/version/1

Inositol-Related Gene Knockouts Mimic Lithium&amp;#x27;s Effect on Mitochondrial Function
Provedor de dados: 17
Autores: Galila Agam; RH Belmaker; Dieder  Moechars; Vered Chalifa-Caspi; Yuly Bersudsky; Inbar Plaschkes; Lilach Toker; Gerard Berry.
Bipolar-disorder, characterized by switches between depressive and manic mood, is treated by mood-stabilizers, lithium being one of them. Among hypotheses suggested, the inositol-depletion hypothesis proposes that lithium attenuates hyperactivation of phosphatidylinositol signaling linked to neurotransmission-related receptors.Available for us are knockout-mice of two genes (IMPA1 or Slc5a3) each encoding for a protein related to inositol metabolism. We previously characterized these mice as exhibiting lithium-like neurochemical and behavioral phenotype. We performed a DNA-microarray study searching for pathways commonly affected by chronic lithium treatment and by the knockout of each of the genes. Here we show up-regulation of mitochondrial function in...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6318/version/1

21 Tesla Rat Heart Magnetic Resonance Microimaging by Paramagnetic Anti-Troponin Bound Polyethylene Based Iron-Oxide Nanoparticles and Image Processing
Provedor de dados: 17
Autores: Rakesh Sharma.
21T MR microimaging with the first use of troponin nanoparticles enhances the visualization of cardiac muscle fibers and offers technical advancement for the future. Diffusion weighting offers fiber tracking and functional analysis. Image processing offers heart probabilistic atlas and maps.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;http://www.ismrm.org/10/program/ELECTRONICPOSTERS.htm
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6650/version/1

GreenPhylDB: A Gene Family Database for plant functional Genomics
Provedor de dados: 17
Autores: Matthieu G. Conte; Marie-Ang&amp;#xe9;lique Laporte; Christophe P&amp;#xe9;rin; Mathieu  Rouard.
With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3136/version/1

Proteomics in the Light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. S.  Hassan; P. Pal  Choudhury.
In this paper, Proteomics have been studied in the light of Integral Value Transformations (IVTs) which was introduced by Sk. S. Hassan et al in 2010. For case study, a Human olfactory receptor OR1D2 protein sequence has been taken and then different IVTs have been used to evolve OR1D2 into some other proteomic like sequences. It has been observed that some of the generated sequences have been mapped to another olfactory receptor in Human or in some other species. Also it has been corroborated through fractal dimension that some of the fundamental protein properties have been nearly intact, even after the mapping. This study will help to comprehend the proteomic evolutionary network with the help of IVTs.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6100/version/1

DNA sequences classification and computation scheme based on the symmetry principle
Provedor de dados: 17
Autores: Xiao-Gang Song; Wen-Yuan Qiu.
The DNA sequences containing multifarious novel symmetrical structure frequently play crucial role in how genomes work. Here we present a new scheme for understanding the structural features and potential mathematical rules of symmetrical DNA sequences using a method containing stepwise classification and recursive computation. By defining the symmetry of DNA sequences, we classify all sequences and conclude a series of recursive equations for computing the quantity of all classes of sequences existing theoretically; moreover, the symmetries of the typical sequences at different levels are analyzed. The classification and quantitative relation demonstrate that DNA sequences have recursive and nested properties. The scheme may help us better discuss the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3116/version/1

p63, p73, &amp;#x26; p53 are Negative Regulators of Epithelial to Mesenchymal Transition (EMT), Invasion &amp;#x26; Metastasis
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
It has recently been shown that microRNAs, such as miRs-145,192, and 215, are regulated by the tumor suppressor p53 through their p53REs.  Considering miRs-145, 192, and 215 promoters contain p53REs suggests that they could be transcriptional targets of p63 and p73 as well.  Remarkably, bioinformatics analysis of miRs-145, 192, and 215 targets suggests that they target ZEB2, suggesting that p53, p63, and p73 by increasing the expression of miRs-192, 215, &amp;#x26; 145, they could inhibit the expression of ZEB2.  ZEB2 has been shown to function as a repressor of the tumor suppressor E-cadherin, suggesting that p53, p73, and p63 by suppressing the expression of ZEB2 through their transcriptional target miRs, they could increase the expression of E-cadherin....
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4109/version/1

An artificial spiking synapse made of molecules and nanoparticles
Provedor de dados: 17
Autores: Fabien Alibart; Stephane Pleutin; David Guerin; Christian Gamrat; Dominique Vuillaume.
Molecule-based devices are envisioned to complement silicon devices by providing new functions or already existing functions at a simpler process level and at a lower cost by virtue of their self-organization capabilities, moreover, they are not bound to von Neuman architecture and this may open the way to other architectural paradigms. Here we demonstrate a device made of conjugated molecules and metal nanoparticles (NPs) which behaves as a spiking synapse suitable for integration in neural network architectures. We demonstrate that this device exhibits the main behavior of a biological synapse. These results open the way to rate coding utilization of the NOMFET in perceptron and Hopfield networks. We can also envision the NOMFET as a building block of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3031/version/1

Generalized Theory of Life
Provedor de dados: 17
Autores: Vyacheslav L. Kalmykov.
The paper is mathematically, physically and biologically inspired - it is a deductive attempt of the biologist to find the most appropriate language for modelling of life. Applications of mathematical structures - groupoids, groups, categories, functors and monads, which are the most effective for the description of the complex objects, are discussed. Some new conceptions and interpretations were introduced: unified classification of complex systems; the generalized conception about stationary states of any autonomous agent (&amp;#x22;Statology&amp;#x22;); the total quantitative criterions of evolutionary direction; the generalized group of symmetry. The definitions of information, entropy, organization, behavior, evolution, creation, life, culture,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7108/version/1

Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences
Provedor de dados: 17
Autores: B. Jayaram.
That only 20 amino acids occur naturally accounting for the structural and functional diversity of proteins remains a mystery. We show here that this is a consequence of the action of a symmetry group, identify the presence of hydrogen bond donor groups, presence of sp3 hybridized [gamma] carbons, absence of [delta] carbons and linearity as properties central to side chain design and quantify the chemical logic of protein sequences.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2135/version/1

CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical model of G1/S checkpoint pathway
Provedor de dados: 17
Autores: Hong  Ling; Sandhya Samarasinghe; Don  Kulasiri.
Cellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this, we...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4950/version/1

The eDAL Suite: Tools and Concepts for Primary Data Citation
Provedor de dados: 17
Autores: Matthias Lange; Christian Colmsee; Steffen Flemming; Jinbo Chen; Matthias Klapperst&amp;#xfc;ck; Uwe Scholz.
Retrieval and citation of primary data is the important factor in the approaching age of &amp;#x201c;data science&amp;#x201d;. Digital data are easily shared, and just as easily wiped or lost. The problem of keeping on-line data accessible and&amp;#xd;&amp;#xa;retrievable is especially difficult for SME like plant breeders plant biotech companies as well as research projects in this domain.&amp;#xd;&amp;#xa;Intension of eDAL is the provisioning of an information retrieval and data citation infrastructure that meets the requirements of the &amp;#x201c;data science&amp;#x201d; age and implements a re-usable platform for data retrieval, data&amp;#xd;&amp;#xa;citation, and data publication. Like a shopping cart, the idea is to combine a search engine and a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4935/version/1

ABC Methods for Bayesian Model Choice
Provedor de dados: 17
Autores: Christian P. Robert.
Approximate Bayesian computation (ABC), also known as likelihood-free  methods, have become a standard tool for the analysis of complex models, primarily in population genetics but also for complex financial models. The development of new ABC methodology is undergoing a rapid increase in the past years, as shown by multiple publications, conferences and even software. While one valid interpretation of ABC based estimation is connected with nonparametrics, the setting is quite different for model choice issues. We examined in Grelaud et al. (2009, Bayesian Analysis) the use of ABC for Bayesian model choice in the specific of Gaussian random fields (GRF), relying on a sufficient property only enjoyed by GRFs to show that the approach was legitimate. Despite...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5961/version/1

DNA SEQUENCE PATTERNS
Provedor de dados: 17
Autores: Sriram Kannan.
There is significance in the molecular weight derived sequence patterns of adenosine, guanosine, cytosine, thymine, methyl cytosine and hydroxyl methyl cytosine if one has to consider the molecular events holistically by including single nucleotide polymorphisms, tumor suppressor gene activity like that of ten eleven translocation gene, CpG methylation, miRNA SNP patterns and SNPs neighboring CpGs. This research article focuses on observing simulation results of validated SNPs in a sequence using substitution patterns of molecular weight of A, G, C, T, 5OHC, 5MC.  The outcome helped to bring out positions in a DNA sequence where in validated bi allelic SNPs were never found to occur and SNPs neighboring methylated CpGs do show disconcordance and a...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4933/version/1

The System Biology Format Converter
Provedor de dados: 17
Autores: Ga&amp;#xeb;l Jalowicki; Nicolas Rodriguez; Martina Kutmon; Jean-Baptiste Pettit; Lu Li; Arnaud Henry; Kedar Nath Natarajan; Camille Laibe; Chris T. Evelo; Nicolas Le Nov&amp;#xe8;re.
The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6363/version/1

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data
Provedor de dados: 17
Autores: Vladimir Trifonov; Laura Pasqualucci; Riccardo Dalla-Favera; Raul Rabadan.
Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5037/version/1

Nationwide Study of Breast Cancer Risk Factors in Latinas
Provedor de dados: 17
Autores: Michael Dean; Latoya Silverton; Julie Sawitzke.
Breast cancer is the most common cancer among American women. Any woman can be affected by breast cancer, with risk for the disease increasing with age.  Risk for breast cancer is also exacerbated in women who have certain genetic alterations. Mutations in the BRCA1 and BRCA2 genes predispose women to breast and ovarian cancer, and are increasingly recognized in prostate and pancreatic cancers (1-3).  In Caucasian and Asian ethnicities BRCA mutations are associated with basal-type/triple-negative disease. However this association between BRCA gene mutations and basal/triple-negative disease has been understudied in other ethnicities (4-6). The incidence and mortality of breast cancer of Hispanics and Native Americans are lower than other ethnicities;...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5691/version/2

Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis
Provedor de dados: 17
Autores: Judith D. Cohn; Dengming Ming; Michael E. Wall.
Dynamics perturbation analysis (DPA) finds regions in a protein structure where proteins are &amp;#x22;ticklish&amp;#x22;, i.e., where interactions cause a large change in protein dynamics. Previously, such regions were shown to predict the location of native binding sites in a docking test set, but the more general applicability of DPA to the prediction of functional sites in proteins was not shown. Here we describe the results of applying an accelerated algorithm, called Fast DPA, to predict functional sites in over 50,000 SCOP domains.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2209/version/1

1st INCF Workshop on Needs for Training in Neuroinformatics
Provedor de dados: 17
Autores: David Willshaw.
The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2563/version/1

UniProt Knowledgebase: a hub of integrated data
Provedor de dados: 17
Autores: Michele Magrane; UniProt Consortium.
Data integration plays an increasingly important role in bringing together the large amounts of diverse information spread across disparate resources and presenting a comprehensive overview of these data to the scientific community. The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialised data collections. UniProtKB also integrates data such as protein sequences, protein-protein interactions, Gene Ontology terms and official gene...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5092/version/1

Objective dysphonia quantification in vocal fold paralysis: comparing nonlinear with classical measures
Provedor de dados: 17
Autores: Max A. Little; Declan A. E. Costello; Meredydd L. Harries.
Clinical acoustic voice recording analysis is usually performed using classical perturbation measures including jitter, shimmer and noise-to-harmonic ratios. However, restrictive mathematical limitations of these measures prevent analysis for severely dysphonic voices. Previous studies of alternative nonlinear random measures addressed wide varieties of vocal pathologies. Here, we analyze a single vocal pathology cohort, testing the performance of these alternative measures alongside classical measures.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We present voice analysis pre- and post-operatively in unilateral vocal fold paralysis (UVFP) patients and healthy controls, patients undergoing standard medialisation thyroplasty surgery, using jitter, shimmer and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3106/version/1

Effect of Non-Coding RNA on Post-Transcriptional Gene Silencing of Alzheimer Disease
Provedor de dados: 17
Autores: Krishnan Namboori; Arun Mohan; Radhagayathri K.U.; Varun Gopal; Vasavi C.S.; Premkumar P; Deepa  Gopakumar; Ramachandran K.I.
A large amount of hidden biological information is contained in the human genome, which is not expressed or revealed in the form of proteins; the usual end product form of gene expression. Instead, most of such information is in the form of non-coding RNAs (ncRNAs). ncRNAs correspond to genes that are transcribed, but do not get translated into proteins. This part of the genome was, till recently, considered as &amp;#x2018;junk&amp;#x2019;. The term &amp;#x2018;junk&amp;#x2019; implied lack of any discernible function of these RNA. More than 98% of the human genomic size encompasses these non-coding RNAs. But, recent research has evidently brought out the indispensible contribution of non-coding RNA in controlling and regulating gene expression. ncRNA such...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4467/version/1

Predicting Protein-Disease Relationships Using Sequence, Physicochemical Properties, and Molecular Function Information
Provedor de dados: 17
Autores: Predrag Radivojac; Kang Peng; Wyatt T. Clark; Brandon J. Peters; Amrita Mohan; Sean M. Boyle; Sean D. Mooney.
One of the most important tasks of modern bioinformatics is the development of computational tools that can be used to understand and treat human disease. To date, a variety of methods have been explored and algorithms for predicting whether a protein is involved in disease are gaining in their utility. Here, we describe an algorithm for detecting protein-disease associations based on the human protein-protein interaction network, known gene-disease associations, protein sequence, and protein functional information at the molecular level. Our method, PhenoPred (&amp;#x22;www.phenopred.org&amp;#x22;:www.phenopred.org), is supervised: first, we map each protein onto the spaces of disease and functional terms based on distance to all annotated proteins in the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2239/version/1

Taking shortcuts with OWL using safe macros
Provedor de dados: 17
Autores: Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland.
Accurate representation of complex domains such as biology demands&amp;#xd;&amp;#xa;powerful and expressive ontology languages such as OWL. However, the&amp;#xd;&amp;#xa;complex nested class expressions required for modeling can be a&amp;#xd;&amp;#xa;hindrance to ontology authoring and adoption. These class expressions&amp;#xd;&amp;#xa;can appear opaque to domain experts, and even users proficient in OWL&amp;#xd;&amp;#xa;can benefit from some kind of syntactic sugar or &amp;#x22;short-cut&amp;#x22;&amp;#xd;&amp;#xa;strategy, especially when authoring large ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;One solution is to have domain experts fill in simple templates (for&amp;#xd;&amp;#xa;example, in Excel) and translate the results into more complex...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5292/version/1

Prediction of novel inhibitors for human RNase1 involved in cardiovascular disease through in silico screening
Provedor de dados: 17
Autores: Kanipakam Hema; Sadnala Giribabu; Sandeep Swargam; Amineni Umamaheswari.
Human pancreatic ribonuclease (RNase1) is a small digestive and pyramidine specific enzyme secreted by the pancreas. RNase1 contributes in the regulation of extracellular RNA by hydrolyzing RNA phosphodiester bonds. High levels of RNase1 in cardiovascular disease patients project the enzyme as an attractive drug target. The known RNase1 inhibitors, citric acid and U1S were searched for structural analogs from Ligand.info database to compile 783 ligands. The ligands&amp;#x27; 3D structures and their tautomeric states were generated using LigPrep. The 3424 prepared conformations were subjected to QikProp analysis and filtered based on Lipinski rule of five and zero reactive functional group.  The 3376 conformations with good ADME (absorption, desorption,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6527/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO)  is an ontology developed, as part of the EvoInfo and EvoIO groups supported by NESCent, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic trees and associated character data matrices. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;CDAO-store is a repository providing a rich set of API&amp;#x2019;s for querying and visualizing phyloinformatics data. It is a triple-store encoding data as RDF triples constructed according to the CDAO concept vocabulary. CDAO-store provides three classes of services: a service for importing data in CDAO format, a PhyloWS interface supporting an...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4586/version/1

Reducing the Probability of False Positive Research Findings by Pre-Publication Validation - Experience with a Large Multiple Sclerosis Database
Provedor de dados: 17
Autores: Martin M. Daumer; Ulrike U. Held; Katja K. Ickstadt; Moritz M. Heinz; Siegfried S. Schach; George G. Ebers.
*Objective*&amp;#xd;&amp;#xa;We have assessed the utility of a pre-publication validation policy in reducing the probability of publishing false positive research findings. &amp;#xd;&amp;#xa;*Study design and setting*&amp;#xd;&amp;#xa;The large database of the Sylvia Lawry Centre for Multiple Sclerosis Research was split in two parts: one for hypothesis generation and a validation part for confirmation of selected results. We present case studies from 5 finalized projects that have used the validation policy and results from a simulation study.&amp;#xd;&amp;#xa;*Results*&amp;#xd;&amp;#xa;In one project, the &amp;#x22;relapse and disability&amp;#x22; project as described in section II (example 3), findings could not be confirmed in the validation part of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/433/version/1

Failure of Abeta(1-40) amyloid fibrils under tensile loading
Provedor de dados: 17
Autores: Raffaella Paparcone; Markus J. Buehler.
Amyloid fibrils and plaques are detected in the brain tissue of patients affected by Alzheimer&amp;#x2019;s disease, but have also been found as part of normal physiological processes such as bacterial adhesion. Due to their highly organized structures, amyloid proteins have also been used for the development of novel nanomaterials, for a variety of applications including biomaterials for tissue engineering, nanolectronics, or optical devices. Past research on amyloid fibrils resulted in advances in identifying their mechanical properties, revealing a remarkable stiffness. However, the failure mechanism under tensile loading has not been elucidated yet, despite its importance for the understanding of key mechanical properties of amyloid fibrils and plaques...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5174/version/1

Structural Modeling and Validation of Rep protein of Begomovirus Strains (TLCBV and TYLCTHV)
Provedor de dados: 17
Autores: Rajneesh Prajapat; Vivek Bajpai; Rajarshi Kumar Gaur.
Homology modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or several similar (homologous) proteins. It would be expected that two proteins of similar origin and function would have reasonable structural similarity. Therefore it is possible to use the known structure as a template for modeling the structure of the unknown structure. Proteins that share the same function generally have similar structures. During alignment if two proteins show maximum sequence identity they also show a similar folding pattern. This principal has became the foundation of homology modeling. &amp;#xd;&amp;#xa;The Geminivirus taxonomic group of plant viruses is characterized by geminate particles and genomes...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5617/version/1

The true story behind the annotation of a pathway
Provedor de dados: 17
Autores: Giovanni Marco G. M. Dall&amp;#x27;Olio; Hafid H. Laayouni.
On 2010 we worked on the annotation of the N-Glycosylation pathway in the Reactome database. During this process, we found some unclear points and errors in other databases, and we reported and helped fix them. After we finished, we realized that the work of reporting errors to a database is basically not acknowledged by the scientific community: this is unfortunate because if only this process would be a bit more recognized and transparent, we could have better data in the databases and a more active community. Moreover, the fact that many databases tend to keep error reporting private creates great issues to the reproducibility of a work.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Another way to look at this talk is: if you dedicate 6 months of your PhD thesis...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5561/version/1

Gender differences in a Drosophila transcriptomic model of chronic pentylenetetrazole induced behavioral deficit
Provedor de dados: 17
Autores: Abhay Sharma; Farhan Mohammad; Priyanka Singh.
A male Drosophila model of locomotor deficit induced by chronic pentylenetetrazole (PTZ), a proconvulsant used to model epileptogenesis in rodents, has recently been described. Antiepileptic drugs (AEDs) ameliorate development of this behavioral abnormality. Time-series of microarray profiling of heads of male flies treated with PTZ has shown epileptogenesis-like transcriptomic perturbation in the fly model. Gender differences are known to exist in neurological and psychiatric conditions including epileptogenesis. We describe here the effects of chronic PTZ in Drosophila females, and compare the results with the male model. As in males, chronic PTZ was found found to cause a decreased climbing speed in females. In males, overrepresentation of Wnt, MAPK,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3460/version/1

A review of journal policies for sharing research data
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background:*  Sharing data is a tenet of science, yet commonplace in only a few subdisciplines.  Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers.  The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methods:*  We investigated these relationships with respect to gene expression microarray data in the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1700/version/1

Web 2.0 and the ever elusive balance between information explosion and data mining
Provedor de dados: 17
Autores: Abhay Krishna.
In a fascinating tussle of perspectives in Volume 6 and issue no 3 of april 2008 Frontiers in Ecology and Evolution, Martin A Nu&amp;#xf1;ez and Gregory M Crustinger enlist ways to brace up with the recent literature. They advocate that PhD students should choose a well studied system to have better chances of success. On the other side of this fascinating tussle Daniel Simberloff and Nathan J Sanders agree with there enthusiastic case and approaches for bracing up with the recent literature. However, they disagree with the play safe strategy of start-ups in ecology and evolution.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For me this tussle of perspectives is really fascinating. It underlines the story of our times. In the times of information explosion, should...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1959/version/1

Practical experiences in concurrent, collaborative ontology building using Collaborative Prot&amp;#xe9;g&amp;#xe9;
Provedor de dados: 17
Autores: Daniel Schober; James Malone; Robert Stevens.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3517/version/1

Betaine aldehyde dehydrogenase (BADH) from Hordeum vulgare- an in-silico study
Provedor de dados: 17
Autores: Kaushal Kumar Bhati; Vijay  Kumar Singh.
Glycine Betaine is a quaternary amino compound that accumulates in stress conditions, mainly abiotic stresses like drought and salinity &amp;#x26; synthesized  by  the  two-step  oxidation  of  choline  via  the intermediate  betaine  aldehyde,  catalyzed  by  Choline  monooxygenase  and  Betaine  aldehyde dehydrogenase  (BADH).&amp;#xd;&amp;#xa;The sequence analysis of key enzymes of Glycine betaine biosynthesis i.e. BADH was carried out using various online proteomic tools available on Expasy and EBL, and then homologous modeling of this enzyme was performed using automated mode SWISS-MODEL &amp;#x26; GENO 3D and models were analyzed on QMEAN.  This was an attempt to find the possible model of BADH, because no physical model of BADH is yet available on...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6360/version/1

Data submission and curation for caArray, a standard based microarray data repository system
Provedor de dados: 17
Autores: X Bian; J Klemm; A Basu; J Hadfield; R Srinivasa; T Parnell; S Miller; W Mason; D Kokotov; M Duncan; P Duvall; L Gurses; T Boal; L Misquitta; D Swan; R Wysong; A Klink; A Johnson; G Fontenay; J Liu; M Colbert; G Komatsoulis.
caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG&amp;#x2122;), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge.  caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG&amp;#x2122;.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3138/version/1

A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin  Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/2

Using Metaneva for Structuring, Managing and Retrieving Animal Data in the Cognitive Neurosciences
Provedor de dados: 17
Autores: Dirk Derom; Randall A. Schmidt; Ian McLeod; Bruce A. Hewitt.
Contemporary cognitive neuroscience data sets are characterized by a lack of a standardized ontology, leading to shortcomings in data reports and data sharing along with possibly outdated modular models of functional brain mechanisms. Neuroinformatics is actively addressing these hiatuses, developing detailed and more powerful workbenches. However, the structuring of data is largely neglected due to the intrinsically different data sets in the neurosciences. Here we present a workbench called Metaneva addressing the need of data structures for the improvement of both data storage and data retrieval. We hereby present both our data structuring approach and the system developed specifically for the storage and retrieval of this Metaneva specific data...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4146/version/1

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
Provedor de dados: 17
Autores: Mikel Ega&amp;#xf1;a Aranguren; Robert Stevens; Erick Antezana.
As ontologies are developed there is a common need to transform them, especially from those that are axiomatically lean to those that are axiomatically rich. Such transformations often require large numbers of axioms to be generated that affect many different parts of the ontology. This paper describes the Ontology Pre-Processor Language (OPPL), a domain-specific macro language, based in the Manchester OWL Syntax, for manipulating ontologies written in OWL. OPPL instructions can add/remove entities, and add/remove axioms (semantics or annotations) to/from entities in an OWL ontology. OPPL is suitable for applying the same change to different ontologies or at different development stages, and for keeping track of the changes made (e.g. in pipelines). It is...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4006/version/1

Managing Multiple Parameter Sets in SBML
Provedor de dados: 17
Autores: Frank Bergmann.
This document describes the elements of a SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4233/version/1

Mitochondrial Molecular Adaptations and Life History Strategies Coevolve in Plants
Provedor de dados: 17
Autores: Neeraja M. Krishnan; Basuthkar J. Rao.
Messenger RNA secondary structure prevents mutations at functionally important sites. Mutations at exposed sites would cause micro-adaptations, niche-specialization, and therefore, can be thought to promote K-strategists. Exposing, rather than protecting, conserved sites, is also potentially adaptive because they probably promote macro-adaptive changes. This presumably fits r-strategists: their population dynamics tolerate decreased survival. We found that helix-forming tendencies are greater at evolutionary conserved sites of plant mitochondrial mRNAs than at evolutionary variable sites in a majority (73%) of species&amp;#x2013;gene combinations. K-strategists preferentially protect conserved sites in short genes, r-strategists protect them most in larger...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1922/version/1

Logical implications for regulatory relations represented by verbs in biomedical texts
Provedor de dados: 17
Autores: Sine Zambach.
Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However some relations are used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular their usage expressed as verbs in different biomedical genres and the properties of the relations.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3560/version/1

Publishing re-usable phylogenetic trees, in theory and practice
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Jamie Whitacre; Ross Mounce; Dan F. Rosauer; Rutger A. Vos; Arlin Stoltzfus.
Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&amp;#x27;data&amp;#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &amp;#xd;&amp;#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6048/version/1

BioPAX Support in CellDesigner
Provedor de dados: 17
Autores: Anushya Muruganujan; Huaiyu Mi.
BioPAX is a pathway data exchange language that is widely used by pathway database resources.  Here we describe a mechanism that allows users to curate pathway data in diagrams using CellDesigner, a pathway graphical editing tool, and save the pathway data in BioPAX format.  We used this mechanism to create BioPAX files for all 165 pathways from the PANTHER database.  In addition, we are also working on graphically visualizing BioPAX data by importing them into CellDesigner.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5679/version/1

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
Provedor de dados: 17
Autores: Colin Batchelor; Thomas Bittner; Karen Eilbeck; Chris Mungall; Jane Richardson; Rob Knight; Jesse Stombaugh; Craig Zirbel; Eric Westhof; Neocles Leontis.
Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared...
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3561/version/1

The nutritional phenotype database&amp;#xb;. A real data structure for systems biology
Provedor de dados: 17
Autores: Chris T. Evelo.
Biology is rapidly developing into a data-driven science and faces not only the challenge of coping with an ever growing amount of data but also that of interpreting its complex diversity. The requirement of systems biology to connect different levels of biological research leads directly to a need for large scale data integration. The nutritional phenotype database (dbNP) addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. In this presentation we will describe how we intend to meet this objective with the nutritional phenotype database. We will outline relevant parts of the system architecture, describe the kinds of data to...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5141/version/1

Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a &amp;#x27;language&amp;#x27; model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/1

ABC SMC for parameter estimation and model selection with applications in systems biology
Provedor de dados: 17
Autores: Tina Toni.
Approximate Bayesian Computation (ABC) methods can be used in situations where the evaluation of the likelihood is computationally prohibitive. They are thus ideally suited for analyzing the complex dynamical models encountered in systems biology, where knowledge of the full (approximate) posterior is often essential.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk gives an overview of an ABC algorithm based on Sequential Monte Carlo (ABC SMC). Different uses of the algorithm will be presented, depending on the application question of interest. The first is the general parameter estimation framework, where the interest lies in estimating the posterior parameter distribution from available experimental data. In the second context we ask whether the model can...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5964/version/1

A Linked Data Approach to Help Identify Therapeutic Targets for Cancer
Provedor de dados: 17
Autores: Helena Deus.
Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer &amp;#x201c;driver&amp;#x201d; mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6169/version/1

Identifying Data Sharing in Biomedical Literature
Provedor de dados: 17
Autores: Heather Piwowar; Wendy W. Chapman.
Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to find shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1721/version/2

The guardians of the genome dependent tumor suppressor miRNAs network
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors.  However, how they function as tumor suppressors remains elusive.  Here I present a number of models that illustrates how the TA-p73/p63 could function as tumor suppressors.  Remarkably, the guardians&amp;#x2014;p53, p63, and p73&amp;#x2014;of the genome are in control of most of the known tumor suppressor miRNAs.  &amp;#xd;&amp;#xa;TA-p73/p63 and p53, by suppressing the expression of c-Myc through TRIM32 and miR-145, they could up regulate the expression of tumor suppressor microRNAs, such as miR-15/16a, miR-29, miR-34, miR-26, let-7a/d/g, miR-30b/c/d/e, miR-146a, and a number of tumor suppressor genes.  It appears that p53/TA-p73/p63-mediated repression...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4112/version/1

Heterogeneity in Ty1-copia group of retroelements in chickpea (Cicer arietinum) genome
Provedor de dados: 17
Autores: Manoj K. Rajput; Kailash C. Upadhyaya.
Retrotransposons constitute a major fraction of plant genomes and these elements may have played a significant role in evolution and sequence organization of genomes. In order to access the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequences were amplified from chickpea genome, using the primers derived from two conserved domains of RT region. Thirty-six RT regions from independent amplicons were cloned and sequenced. On the basis of homology of deduced amino acids, the RT sequences could be grouped into three major families. The intra-family divergence at amino acid level ranges from 2 to 19%. Though intra-family RT sequences were conserved but no two sequences were identical. The results indicate a high degree of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/697/version/1

Molecular Static and Dynamic Analyses reveal Flaw in Murine Model used by US FDA to Detect Drug Carcinogenicity
Provedor de dados: 17
Autores: Trevor Marshall.
The US FDA currently accepts carcinogenicity studies of pharmaceutical drugs based on murine models. In addition to 6 month studies with p53(+/-) and ras.H2 transgenic mice, lifetime studies (typically 2 years) in WT mice or rats are also considered as evidence that a drug lacks carcinogenic activity. This model is not always exhaustive. For example, during the acceptance testing of the ARB Olmesartan[1], possible carcinogenicity observed in hamsters was not able to be duplicated in rats, or in transgenic mice. We have previously used the static molecular modeling of AutoDock to demonstrate that Olmesartan has agonostic activity in the PDB:1DB1 model of the human VDR Nuclear Receptor[2], while it has antagonistic activity in the PDB:1RK3 model of the rat...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Immunology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/52/version/1

Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders
Provedor de dados: 17
Autores: Anna Glinskii; Shuang Ma; Jun Ma; Denise Grant; Chang-Uk  Lim; Ian Guest; Stewart Sell; Ralph Buttyan; Gennadi Glinsky.
Biological and mechanistic relevance of intergenic disease-associated genetic loci (IDAGL) containing highly statistically significant disease-linked SNPs remains unknown. Here we present the experimental and clinical evidence revealing important role of IDAGL in human diseases. Targeted RT-PCR screen coupled with sequencing of purified PCR products detects widespread transcription at multiple intergenic disease-associated genomic loci (IDAGL) and identifies 96 small non-coding trans-regulatory RNAs of ~ 100-300 nt in length containing SNPs associated with 21 common human disorders (snpRNAs). Functionality of snpRNAs is supported by multiple independent lines of experimental evidence demonstrating their cell-type-specific expression and evolutionary...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6069/version/1

On Asymmetry in Biology and Nature
Provedor de dados: 17
Autores: I. C. Baianu.
Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by &amp;#x2018;perfect&amp;#x2019; order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered &amp;#x2018;structure&amp;#x2019; that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7134/version/1

Structure Prediction and Functional Characterization of ERG Proteins Involved in Ergosterol Biosynthetic Pathway of Candida albicans
Provedor de dados: 17
Autores: Sudeep  Roy; Suaib  Luqman; Ashok  Sharma.
The ERG proteins and enzymes of the ergosterol biosynthetic pathway has been the subject of intensive investigation as a target for several classes of antifungal agents used to treat C. albicans infection. Over the past few decades, a number of drugs and inhibitors with wide spectrum of activity, low toxicity and defined targets have been introduced. Several lines of evidence suggest that allylamines targets squalene epoxidase (ERG1), morpholines affects sterol C8-C7 isomerase (ERG2) and sterol reductase (ERG24), azoles inhibits a cytochrome P450 (ERG11) responsible for the 14 &amp;#x3b1;-demethylation of lanosterol and C-5 sterol desaturase (ERG3) and polyenes binds to ergosterol that leads to the damage of cell plasma membrane, ensuing in leakage of...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6709/version/1

Practical experiences in concurrent, collaborative ontology building using Collaborative Prot&amp;#xe9;g&amp;#xe9;
Provedor de dados: 17
Autores: Daniel Schober; James Malone; Robert Stevens.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3517/version/2

Minimal Information About Sample Preparation for Phosphoproteomics
Provedor de dados: 17
Autores: Montserrat Carrascal; David Ovelleiro; Marina Gay; Joaquin Abian.
This guideline describes parameters and conditions involved in phosphopeptide sample preparation. It covers from the description and preparation of the cells and tissues to the fractionation and specific enrichment of phosphopeptides for MS analysis. The guideline is prepared in order to easily cope with many of the experimental designs used in phosphoproteomic studies. &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;The document is subdivided as follows:&amp;#xd;&amp;#xa;1. General features&amp;#xd;&amp;#xa;2. Sample processing&amp;#xd;&amp;#xa;3. Protein Purification/Fractionation&amp;#xd;&amp;#xa;4. Peptide Purification/Fractionation&amp;#xd;&amp;#xa;5. Phosphopeptide enrichment&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3131/version/1

Systems Biology Graphical Notation: Entity Relationship language Level 1
Provedor de dados: 17
Autores: Nicolas Le Nov&amp;#xe8;re; Stuart Moodie; Anatoly Sorokin; Falk Schreiber; Huaiyu Mi.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/3719/version/2

Toward a Complete Phyloreferencing Language
Provedor de dados: 17
Autores: T. Michael Keesey.
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few &amp;#x201c;standard&amp;#x201d; forms (node&amp;#x2011;, branch&amp;#x2011;, and perhaps apomorphy&amp;#x2011;based clades) without the capacity to represent more &amp;#x201c;exotic&amp;#x201d; forms (e.g., ancestor&amp;#x2011;based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4652/version/2

Ten Simple Rules for Searching and Organizing the Scientific Literature
Provedor de dados: 17
Autores: Denis C. Bauer.
The exponentially increasing number of published papers (1.4 million per year by one estimate) makes it more and more difficult for us to manage the flood of scientific information. Each of us has acquired some protocol to find and organize journal articles and other references over the course of our careers. Most of those protocols are likely to have been formed by old routines or idleness rather than a structured approach to save time and frustration over the long run. Furthermore, with the Web 2.0 revolution, new ways of handling information are emerging (O&amp;#x2019;Reilly 2005). For example, traditional standalone tools for reference management like EndNote  are being supplemented by centralized resources like RefWorks  and social bookmarking sites...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3867/version/1

A novel mathematical tool for generating highly conserved protein domain via different organismal genomic landscapes
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in nature....
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4850/version/1

Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Provedor de dados: 17
Autores: Dagmar K&amp;#xf6;hn; Nicolas Le Nov&amp;#xe8;re; Christian Kn&amp;#xfc;pfer.
Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3137/version/1

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression
Provedor de dados: 17
Autores: Thomas  B. Parker; Peter Szucs; Walt  F. Mahaffee; Jean-Luc Jannink; John A. Henning.
Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1386/version/2

Nucleosome-mediated cooperativity between transcription factors
Provedor de dados: 17
Autores: Leonid A. Mirny.
Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2796/version/1

Molecular Bio-imprinting of Biocatalysts
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the  depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5665/version/1

In silico design of novel leads for inhibition of human beta-2-microglobulin
Provedor de dados: 17
Autores: Pallapotu Navya; Dibyabhaba Pradhan; Amineni Umamaheswari.
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy.  Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmacological properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was pursued in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schr&amp;#xf6;dinger software suite 2010 (maestro v9.1), docked...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6569/version/1

Discovery of transcription factor binding sites through integration of generic motif finders
Provedor de dados: 17
Autores: Edward Wijaya; Siu-Ming Yiu; Thanh Son Ngo; Rajaraman Kanagasabai; Wing-Kin Sung.
Locating transcription factor binding sites is a key step in understanding gene regulation. Due to its importance, many _de novo_ motif-finding methods have been proposed. Individually, these motif finders perform unimpressively overall based on Tompa&amp;#x27;s benchmark datasets. Moreover, these motif finders vary in their definitions of what constitute a motif, and in their methods for finding statistically overrepresented motifs. There is no clear way for biologists to choose the motif finder that is most suitable for their task. The purpose of this work is to describe a method called MotifVoter to identify transcription factor binding sites by integrating the results found by motif finders of different models. Validation of our method on...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1251/version/1

SNOMED CT&amp;#x2019;s Ontological Commitment
Provedor de dados: 17
Autores: Stefan Schulz; Ronald Cornet.
SNOMED CT is a clinical terminology that describes the meaning of terms by logical axioms. This requires an ontological commitment, i.e. precise agreements about the ontological nature of the entities referred to. We provide evidence that SNOMED implicitly supports at least three different kinds of commitments, viz. (i) independently existing entities, (ii) representational artifacts, and (iii) clinical situations. Our analysis shows how the truth-value of a sentence changes according to one of these perspectives. We argue that a clear understanding of to what kind of entities SNOMED CT concepts extend is crucial for the proper use and maintenance of SNOMED CT.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3465/version/1

Types, models and instances: a perspective from neuroscience
Provedor de dados: 17
Autores: Robert C. Cannon.
In order to share neuroscience models effectively, there is a need to clearly separate out the structure, equations and parameters so that each model only specifies those bits that are unique to itself. This will enable specialized simulation tools to recognize structures they can handle without having to process the equations directly. Two projects, NeuroML2 and NineML are working in this direction. As an example, we show how the Hodgkin Huxley equations can be decomposed into separate component type definitions and parameter sets in such as way that the majority of Hodgkin-Huxley style ion channel models can be expressed in only a few lines.
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5119/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/1

Wikis in scholarly publishing
Provedor de dados: 17
Autores: Daniel Mietchen; Gregor Hagedorn; Konrad U. F&amp;#xf6;rstner; M Fabiana Kubke; Claudia Koltzenburg; Mark J. Hahnel; Lyubomir Penev.
Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on &amp;#x22;Species-ID&amp;#x22;:http://species-id.net/w/index.php?title=Wikis_in_scholarly_publishing&amp;#x26;oldid=3815 - a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5891/version/1

Cationic State Distributions over Chlorophyll Pairs in Photosystem I and II
Provedor de dados: 17
Autores: Keisuke Saito; Hiroshi Ishikita.
Photosystem I (PSI) and II (PSII) possess chlorophyll pairs P~A~/P~B~ and P~D1~/P~D2~, respectively. These chlorophylls are the primary electron donors in the light-induced electron transfer. After the electron transfer, the radical cation remains on these chlorophyll pairs, forming [P~A~/P~B~]^&amp;#xb7;+^ and [P~D1~/P~D2~]^&amp;#xb7;+^. The positive charge distributions over the two chlorophylls were reported to be 10/90-50/50 for P~A~^&amp;#xb7;+^/P~B~^&amp;#xb7;+^ [1,2] and 70/30-80/20 for P~D1~^&amp;#xb7;+^/P~D2~^&amp;#xb7;+^ [3,4]. To clarify the origin of the distributions, we calculated ratios of P~A~^&amp;#xb7;+^/P~B~^&amp;#xb7;+^ and P~D1~^&amp;#xb7;+^/P~D2~^&amp;#xb7;+^ with a quantum mechanical/molecular mechanical (QM/MM) approach and the...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6486/version/1

SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs
Provedor de dados: 17
Autores: Qipeng Zhang; Ming Lu; Qinghua Cui.
MicroRNAs are one class of important gene regulators at the post-transcriptional level by binding to the 3&amp;#x2019;UTRs of target mRNAs. It has been reported that human microRNAs are evolutionary conserved and show lower single nucleotide polymorphisms (SNPs) than their flanking regions. However, in this study, we report that the human-specific microRNAs show a higher SNP density than both the conserved microRNAs and other control regions, suggesting rapid evolution and positive selection has occurred in these regions. Furthermore, we observe that the human-specific microRNAs show greater SNPs minor allele frequency and the SNPs in the human-specific microRNAs show fewer effects on the stability of the microRNA secondary structure, indicating that the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2127/version/1

Systems Biology Graphical Notation: Process Diagram Level 1
Provedor de dados: 17
Autores: Nicolas Le Novere; Stuart Moodie; Anatoly Sorokin; Michael Hucka; Falk Schreiber; Emek Demir; Huaiyu Mi; Yukiko Matsuoka; Katja Wegner; Hiroaki Kitano.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2320/version/1

A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/1

Scaffolder - Software for Reproducible Genome Scaffolding.
Provedor de dados: 17
Autores: Michael D. Barton; Hazel A. Barton.
Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: The software outlined here, &amp;#x201c;Scaffolder,&amp;#x201d; is implemented in the Ruby programming language and can be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5779/version/1

Independent elaboration of steroid hormone signaling pathways in Metazoans
Provedor de dados: 17
Autores: Gabriel V. Markov; Raquel Tavares; Chantal Dauphin-Villemant; Barbara A. Demeneix; Michael E. Baker; Vincent Laudet.
Steroid hormones regulate many physiological processes in vertebrates, nematodes and arthropods through binding to nuclear receptors (NR), a metazoan-specific family of ligand-activated transcription factors.  The main steps controlling the diversification of this family are now well understood.  In contrast, the origin and evolution of steroid ligands remain mysterious although this is crucial for understanding the emergence of modern endocrine systems.  Using a comparative genomic approach, we analyzed complete metazoan genomes to provide a comprehensive view of the evolution of major enzymatic players implicated in steroidogenesis at the whole Metazoan scale.  Our analysis reveals that steroidogenesis has been independently elaborated in the three main...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3374/version/1

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, input should equal the output. What I suggest here is that if the system is out of homeostasis, the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6741/version/1

The use of Web Ontology Language (OWL) to Combine Extant Controlled Vocabularies in Biodiversity Informatics Appears Redundant
Provedor de dados: 17
Autores: Roger D. Hyam.
Implementation of PESI requires data to be combined from multiple source databases. Some of the shared fields in the source databases used different controlled vocabularies of terms. OWL DL was investigated as a mechanism to build an extensible, shared ontology of species occurrence terms that permitted the source database to continue using and extending their own vocabularies whilst formally mapping to a more generic shared vocabulary. The merits of this approach were explored and it was concluded that the building of such a complex mapping ontology probably wasn&amp;#x27;t worthwhile. The level of semantic complexity involved outweighed the costs of simply imposing a flat list of well defined terms onto data suppliers. The main problem with exiting...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5168/version/2

Exploring binding site of human RBP4 towards discovery of novel inhibitor for treatment of cardiovascular diseases
Provedor de dados: 17
Autores: C Lakshmi Narayana Rao; LA  Raziya Beevi; Amineni Umamaheswari.
Retinol binding proteins (RBPs) are transport proteins that act by solubilizing and protecting their labile ligands in aqueous spaces. In addition, RBPs have diverse and specific functions in regulating the disposition, metabolism and activities of retinoids. Elevated levels of retinol-binding protein 4 (RBP4) are observed in cardiovascular disease conditions, which prompts it as a potential drug target. Therefore, computational approach methods were implemented herein to design a novel inhibitor for RBP4. Crystal structure (2wq9) of RBP4 was retrieved and investigated to locate retinol binding site residues (Lys29, Pro32, Leu35, Phe36, Leu37, Phe45, Ala55, Ala57, Met73, Val74, Gly75, Met88, Try90, His104, Gln117, Arg121, Try133, Phe135, Phe137). Five...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6587/version/1

LBFO: toward an artificial language for ontology development
Provedor de dados: 17
Autores: Leonard  F. Jacuzzo.
The syntax of LBFO represents the initial step toward the creation of a rigorously characterized, recursively defined, artificial language for the sole purpose of ontology development. The underlying idea is that maximally fruitful application of ontology requires accurate representation of reality in accordance with current textbook science. Hence, creating a robust, accurate representation of reality is a fundamental concern. &amp;#xd;&amp;#xa;An ontology represents general types of entities and relations between them. A domain ontology represents the general types and relations for a given domain of research. A top-level ontology represents the general types of entities in any domain of research. Ontologies serve many purposes in computerized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4001/version/1

Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Bijay Jassal; Esther E. Schmidt; Guanming Wu; Imre Vastrik; David Croft; Bernard de Bono; Gopal Gopinath; Marc Gillespie; Steven Jupe; Gavin O&amp;#x27;Kelly; Lisa Matthews; Phani V. Garapati; Michael Caudy; Alexander Kanapin; Bruce May; Shahana Mahajan; Ewan Birney; Peter  D&amp;#x27;Eustachio; Lincoln Stein.
Reactome (&amp;#x22;http://www.reactome.org&amp;#x22;:http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data...
Tipo: Poster
Palavras-chave: Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3200/version/1

P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function
Provedor de dados: 17
Autores: Michael S. Livstone; Rose Oughtred; Sven Heinicke; Fan Kang; Benjamin Vernot; Aiton Goldman; Dannie Durand; David Botstein; Kara Dolinski.
P-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms into families of homologs and provides curated evidence from the literature addressing these relationships.  The web page for each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD, papers describing complementation experiments, and OMIM gene and disease information.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As participants in the Gene Ontology Consortium&amp;#x2019;s Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins.  We have expanded P-POD to include the protein complement of the twelve Reference Genomes.  In...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3119/version/1

On attraction of slime mould Physarum polycephalum to plants with sedative properties
Provedor de dados: 17
Autores: Andrew Adamatzky.
A plasmodium of acellular slime mould Physarum polycephalum is a large single cell with many nuclei. Presented to a configuration of attracting and repelling stimuli a plasmodium optimizes its growth pattern and spans the attractants, while avoiding repellents, with efficient network of protoplasmic tubes. Such behaviour is interpreted as computation and the plasmodium as an amorphous growing biological computer. Till recently laboratory prototypes of slime mould computing devices (Physarum machines) employed rolled oats and oat powder to represent input data. We explore alternative sources of chemo-attractants, which do not require a sophisticated laboratory synthesis. We show that plasmodium of P. polycephalum prefers sedative herbal tablets and dried...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5985/version/1

cn.FARMS: a probabilistic model to detect DNA copy numbers
Provedor de dados: 17
Autores: Djork-Arn&amp;#xe9;  Clevert; Andreas Mitterecker; Andreas Mayr; Robert Burger; An  De Bondt; Marianne Tuefferd; Willem Talloen; Hinrich G&amp;#xf6;hlmann; Sepp Hochreiter.
Motivation: Existing pre-processing methods for DNA microarrays designed to detect copy number variations (CNVs) lead to high false discovery rates (FDRs). High FDRs misguide researchers especially in the medical context where CNVs are wrongly associated with diseases. We propose a probabilistic latent variable model, cn.FARMS, for array-based CNV analysis which controls the FDR without loss of sensitivity. At a DNA region, cn.FARMS constructs a model by a Bayesian maximum a posteriori estimation where the unobserved, latent variable represents the copy number that is measured by observed genetic markers (probes). The latent variable&amp;#x2019;s prior prefers parameters which represent the null hypothesis, (same copy number for all samples), from which...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4712/version/1

Grid Potential Analysis and Docking Studies on a Dataset of  N-Arylsulfonyl-3-AcetylIndoles as Anti-HIV Agent
Provedor de dados: 17
Autores: Surendra Kumar; Meena Tiwari.
A grid potential analysis employing the AutoGPA module in MOE2009.10 was performed on a dataset of 42 molecules of N-arylsulfonyl-3-acetylindoles as anti-HIV agent. The molecular docking simulations were also employed to position the inhibitors to their binding site to determine the most appropriate binding mode for different conformations of molecule. The uniqueness of AutoGPA module is that it automatically builds the 3D-QSAR model on the pharmacophore based molecular alignment. The best AutoGPA 3D-QSAR model obtained in the present study gives the cross-validated q2 value of 0.588 and r2pred value of 0.701 among the fifty six 3D-QSAR model developed. Furthermore, the steric and electrostatic contour maps for AutoGPA model along with the 3D structure of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6932/version/1

Extending Tlusty&amp;#x27;s method to the glycome: Tuning the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/1

The Human Microbiome and Recurrent Abdominal Pain in Children
Provedor de dados: 17
Autores: James Versalovic; Robert J. Shulman; Kevin Riehle; Delphine M. Saulnier; Toni-Ann Mistretta; Maria A. Diaz; Sabeen Raza; Debasmita Mandal; Xiang Qin; Susan Lynch; Joseph Petrosino; Richard Gibbs.
This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS).  Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain.  3. Perform functional gut metagenomics by evaluation of whole...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5228/version/2

Open Science: Tools, approaches, and implications
Provedor de dados: 17
Autores: Shirley Wu; Cameron Neylon.
The Pacific Symposium on Biocomputing is an annual meeting whose topics are determined by proposals submitted by members of the community. This document is the proposal for a session on Open Science, submitted for consideration for the PSB meeting in 2009.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1633/version/1

The SBML Level 3 Annotation package: an initial proposal
Provedor de dados: 17
Autores: Neil Swainston.
The SBML Level 3 Annotation package proposal intends to extend the current Level 3 Core annotations by increasing the range of RDF features supported.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Such an extension will support RDF Reification, annotation of SBML attributes, specification of relationships between annotations, negation of annotations and cross-references and cross-element annotations.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5001/version/1

Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery
Provedor de dados: 17
Autores: Ramil Mauleon; Kenneth McNally; Hei Leung; Richard Bruskiewich; Ruaraidh Sackville-Hamilton.
Rice diversity is the foundation for rice improvement programs. At IRRI, over 100,000 rice accessions are deposited, and intelligent use of this diversity can not only help solve current production problems but also create future production opportunities and tackle climate change challenges. To fully explore and utilize rice diversity, two ingredients are needed: 1 - the genetic blueprints of diverse rice accessions in use, 2 - plant populations with recombined genotypes allowing expression of phenotypic variation and discovery of new genes/QTLs  for use in breeding programs. Sequencing of the genomes &amp;#x26; obtaining SNP genotypes of many rice accessions is feasible due to decreasing cost of advanced DNA sequencing technologies. Coupled with the...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5114/version/1

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, &amp;#xd;&amp;#xa;which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/1

Lightning talk: PyPop - a software pipeline for large-scale multilocus population genomics
Provedor de dados: 17
Autores: Alex K. Lancaster; Richard M. Single; Owen D. Solberg; Mark P. Nelson; Glenys Thomson.
PyPop (Python for Population Genomics) is an open-source framework for performing large-scale population genetic analyses on multilocus genotype and allele frequency data. It computes tests and measures of Hardy-Weinberg equilibrium (locus-level and individual genotype-level), linkage disequilibrum, and selection, and estimates multi-locus haplotypes. PyPop supplements and extends existing population genetic software incorporating them as modules, modified to accommodate highly polymorphic data, rather than reimplementing them from scratch. It facilitates evolutionary analyses by integrating population genetic statistics within and across populations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Originally developed to analyze the highly polymorphic genetic data of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4700/version/1

Clonal Complexes in Biomedical Ontologies
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3476/version/1

Integral presentation of Experimental Results and Bioinformatic Analyses on _Ciona_ _intestinalis_ Proteins
Provedor de dados: 17
Autores: Kouki Yonezawa; Keisuke Ueno; Katsuhiko Mineta; Toshinori Endo.
For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of _Ciona intestinalis_, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for _Ciona_ proteins.  In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta _et al_., and cross-references with JGI version 1 and ENSEMBL.  A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database.  The information is summarized in a single page for a protein.  Together with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5088/version/1

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/version/1

PECAn: workflow management for data assimilation and forecasting
Provedor de dados: 17
Autores: David LeBauer; Dan Wang; Xiaohui Feng; Michael Dietze.
*Background/Question/Methods*  Ecosystem models use physiological traits and environmental data to model land-air carbon exchange. Such models can integrate heterogeneous ecological and environmental data, but rarely account for the contribution of each input to the overall uncertainty in model output. Quantifying uncertainty in each model input and propagating uncertainty through model ensembles directly estimates overall uncertainty in model output. Identification of data that would most effectively constrain uncertainty can also be directly inferred by processing output. Real-time data assimilation and forecasting benefits from a method that is transparent, scalable, and adaptable. A tool that manages these steps while tracking the provenance of data...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5533/version/1

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome
Provedor de dados: 17
Autores: A. Bignell; A. Frankish; B. Aken; M. Diekhans; F. Kokocinski; M. Lin; M. Tress; J. Van Baren; I. Barnes; T. Hunt; D. Carvalho-Silva; C. Davidson; S. Donaldson; J. Gilbert; E. Hart; M. Kay; R. Kinsella; D. Lloyd; J. Loveland; J. E. Mudge; C. Snow; J. Vamathevan; L. Wilming; M. Brent; M. Gerstein; R. Guig&amp;#xf3;; R. Harte; M. Kellis; S. Searle; J. Harrow; T. Hubbard.
The Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute produced the manually annotated geneset for the Encyclopedia of DNA Elements (ENCODE) pilot project and, as part of the Gencode subgroup, are reprising this role in the scale up to cover the whole human genome. Our manual annotation is checked computationally and validated experimentally. Loci and transcripts predicted to be absent from the initial annotation are identified by comparison with a number of state-of-the-art algorithms for identifying exons, splice sites, transcripts and pseudogenes. Where novel features are confirmed the annotation is updated. Annotated coding transcripts are analysed to assess their coding potential by investigating...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3155/version/1

A database of orthologous exons in primates for comparative analysis of RNA-seq data
Provedor de dados: 17
Autores: Ran Blekhman.
RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7054/version/1

Prevalence and Patterns of Microarray Data Sharing
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Sharing research data is a cornerstone of science. Although many tools and policies exist to encourage data sharing, the prevalence with which datasets are shared is not well understood. We report our preliminary results on patterns of sharing microarray data in public databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The most comprehensive method for measuring occurrences of public data sharing is manual curation of research reports, since data sharing plans are usually communicated in free text within the body of an article. Our early findings from manual curation of 100 papers suggest that 30% of investigators publicly share their full microarray datasets. Of these, 70% of the datasets are deposited at NCBI&amp;#x27;s Gene Expression Omnibus (GEO) database,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1701/version/1

Minimum Information about a Neuroscience Investigation (MINI): Electrophysiology
Provedor de dados: 17
Autores: Frank Gibson; Paul G. Overton; Tom V. Smulders; Simon R. Schultz; Stephen J. Eglen; Colin D. Ingram; Stefano Panzeri; Phil Bream; Miles Whittington; Evelyne Sernagor; Mark Cunningham; Christopher Adams; Christoph Echtermeyer; Jennifer Simonotto; Marcus Kaiser; Daniel C. Swan; Martyn Fletcher; Phillip Lord.
This module represents the formalised opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission&amp;#xd;&amp;#xa;to the CARMEN system (&amp;#x22;http://www.carmen.org.uk&amp;#x22;:www.carmen.org.uk).
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/1720/version/2

`The frozen accident&amp;#x27; as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
Provedor de dados: 17
Autores: James  F. Glazebrook; Rodrick  Wallace.
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks.  The approach to most of these questions involves using elements of Shannon&amp;#x27;s rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5717/version/1

ENA as an Information Hub
Provedor de dados: 17
Autores: Petra ten Hoopen; Ruth Akhtar; Richard Gibson; Bob Vaughan; Nadeem Faruque; Guy Cochrane.
The European Nucleotide Archive (ENA; &amp;#x22;http://www.ebi.ac.uk/ena/&amp;#x22;:http://www.ebi.ac.uk/ena/) is a comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes, respectively). Resources beyond...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5108/version/1

Towards a Taxonomically Intelligent Phylogenetic Database
Provedor de dados: 17
Autores: Roderic Page.
This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1028/version/1

Data Curation in Biology - Past, Present and Future
Provedor de dados: 17
Autores: Janet Thornton.
Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will describe how we have used data curation in my own research group - and also present an overview of curation at the EBI. With new technical developments and the move towards the semantic web, the role of curation in the future needs to develop to take advantage of these new opportunities. This will be discussed.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3225/version/1

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
Provedor de dados: 17
Autores: Andrey Ptitsyn; Shane Kanatous.
*_Background:_* The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (_Leptonychotes weddellii_) genes.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*_Results:_* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3380/version/1

Curating Genetic Association Literature for Common Diseases
Provedor de dados: 17
Autores: Elana Silver; Eran Halperin; Kord M. Kober; Badri Padhukasahasram; Nila Patil; Michelle Sommargren; Dietrich A. Stephan; Daryl J. Thomas; Heather Trumbower; Michele Cargill.
Papers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add to an already large body of literature which includes candidate gene studies, genome wide association studies, review papers, and meta-analyses. Related papers describe the basic epidemiology of these common diseases, as well as interactions between genes and environment, other genes, and drugs (pharmacogenomics), all of which may affect disease predisposition and management. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As the field of personalized genomics continues to grow and mature, this body of literature is being synthesized in various ways. One aspect of utmost importance is to track gene-disease associations over time to see if...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3174/version/1

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur &amp;#x2013; a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B) The Ribosomal Database (RDP) nai&amp;#x308;ve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/3

The Mass-Action-Law Based GPS Concept for Bio-Informatics
Provedor de dados: 17
Autores: Ting-Chao Chou.
The unified theory of dose and effect, as indicated by the median-effect equation for single and multiple entities and for the first and higher order kinetic/dynamic, has been established by T.C. Chou and it is based on the physical/chemical principle of the mass-action law (_J. Theor. Biol._ 59: 253-276, 1976; _Pharmacological Rev._ 58: 621-681, 2006). Rearrangements of the median-effect equation lead to Michaelis-Menten, Hill, Scatchard, and Henderson-Hasselbalch equations. The &amp;#x201c;median&amp;#x201d; serves as the &amp;#x201c;universal reference point&amp;#x201d; and the &amp;#x201c;common link&amp;#x201d; for the relationship of all entities at all dynamic orders, and is also the &amp;#x201c;harmonic mean&amp;#x201d; of kinetic dissociation...
Tipo: Presentation
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2064/version/1

Expression cartography of human tissues using self organizing maps
Provedor de dados: 17
Autores: Henry Wirth; Markus L&amp;#xf6;ffler; Martin von Bergen; Hans Binder.
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.&amp;#xd;&amp;#xa;Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5825/version/2

Increasing Access To Bioinformatics Resources: Increase Community Curation by Increasing Your Community
Provedor de dados: 17
Autores: Jennifer M. Williams.
The amount of biological data has risen exponentially over the last decade. Along with this rise, the number and types of bioinformatics resources has risen such that the sheer number of bioinformatics resources is overwhelming. For these resources to attain their full potential, they must be efficiently and extensively utilized. But in such a plethora of resources, how does a researcher new to a field find the resources that will meet their needs. Once a resource is found, how does the researcher quickly learn to utilize that resource fully? There are resource lists such as those provided by the journal Nucleic Acid Research (NAR), BioMed Central and the Univ. of Pittsburgh Health Sciences Library, and most resources include their own documentation. But...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3163/version/1

Nonlinear Models of Neural and Genetic Network Dynamics
Provedor de dados: 17
Autores: I. C. Baianu.
A categorical and &amp;#x141;ukasiewicz-Topos framework for &amp;#x141;ukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7114/version/1

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/version/2

Open Data in Science
Provedor de dados: 17
Autores: Peter Murray-Rust.
Open Data (OD) is an emerging term in the process of defining how scientific data may be published and re-used without price or permission barriers. Scientists generally see published data as belonging to the scientific community, but many publishers claim copyright over data and will not allow its re-use without permission. This is a major impediment to the progress of scholarship in the digital age. This article reviews the need for Open Data, shows examples of why Open Data are valuable and summarizes some early initiatives in formalizing the right of access to and re-use of scientific data.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1526/version/1

Multi-Cancer Computational Analysis Reveals Metastasis-Associated Variant of Desmoplastic Reaction Involving INHBA and THBS2
Provedor de dados: 17
Autores: Hoon Kim; John Watkinson; Vinay Varadan; Dimitris Anastassiou.
Despite extensive research, the details of the metastasis-associated biological mechanisms are largely unknown. Here, we analyze data from multiple cancers using a novel computational method identifying sets of genes whose coordinated overexpression indicates the presence of a particular phenotype. We conclude that there is one shared &amp;#x201c;core&amp;#x201d; metastasis-associated gene expression signature corresponding to a specific variant of desmoplastic reaction, present in a large subset of samples that have exceeded a threshold of invasive transition specific to each cancer, indicating that the biological mechanism is triggered at that point. For example this threshold is reached at stage IIIc in ovarian cancer and at stage II in colorectal...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4503/version/1

My experiment with open science: Why the benefits of sharing go beyond source code
Provedor de dados: 17
Autores: Carl Boettiger.
I briefly describe three themes that help maximize the benefits of an open science approach towards code, literature, discussions, and lab notebooks.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4602/version/1

The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control
Provedor de dados: 17
Autores: Erick Antezana; Vladimir Mironov; Mikel Egana; Robert Stevens; Ward Blond&amp;#xe9;; Bernard De Baets; Martin Kuiper.
The Cell Cycle Ontology (CCO) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process by combining, interlinking and enriching knowledge from various sources. CCO uses Semantic Web technologies, and it is accessible via the web for browsing, visualising, advanced querying, and computational reasoning. CCO facilitates a detailed analysis of cell cycle related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building. The ontology is available on &amp;#x22;http://www.cellcycleontology.org&amp;#x22;:http://www.cellcycleontology.org. Visual exploration can be done via the BioPortal, the...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3563/version/1

Inter-Tunneling Mechanism of Colliding Population Waves
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6990/version/1

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records.  This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms.  Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis.  The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are.  Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are.  The findings...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/2

KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis
Provedor de dados: 17
Autores: Nozomu Sakurai.
Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 (&amp;#x22;http://kpv.kazusa.or.jp/kpv4/&amp;#x22;:http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bez&amp;#xed;er curves on metabolic pathway maps. For up to 4 maps...
Tipo: Presentation
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5065/version/1

In-silico analysis and identification of novel lead molecule for human IGFBP-4 involved in cardiovascular diseases
Provedor de dados: 17
Autores: Kavali  Roopesh; Manne Munikumar; Amineni Umamaheswari.
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure. IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was persuaded in the present study to propose potential inhibitors of IGFBP-4. Two inhibitors (mainly from literature search) were selected to initiate high throughput virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH,...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6530/version/1

ChemCloud: Chemical e-Science Information Cloud
Provedor de dados: 17
Autores: Alexandru Todor; Adrian Paschke; Stephan Heineke.
Our Chemical e-Science Information Cloud (ChemCloud) &amp;#x2013; a Semantic Web based eScience infrastructure &amp;#x2013; integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5642/version/1

Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth  Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon Cockell; Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall&amp;#x2019;Olio; Chris Miller.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered. Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see description from Joel Spolsky), a comparable site for programmers.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Users find the site valuable both for answers to questions they have and as a reference. Since the content can also be viewed without registration the site likely reaches a larger audience. For instance, BioStar questions are often referenced on Twitter and FriendFeed. This leads to...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6043/version/1

Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
ZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis.  I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2.  Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, &amp;#x26; miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI.  ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors.  By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4385/version/1

TreeRipper: towards a fully automated optical tree  recognition software
Provedor de dados: 17
Autores: Joseph Hughes.
Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. &amp;#xd;&amp;#xa;TreeRipper is a command line c++ program for the fully-automated recognition of multifurcating phylogenetic trees. The program accepts a range of input image formats  (PNG, JPG/JPEG, GIF, TIFF or PDF ). Then follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4997/version/1

Translational Oncogenomics and Human Cancer Interactome Networks
Provedor de dados: 17
Autores: I. C. Baianu.
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6190/version/2

Multi-scale network biology model &amp;#x26; the model library
Provedor de dados: 17
Autores: Jianghui Xiong.
Multi-scale network biology model &amp;#x26; the model library
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5778/version/1

The Multigeneic _Rhg1_ Locus: A Model For The Effects on Root Development, Nematode Resistance and Recombination Suppression.
Provedor de dados: 17
Autores: David A. Lightfoot; Ali Srour; Jawad Afzal; Navinder Saini.
Soybean (Glycine max L. Merr.) resistance to populations (HgType) of _Heterodera glycines I._, the soybean cyst nematode (SCN), requires a functional allele at rhg1. An apoptosis-like response in the giant cells formed around the nematode results 24-48 h after feeding commences. This study aimed to identify the role of the three genes within the rhg1 locus, a receptor like kinase (RLK), a laccase and an ion anti-porter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles. Features of the rhg1 locus, the candidate genes and their nascent transcripts and proteins in roots were elucidated. First, evidence for a syntenic gene cluster was found and the effectiveness of SNP probes for distinguishing the homeolog sequence variant on...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2726/version/1

Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model
Provedor de dados: 17
Autores: Ofer Rahat; Uri Alon; Yaakov Levy; Gideon Schreiber.
Proteins are built from basic structural elements and their systematic characterization is of interest. Searching for recurring patterns in protein contact maps, we found several network motifs, patterns that occur more frequently in experimentally determined protein contact maps than in randomized contact maps with the same properties. Some of these network motifs correspond to sub-structures of alpha helices, including topologies not previously recognized in this context. Other motifs characterize beta-sheets, again some of which appear to be novel. This topological characterization of patterns serves as a tool to characterize proteins, and to reveal a high detailed differences map for comparing protein structures solved by X-ray crystallography, NMR and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1490/version/1

The Role of the Gut Microbiota in Ulcerative Colitis
Provedor de dados: 17
Autores: Vincent B. Young; Eugene B. Chang; Folker Meyer; Mitchell L. Sogin; Thomas M. Schmidt; James Tiedje.
The overall goal of our Demonstration Project is to address the hypothesis that the gut microbiota plays a critical role in the pathogenesis of inflammatory bowel disease (IBD). To circumvent the confounding effects of mucosal inflammation and medications that independently bias microbial selection, we have set out to study a unique clinical model of ulcerative colitis (pouchitis) where the development and status of the gut microbiota can be assessed prospectively and relative to the outcome of disease. Pouchitis is an inflammatory condition of a surgically-created pseudorectum that is unique to ulcerative colitis and rarely occurs when this procedure is performed for treatment of other non-IBD diseases.  Since the incidence of developing pouchitis within...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5254/version/1

Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31
Provedor de dados: 17
Autores: N S. Sardeshmukh; S G. Sanmukh; E Nakkeeran.
The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6784/version/1

Efficient learning in Approximate Bayesian Computation
Provedor de dados: 17
Autores: Mohammed  Sedki; Pierre  Pudlo.
Efficient learning in Approximate Bayesian Computation
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5962/version/1

The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases
Provedor de dados: 17
Autores: Matthias Lange; Karl Spies; Christian Colmsee; Steffen Flemming; Matthias Klapperst&amp;#xfc;ck; Uwe Scholz.
Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4337/version/1

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Stefan Hoops; Sarah M. Keating; Nicolas Le Nov&amp;#xe8;re; Sven Sahle; Darren Wilkinson.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2715/version/1

Metabolic, Replication and Genomic  Category of Systems in Biology,  Bioinformatics and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x2019;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth. Genomic systems are also considered as molecular realizations of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7051/version/1

An exercise on developing an ontology-epistemology about schizophrenia and neuroanatomy
Provedor de dados: 17
Autores: Rodolpho Freire; Danilo Nunes Santos; Marcos  Vinicius dos Santos; Paulo Eduardo Santos.
This paper describes preliminary ideas on formalizing some concepts of neuroanatomy into ontological and epistemological terms. We envisage the application of this ontology on the assimilation of facts about medical knowledge about neuroimages from schizophrenic patients.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3483/version/1

Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal Scanning
Provedor de dados: 17
Autores: Paul Browne; Ruth Eberhardt.
Most sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool &amp;#x22;SPIN&amp;#x22;:http://www.ebi.ac.uk/swissprot/Submissions/spin. Curators use a range of sequence analysis tools to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be kept confidential...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3120/version/1

Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net
Provedor de dados: 17
Autores: Michael Hucka.
Systems biology has arisen through the convergence of theoretical, computational, and mathematical modeling of systems and the need to understand the wealth of information being rapidly generated in biology.  Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics.  Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other&amp;#x27;s results in practical and unambiguous ways....
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/20/version/1

Chemistry Crowdsourcing and Open Notebook Science
Provedor de dados: 17
Autores: Jean-Claude Bradley; Kevin Owens; Antony Williams.
This is a pre-proposal written for the NSF program  CDI (Cyber-Enabled Discovery and Innovation) in Jan 2008.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The current system of dissemination of scientific data and knowledge is far less efficient than it needs to be to facilitate improved collaborative science, especially considering current publication vehicles and infrastructure.  There is a growing movement promoting more Open Science with the belief that a more transparent scientific process can perform far more effectively.  The logical extension of this concept is full transparency - exposing a researcher&amp;#x27;s complete record of progress to the public in near real time. Not only will such a process enable ongoing data sharing it also provides an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1505/version/1

Ligand based virtual screening studies to design drug molecules for human PIN1 causing cardiovascular disease
Provedor de dados: 17
Autores: C Ramana; Manne  Munikumar; Amineni Umamaheswari.
PIN1 is a member of the cis/trans peptidyl-prolyl isomerase family which plays critical roles in cell-cycle regulation. Over expression of PIN1 in endothelial cells causes cardiovascular disease. The present study has focused on computational analysis to identify the potential inhibitors for PIN1. The human PIN1 crystal structure was retrieved from the protein data bank and prepared using protein preparation wizard of Maestro v9.2.  Fourteen PIN1 inhibitors reported in recent literature were acquired and searched for structural analogs using Ligand.Info tool. 5675 PIN1 inhibitor analogs yielded were converted to 3D structures using LigPrep with constraints of ADME evaluation and toxicity assessments.  The 3D ligand dataset was docked to PIN1 through...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6604/version/1

SABIO-RK: Curated Kinetic Data of Biochemical Reactions
Provedor de dados: 17
Autores: Ulrike Wittig.
SABIO-RK (&amp;#x22;http://sabio.villa-bosch.de/SABIORK/&amp;#x22;:http://sabio.villa-bosch.de/SABIORK/) is a curated, web-accessible database for modellers and wet-lab scientists to get comprehensive information about biochemical reactions and their kinetic properties. It integrates data from different origin in order to facilitate the access to reaction kinetics data and corresponding information. Since most of the kinetic data is exclusively found in the literature SABIO-RK offers data manually extracted from the literature and related information obtained from other publicly available biological databases. For instance, the kinetic data are related to reactions, organisms, tissues and cellular locations. The type of the kinetic mechanism and...
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3085/version/1

Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
New antibiotics against multidrug-resistant bacteria are urgently needed, but rapid acquisition of resistance limits their usefulness. Endogenous antimicrobial peptides (AMPs) with moderate selectivity, but multimodal mechanism of action, have remained effective against bacteria for millions of years. Their therapeutic application, however, requires optimizing the balance between antibacterial activity and selectivity, so that rational design methods for increasing selectivity are highly desirable. We have created training (n=36) and testing (n=37) sets from frog-derived AMPs with determined therapeutic index (TI). The &amp;#x27;sequence moments&amp;#x27; concept then enabled us to find a one-parameter linear model resulting in a good correlation between...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/1

BRIF Workshop Introduction
Provedor de dados: 17
Autores: Anne Cambon-Thomsen.
This presentation aims at introducing the place of BRIF in the landscape of data sharing, the BRIF concept, a presentation of the working group, the ongoing debates and the workshop objectives.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5658/version/1

The Hymenoptera Genome Database
Provedor de dados: 17
Autores: Monica C. Munoz-Torres; Justin T. Reese; Christopher P. Childers; Anna K. Bennett; Jaideep P. Sundaram; Donald  C. Vile; Christine G. Elsik.
The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of hymenopteran insect species. This relational database implements open-source software and components providing access to curated data contributed by an extensive, active research community. HGD includes the genome sequences and annotation data of honey bee _Apis mellifera_ and its pathogens (&amp;#x22;http://BeeBase.org&amp;#x22;:BeeBase.org) the parasitoid wasp _Nasonia vitripennis_ (&amp;#x22;http://NasoniaBase.org&amp;#x22;:NasoniaBase.org) and a portal to the genomes of six species of ants. Together, these species cover approximately 200 MY in the phylogeny of Hymenoptera, allowing to leverage genetic, genome sequence, and gene expression data, as well as the...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5182/version/1

Manual Curation of Vertebrate Proteins  in the UniProt Knowledgebase.
Provedor de dados: 17
Autores: Michael  J. Gardner; Lionel  Breuza; The UniProt  Consortium.
The UniProt Knowledgebase (UniProtKB) aims to provide the scientific community with a comprehensive, consistent and authoritative resource for protein sequence and functional information. Given the importance of human and vertebrate model data in biomedical research, a major focus is the high-quality manual curation of human proteins and their vertebrate orthologues. Manual curation involves (1) the extraction of experimental results from scientific literature to enrich protein records with a wide range of information including function, structure, interactions and subcellular location, (2) the manual verification of each sequence and clarification of discrepancies between sequence reports, and (3) the assessment of the output of a range of analysis...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5165/version/1

Design of RNAi reagents for invertebrate model organisms and human disease vectors
Provedor de dados: 17
Autores: Thomas Horn; Michael Boutros.
RNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters. Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and evaluate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6665/version/1

One lump or two?
Provedor de dados: 17
Autores: Kieran Smallbone.
We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of  a cloned population of cells with their environment as though it were one large cell. The question is as to whether any dynamics are lost by this assumption, and as to whether it might be more appropriate to instead model each cell individually. We show that it is sufficient to model at an intermediate level of granularity, representing the population as two interacting lumps of tissue.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4033/version/1

Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer)
Provedor de dados: 17
Autores: C Y Kok; S A Forbes; N Bindal; S Bamford; C G Cole; M Jia; D Breare; R Shepherd; A Menzies; K Leung; J Teague; M R Stratton; P A Futreal.
&amp;#x22;COSMIC, the Catalogue Of Somatic Mutations In Cancer&amp;#x22;:http://www.sanger.ac.uk/cosmic is designed to store and display somatic mutation information relating to human cancers, combining detailed information on publications, samples and mutation types. The information is curated both from the primary literature and the laboratories at the Cancer Genome Project, Sanger Institute, UK, and then semi-automatically entered into the COSMIC database. The v47 release (May 2010) contained the curation of 9202 papers describing 116,977 mutations across 466,851 samples. In order to provide consistent annotation of the data, COSMIC has developed a classification system for cancer histology and tissue ontology, and adapted HGVS mutation nomenclature...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5106/version/1

Exploring NAG active site of human CD59 towards discovery of novel activators for treatment of atherosclerosis
Provedor de dados: 17
Autores: Challa Lakshmi Narayana Rao; Dibyabhaba Pradhan; Amineni Umamaheswari.
CD59 is a potent inhibitor of the complement membrane attack complex (MAC) action that acts by binding to the C8 and C9 complements of the assembling MAC, thereby preventing incorporation of the multiple copies of C9 required for complete formation of the osmolytic pore. Human CD59 low expression leads to atherosclerosis. Therefore, computational approach methods were implemented herein to design novel activators for CD59. Crystal structure (PDB ID: 1CDR) of CD59 was investigated to locate N-acetyl glucosamine (NAG) active site residues (Leu1, Gln2, Val17, Asn18, Ser20, Ser21, Asp22 and Asp67). CD59 is known for its binding affinity towards NAG and Alpha-L-Fucose, hence, were explored against more than one million entries of Ligand.Info metadatabase to...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6531/version/1

Using open access literature to guide full-text query formulation
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background* &amp;#xd;&amp;#xa;Much scientific knowledge is contained in the details of the full-text biomedical literature.  Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume.  Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar.  However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users.  We propose improving the formulation of full-text queries...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4267/version/2

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Leonid Mirny; Zeba Wunderlich.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/1

The Immune Response in Patients with SARS: differential gene expression profiling.
Provedor de dados: 17
Autores: Peter Natesan Pushparaj; Jayapal J. Manikandan; Alirio Jose A. J. Melendez.
Severe acute respiratory syndrome (SARS) emerged in 2003, as a new epidemic form of life-threatening infection. As of 26th September 2003, there were 8422 cases of SARS from 29 countries with 908 deaths (WHO). However, the pathogenesis of SARS is poorly understood. To understand the host response to this pathogen, we profiled the gene expression patterns of peripheral blood mononuclear cells (PBMC) from SARS patients compared to healthy controls using one of the latest techniques, high density oligonucleotide expression probe array (HG-Focus array, Gene Chip, Affymetrix, Santa Clara, CA). High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively&amp;#xd;&amp;#xa;used in many areas of biomedical...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1145/version/1

Inverse relationship between genetic diversity and epigenetic complexity
Provedor de dados: 17
Autores: Shi Huang.
Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence.  This observation provoked the molecular clock hypothesis and in turn the &amp;#x2018;Neutral Theory&amp;#x2019;, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year.  Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence.  It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets.  Here, an inverse relationship between genetic diversity and epigenetic...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1751/version/2

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a cognitive paradigm for protein folding regulation will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/2

A dynamical model of genetic networks describes cell differentiation
Provedor de dados: 17
Autores: Roberto Serra; Villani Marco; Alessia Barbieri.
Cell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4741/version/1

caNanoLab &amp;#x2013; A Tool To Benefit Biomedical Nanomaterials Research
Provedor de dados: 17
Autores: Michal Lijowski.
The cancer Nanotechnology Laboratory Web portal (&amp;#x22;http://cananolab.nci.nih.gov/caNanoLab/welcome.do&amp;#x22;:http://cananolab.nci.nih.gov/caNanoLab/welcome.do) is designed to promote sharing of nanomedicine data and to provide support for the annotation of nanoparticles with information about their composition, function, and characterization. The project is a part of NCI cancer Biomedical Informatics Grid (caBIG&amp;#xae;), and includes a collaboration among the NCI Center for Biomedical Informatics and Information Technology (CBIIT), the NCI Nanotechnology Characterization Laboratory (NCL), and the NCI Alliance for Nanotechnology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Currently, caNanolab contains nanomaterial data of 765 &amp;#x22;public&amp;#x22;...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5175/version/1

Curation and annotation for BioModels Database, a resource of published quantitative kinetic models
Provedor de dados: 17
Autores: Chelliah Vijayalakshmi; Lukas Endler; Camille Laibe; Chen Li; Nicolas Le Nov&amp;#xe8;re.
BioModels Database (&amp;#x22;http://www.ebi.ac.uk/biomodels/&amp;#x22;:http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3124/version/1

Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding
Provedor de dados: 17
Autores: Hossein Zare; Mostafa  Kaveh; Arkady  Khodursky.
Transcriptional networks consist of multiple regulatory layers corresponding to the activity of global regulators, specialized repressors and activators of transcription as well as proteins and enzymes shaping the DNA template. Such intrinsic multi-dimensionality makes uncovering connectivity patterns difficult and unreliable and it calls for adoption of methodologies commensurate with the underlying organization of the data source. Here we present a new computational method that predicts interactions between transcription factors and target genes using a compendium of microarray gene expression data and the knowledge of known interactions between genes and transcription factors. The proposed method called Kernel Embedding of REgulatory Networks (KEREN) is...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5008/version/1

VO: Vaccine Ontology
Provedor de dados: 17
Autores: Yongqun He; Lindsay  Cowell; Alexander D. Diehl; Harry  Mobley; Bjoern Peters; Alan  Ruttenberg; Richard H. Scheuermann; Ryan  R. Brinkman; Melanie  Courtot; Chris  Mungall; Zuoshuang  Xiang; Fang Chen; Thomas Todd; Lesley  Colby; Howard  Rush; Trish  Whetzel; Mark A. Musen; Brian D. Athey; Gilbert  S. Omenn; Barry  Smith.
Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO,...
Tipo: Poster
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3552/version/1

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library
Provedor de dados: 17
Autores: Roderic Page.
The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article finding service is exposed as a standard OpenURL resolver on the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4928/version/1

Reputation, authority and incentives. Or: How to get rid of the Impact Factor
Provedor de dados: 17
Autores: Bj&amp;#xf6;rn Brembs; Peter Binfield.
A short intro into the impact factor and its limitations and potential successors.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2801/version/1

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background&amp;#xd;&amp;#xa;    Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Materials and Methods&amp;#xd;&amp;#xa;    We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/2

The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
Provedor de dados: 17
Autores: James C. Wilgenbusch; Wen Huang; Kyle A. Gallivan.
Phylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several  nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4605/version/1

XML in Motion from Genome to Drug
Provedor de dados: 17
Autores: C. Gopi Mohan.
Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/287/version/1

Systems Biology Graphical Notation: Activity Flow language Level 1
Provedor de dados: 17
Autores: Huaiyu Mi; Falk Schreiber; Nicolas Le Nov&amp;#xe9;re; Stuart Moodie; Anatoly Sorokin.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3724/version/1

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4636/version/1

COMBINE - a vision
Provedor de dados: 17
Autores: Nicolas Le Novere.
A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this format, coupled to a wide software support, fostered the emergence of an entire area of research centered on model processing such as encoding, annotation, merging, comparison and integration with other datasets. Recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. In neuroscience, other fledgling efforts cover for instance multi-compartment neurons with NeuroML, and neuronal networks with NineML. More are needed to cover the wide spectrum of...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5992/version/1

MIREOT: the Minimum Information to Reference an External Ontology Term
Provedor de dados: 17
Autores: Melanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan R. Brinkman; Alan Ruttenberg.
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3574/version/1

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background&amp;#xd;&amp;#xa;    Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Materials and Methods&amp;#xd;&amp;#xa;    We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/1

Genomic Replikin Counts of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin CountsTM  of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6991/version/1

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur [1] &amp;#x2013; a C++ - based software package used for clustering 16SrRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B)The Ribosomal Database (RDP) naive Bayesian classifier [2] assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime [3] &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/1

Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an approach for identifying such &amp;#x201c;erroneous mappings&amp;#x201d; using Distributed Description Logics. Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings, and provide preliminary results...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3456/version/1

The CALBC RDF Triple store: retrieval over large literature content
Provedor de dados: 17
Autores: Samuel Croset; Christoph Grabm&amp;#xfc;ller; Chen Li; Silvestras Kavaliauskas; Dietrich Rebholz-Schuhmann.
Background&amp;#xd;&amp;#xa;Integration of the scientific literature into a biomedical research infrastructure requires the processing of the literature, identification of the contained named entities (NEs) and concepts, and to represent the content in a standardised way.  Little efforts have been spent on the integration of content from the literature text into RDF Triple Stores.&amp;#xd;&amp;#xa;The CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus I (SSC-I). The four semantic groups were chemical entities and drugs (CHED), genes and proteins (PRGE), diseases...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5383/version/2

Quest for the descent of the Escherichia coli outbreak strain TY2482 &amp;#x2013; out of Germany?
Provedor de dados: 17
Autores: Tiruvayipati S. Avasthi; Narender Kumar; Ramani Baddam; Niyaz Ahmed.
The recent outbreak of the Escherichia coli infection in north Germany reportedly has killed 35 people and sickened about 4000. Infections were reported in 2001 and 2002 in Germany and Central Africa respectively. In order to dissect all possible connections among the three infection/outbreak strains and to extract the most virulent genes responsible for the augmented  pathogenicity of the present German strain (2011), whole genome sequence data of the two isolates (E. coli TY_2482 &amp;#x26; LB226692) were analyzed. We report that the German outbreak strain isolated in 2011 is a seasoned clone of the 2002 isolate sequenced from Central Africa (55989) and perhaps a direct descendent of the German EAEC strain reported in 2001 infection cases.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6034/version/2

Modeling cardiac rhythm and heart rate using BFO and DOLCE
Provedor de dados: 17
Autores: Lynda Temal; Arnaud Rosier; Olivier Dameron; Anita Burgun.
This paper presents an application ontology for modeling cardiac rhythm and its anomalies such as tachycardia and bradycardia. We use BFO and DOLCE as ontological reference framework in order to compare their impact on ontology design. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3558/version/1

FDserver: A web service for protein folding research
Provedor de dados: 17
Autores: Bin-Guang Ma; Ling-Ling Chen; Hong-Yu Zhang.
*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.&amp;#xd;&amp;#xa;*Availability:* http://sdbi.sdut.edu.cn/FDserver
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2349/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5271/version/1

Structural characterization of an endoglucanase from _Serpula lacrymans_ var. lacrymans S7.9
Provedor de dados: 17
Autores: Csaba Zoltan Kibedi Szabo; Judit Galicza; Istvan Weyda; Csaba Dezso Andras.
Lately cellulase enzymes from fungi and also bacteria, have received much attention due to their application in bioethanol production from lignocellulosic feedstock. Dry rot fungus (_Serpula lacrymans_) is known to be the most damaging destroyer of indoor wood construction materials in temperate regions. Therefore the very recent sequencing of this fungus genome has opened new possibilities. We describe here the analysis of the primary, secondary and tertiary structure of a 255 amino acid sequence endoglucanase, from _S. lacrymans_ var. lacrymans S7.9, having a molecular weight of 26746. We also provide the amino acids from the active site.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6575/version/1

DDBJ Sequence Read Archive / DDBJ Omics Archive
Provedor de dados: 17
Autores: Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura.
Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields.  DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI.  In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms.  DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy.  Since 2004, DDBJ has operated CIBEX as a repository database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5085/version/1

3D Structure Development of Chikungunya Virus and its Structural Characterization &amp;#x2013; an In silico approach
Provedor de dados: 17
Autores: Anuraj Nayarisseri; Mukesh Yadav; Dowlathabad Muralidhara Rao; Sonam Kukreja; Sheaza  Ahmed; Pooja  Singh.
The 3 Dimensional structure of a protein is an expedient for structure based drug design and identifying the conformational epitopes that are foremost for designing the vaccines. Chikungunya (CHIKV) is a heat sensitive RNA virus which causes a viral disease which is transmitted in humans by human-mosquito-human transmission. Disease mostly found in the tropic and subtropical countries mainly in South India and in few other Asian countries. The primary transmission agents of Chikungunya Virus are yellow fever mosquito (_Aedes aegypti_) and forest day mosquito (_Aedes albopictus_). The forest day mosquito bites during day time and hence day time mosquito bite is the main reason for transmission. The main distinctive of the disease is a fever along with an...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5143/version/1

The Mass-Action-Law Based GPS Concept for Bio-Informatics
Provedor de dados: 17
Autores: Ting-Chao Chou.
The unified theory of dose and effect, as indicated by the median-effect equation for single and multiple entities and for the first and higher order kinetic/dynamic, has been established by T.C. Chou and it is based on the physical/chemical principle of the mass-action law (_J. Theor. Biol._ 59: 253-276, 1976; _Pharmacological Rev._ 58: 621-681, 2006). Rearrangements of the median-effect equation lead to Michaelis-Menten, Hill, Scatchard, and Henderson-Hasselbalch equations. The &amp;#x201c;median&amp;#x201d; serves as the &amp;#x201c;universal reference point&amp;#x201d; and the &amp;#x201c;common link&amp;#x201d; for the relationship of all entities at all dynamic orders, and is also the &amp;#x201c;harmonic mean&amp;#x201d; of kinetic dissociation...
Tipo: Presentation
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2064/version/2

Biocuration Workflow Catalogue
Provedor de dados: 17
Autores: Gully Burns; Martin Krallinger; Kevin Cohen; Cathy Wu; Lynette Hirschman.
As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. We presented this work as a slideshow and publish this account of the catalog as...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3250/version/1

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology.  Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The methods and improvement to the CL in...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3635/version/1

UniRule - Automatic Annotation In UniProtKB
Provedor de dados: 17
Autores: Alan J. Bridge; Diego Poggioli; Claire O&amp;#x27;Donovan.
The UniProt KnowledgeBase (UniProtKB) provides a stable, comprehensive, freely accessible, centralized resource on protein sequences and functional annotation. UniProtKB consists of two sections: UniProtKB/SwissProt, a section containing records that are manually annotated with information extracted from the literature and curator-evaluated computational analysis, and UniProtKB/TrEMBL, a section containing computationally analysed records enriched with automatic annotation and classification. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Automatic annotation is an essential complement to manual annotation, which cannot keep pace with either current or projected rates of growth of UniProtKB. To this end UniProt is developing an integrated annotation system termed...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5247/version/1

BioPAX: next steps for Semantic Web / CV workgroup
Provedor de dados: 17
Autores: Andrea Splendiani.
Outline of the next steps which will be proposed as actions in the Semantic Web/ Linking/ CV workgroup of BioPAX.&amp;#xd;&amp;#xa;One main focus will be to clean the RDF representation and adopt some basic relations, in order to address use cases in data-integration, pathway analysis and simple ontology/pathway integration.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4968/version/1

Automatisation in UniProtKB / Swiss-Prot Annotation: New Rules and Tools
Provedor de dados: 17
Autores: The HAPMAP Team; The PROSITE Team; Edouard de Castro; Alan Bridge; UniProt Consortium.
The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are being produced at an ever increasing rate.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3215/version/1

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome
Provedor de dados: 17
Autores: Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu.
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270&amp;#x2013;15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3432/version/1

SED-ML Web Tools
Provedor de dados: 17
Autores: Frank T. Bergmann.
This presentation gives a brief update of the current state of the libSedML library and its new capabilities (like the simulation of CellML models) and the SED-ML Script Editor.  &amp;#xd;&amp;#xa;Following I introduce the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The web application also provides a W3C Web Service, exposing all functionality.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6328/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4120/version/4

DNA expression microarrays may be the wrong tool to identify biological pathways
Provedor de dados: 17
Autores: Adrian Mondry; Marie Loh; Alessandro Giuliani.
DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen&amp;#x2019;s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 &amp;#x3c; k &amp;#x3c; 0.79) between the analysis methods used.  Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1036/version/1

Evolution of the Sequence Ontology terms and relationships
Provedor de dados: 17
Autores: Karen Eilbeck; Christopher J. Mungall.
The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3495/version/1

Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Provedor de dados: 17
Autores: Sonal Mishra; Abha Meena; Sema Singh; Dharmendra Kumar Yadav; Feroz  Khan; Rakesh K. Shukla.
The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5790/version/1

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome
Provedor de dados: 17
Autores: Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu.
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270&amp;#x2013;15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3432/version/2

Molecular Modeling study of Protein Kinase PKnB from Mycobacterium Tuberculosis with derivatives of 1, 3, 4- Thiadiazoles
Provedor de dados: 17
Autores: Vivek Gupta; Asif Naqvi; Jayendra Tanwar; Kaushlesh Mishra.
Tuberculosis causes more than two million deaths per year. Faced with this global threat it is crucial to better understand the physiology of the causative organism, Mycobacterium Tuberculosis, in order to develop efficient therapeutic strategies. PKnB from Mycobacterium tuberculosis is a crucial receptor-like protein kinase involved in signal transduction. M. tuberculosis PKnB is a trans-membrane Ser/Thr protein kinase (STPK) highly conserved in Gram-positive bacteria and apparently essential for Mycobacterial viability. We have attempted with the help of virtual screening and docking approaches to expound the extent of specificity of protein kinase B towards different classes of Thiadiazoles (an anti-tubercular agent).  The selected Thiadiazoles were...
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6136/version/1

WikiPathways: Community Curation of Biological Pathways
Provedor de dados: 17
Autores: Alexander Pico.
Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed &amp;#x22;WikiPathways&amp;#x22;:http://www.wikipathways.org ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria. WikiPathways is entering a phase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5361/version/1

A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006).  It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/1

Evaluation of protein surface roughness index using its heat denatured aggregates
Provedor de dados: 17
Autores: Hrishikesh Mishra; Tapobrata Lahiri.
Recent research works on potential of different protein surface describing parameters to predict protein surface properties gained significance for its possible implication in extracting clues on protein&amp;#x27;s functional site. In this direction, Surface Roughness Index, a surface topological parameter, showed its potential to predict SCOP-family of protein. The present work stands on the foundation of these works where a semi-empirical method for evaluation of Surface Roughness Index directly from its heat denatured protein aggregates (HDPA) was designed and demonstrated successfully. The steps followed consist, the extraction of a feature, Intensity Level Multifractal Dimension (ILMFD) from the microscopic images of HDPA, followed by the mapping of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3693/version/1

Implementation of computational methods for designing potential inhibitors against human p38&amp;#x3b1; protein
Provedor de dados: 17
Autores: Durga Devi M; Dibyabhaba  Pradhan; Manne Munikumar; Amineni Umamaheswari.
p38&amp;#x3b1;, a non-receptor serine/threonine kinase, plays an essential role in cell proliferation, cell differentiation, apoptosis, production of cytokines such as IL1&amp;#x3b2; and TNF&amp;#x3b1;, senescence and tumorigenesis. Over expression of p38&amp;#x3b1; enhances the production of cytokines, leading to inflammation causing cancers. Therefore, the protein p38&amp;#x3b1; is selected as a target for the inhibition of progression of inflammatory cancers. SB203580, BIRB796, 2H-quinolizine-2-one, 7-alkyl-1,5-bis&amp;#x2013;aryl-pyrazolo pyridinones, aML3403, N-pyrimidyl amides, Fused pyrazoles, SD0006, 4-3-(4-fluoro phenyl )-1H-pyrazol-4-yl)pyridine are the nine published inhibitors for the p38&amp;#x3b1;, but they show side effects like liver...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5456/version/1

LogMap 2.0: towards logic-based, scalable and interactive ontology matching
Provedor de dados: 17
Autores: Ernesto Jimenez-Ruiz; Bernardo Cuenca Grau; Yujiao Zhou.
In this paper we present a much improved version of LogMap, a highly scalable ontology matching system with &amp;#x2018;built-in&amp;#x2019; reasoning and diagnosis capabilities. LogMap 2.0 is not only more scalable and robust than its predecessor, but it also provides the necessary infrastructure for domain experts to interactively contribute to the matching process.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6670/version/1

Evaluating Modelling  Approaches for Medical  Image Annotations
Provedor de dados: 17
Autores: Jasmin Opitz; Bijan Parsia; Ulrike Sattler.
Information system designers face many challenges with regards to selecting appropriate semantic technologies and deciding on a modeling approach for their system. However, there is no clear methodology yet to evaluate &amp;#x201c;semantically enriched&amp;#x201d; information systems. In this paper we present a case study on different modeling approaches for annotating medical images and introduce a conceptual framework that can be used to analyze the fitness of information systems and help designers to spot the strengths and weaknesses of various modeling approaches as well as managing trade-o&amp;#xfb00;s between modeling e&amp;#xfb00;ort and their potential benefits.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5609/version/1

Using ABC for model design and inference across biological scales
Provedor de dados: 17
Autores: Oliver  Ratmann.
Using ABC for model design and inference across biological scales.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5960/version/1

A quick trip through openness, freedom and transparency
Provedor de dados: 17
Autores: Konrad U. Foerstner.
This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open science/knowledge. A video of the talk is available on the author&amp;#x27;s website.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1225/version/1

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY
Provedor de dados: 17
Autores: Nick Juty; Nicolas Le Nov&amp;#xe8;re; Dagmar Waltemath; Christian Knuepfer.
The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the &amp;#x27;Repressilator&amp;#x27; model (Elowitz and Leibler, 2000).
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5122/version/1

Human Heart Development Pathways
Provedor de dados: 17
Autores: Samuel Sklar; Alexander Pico.
This pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impact the regional specificity of the human heart. Activating signals are indicated by arrows while inhibitory signals are indicated by T-bars. Special thanks to Kim Cordes for her assistance in revising this pathway, based on recent heart development research. A live version of the pathway can be found at http://www.wikipathways.org/index.php/Pathway:WP1591
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6500/version/1

Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy
Provedor de dados: 17
Autores: I. C. Baianu; Schuyler S. Korban; Doina M. Costescu.
Novel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6207/version/1

More damn lies about data access
Provedor de dados: 17
Autores: Myles Axton.
More data than we can handle is no excuse to give up our efforts to promote data access, but it may make us think about new ways to make it sustainable.&amp;#xd;&amp;#xa;[This draft was written in the hope that participants of the Sage Congress will write an Nature Genetics Editorial in the manner of Tom Sawyer&amp;#x2019;s white fence (Twain M. 1876). All contributions received by April 10th 2011 will be attributed.]&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5873/version/1

Pandemic (H1N1) 2009 Cluster Analysis: A Preliminary Assessment
Provedor de dados: 17
Autores: Charles Wick; Michael Stanford; Rabih Jabbour; Samir Deshpande; Patrick McCubbin; Evan Skowronski; Alan Zulich.
Pandemic (H1N1) 2009 virus has been causing major concerns around the world because of its epidemic potential, rapid dissemination, rate of mutations, and the number of fatalities. One way to gain an advantage over this virus is to use existing rapid bioinformatics tools to examine easily and inexpensively generated genetic sequencing data. We have used the protein sequences deposited with the National Center for Biotechnology Information (NCBI) for data mining to study the relationship among the Pandemic (H1N1) 2009 proteins. There are 11 proteins in the Pandemic (H1N1) 2009 virus, and analysis of sequences from 65 different locations around the globe has resulted in two major clusters. These clusters illustrate the Pandemic H1N1 2009 virus is already...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3773/version/1

Providing a Realist Perspective on the eyeGENE Database System
Provedor de dados: 17
Autores: Werner Ceusters.
One of the achievements of the eyeGENE Network is a repository of DNA samples of patients with inherited eye diseases and an associated database that tracks key elements of phenotype and genotype information for each patient. Although its database structure serves its direct research needs, eyeGENE has set a goal of enhancing this structure to become increasingly well integrated with medical information standards over time. This goal should be achieved by ensuring semantic interoperability with other information systems but without adopting the incoherencies and inconsistencies found in available biomedical standards. Therefore, eyeGENE&amp;#x2019;s current pragmatic perspective with focus on data and information, rather than what the information is about,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3467/version/1

Accelerated Macromolecular Solution Structure Recovery
Provedor de dados: 17
Autores: Petrus Zwart; Haiguang Liu.
Small Angle X-ray Scattering (SAXS) is a standard technique for the determination of low-resolution shapes of macromolecules and their complexes, adding important insights in understanding biological function. We present a novel and computationally efficient method for shape reconstruction from SAXS data. High-quality molecular shapes are calculated in less than two minutes, providing real-time feedback during SAXS experiments.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6521/version/1

MEMOFinder: combining _de_ _novo_ motif prediction methods with a database of known motifs
Provedor de dados: 17
Autores: Bartek Wilczynski; Milosz  Darzynkiewicz; Jerzy  Tiuryn.
*Background:* Methods for finding overrepresented sequence motifs are useful in several key areas of computational biology. They aim at detecting very weak signals responsible for biological processes requiring robust sequence identification like transcription-factor binding to DNA or docking sites in proteins. Currently, general performance of the model-based motif-finding methods is unsatisfactory; however, different methods are successful in different cases. This leads to the practical problem of combining results of different motif-finding tools, taking into account current knowledge collected in motif databases.&amp;#xd;&amp;#xa;*Results:* We propose a new complete service allowing researchers to submit their sequences for analysis by four different...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2289/version/1

ChemTextMiner: An open source tool kit for mining  medical literature abstracts
Provedor de dados: 17
Autores: Muthukumarasamy  Karthikeyan; Yogesh  Pandit; Deepak  Pandit; Ganesh Nainaru; Sunil  Nalwade; Renu  Vyas; Esha  Jain.
Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The methods, tools and data used for building biological networks using a distributed computing environment previously used for ChemXtreme[1]...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6435/version/1

Docking studies to explore novel lead molecules for human Spleen tyrosine kinase involved in chronic lymphocytic leukemia
Provedor de dados: 17
Autores: Naveen  Kadaari; Dibyabhaba  Pradhan; Manne  Munikumar; Amineni  Umamaheswari.
B-cell chronic lymphocytic leukemia (CLL) is the most prevalent B-cell malignancy in adults. Despite advances in treatment, the disease remains incurable, warranting further efforts to identify novel molecular targets and inhibitors. Spleen tyrosine kinase (SYK) plays a pivotal role for B-lymphocyte development and maturation in the B-cell receptor (BCR) signaling pathway and hence represents a potential therapeutic target for CLL. The present study is directed towards finding novel inhibitors of SYK through ligand based virtual screening. The co-crystal structure of SYK was investigated to locate active site residues (Glu-449, Ala-451 Arg-498, Asn-499, Ser-511, and Asp-512). Five SYK specific published inhibitors (Gleevec, staurosporine, Bay61-3606, R-406...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5460/version/1

SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web
Provedor de dados: 17
Autores: Norio Kobayashi; Manabu Ishii; Yuko Yoshida; Yuko Makita; Akihiro Matsushima; Yoshiki Mochizuki; Tetsuro Toyoda.
Integration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena.  Scientists&amp;#x2019; Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a semantically defined relationship between these bio-items.  These triples are curated from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from published databases by computer programs.  SciNetS internally forms a metadata network by maximally concatenating...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5083/version/1

A network-based signaling mechanism of cancer development and progression
Provedor de dados: 17
Autores: Edwin Wang.
We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer mutating genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylating genes are enriched in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or oncogene-signaling blocks,...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2238/version/1

BioMed Central - open data guidance for authors
Provedor de dados: 17
Autores: Naomi Attar.
All research articles published by BioMed Central are open access. In keeping with the spirit of open access publishing, we aim to maximize the availability of data associated with these articles.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6234/version/1

Structural insight to Streptococcus mitis thymidylate kinase: a potential common drug target of infective endocarditis
Provedor de dados: 17
Autores: Vani  Priyadarshini; Dibyabhaba Pradhan; Manne Munikumar; Amineni Umamaheswari.
The incidence of infective endocarditis (IE) represents the fourth leading cause of life-threatening infectious disease with a yearly incidence of 15,000 to 20,000 new cases despite advances in antimicrobial therapy, development of better diagnostic and surgical techniques. The diverse group of causative microbes of IE is one of major obstacle towards development of effective antimicrobial drug. This has triggered exploration of common potential novel drug target from available whole genome sequences of predominant pathogens causing IE in SVIMS hospital through comparative subtractive genomic approach and metabolic pathway analysis. Streptococcus mitis is the most predominant IE pathogen in SVIMS hospital. Thymidylate kinase of Streptococcus mitis plays a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5158/version/1

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)
Provedor de dados: 17
Autores: Satya N. V. Arjunan.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4201/version/1

Concurrent, Collaborative &amp;#xb;Ontology Building&amp;#xb; with Collaborative Prot&amp;#xe9;g&amp;#xe9; (CP)
Provedor de dados: 17
Autores: Daniel Schober.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3516/version/1

SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format
Provedor de dados: 17
Autores: Wolfram Liebermeister; Falko Krause; Jannis Uhlendorf; Timo Lubitz; Edda Klipp.
Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on MIRIAM annotations in the original...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3093/version/1

Normalization And Matching Of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Meik Bittkowski; Henriette Slogsnat; Jasmin Saric; Isabel Rojas; Wolfgang M&amp;#xfc;ller.
We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name  of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6505/version/1

A Target Restricted Assembly Method (TRAM) for Phylogenomics
Provedor de dados: 17
Autores: Kevin P. Johnson; Kimberly K. O. Walden; Hugh M. Robertson.
While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications.  Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes.  This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4612/version/1

Letting the Cat Out of the Bag: &amp;#xb;OBO and the Semantic Web
Provedor de dados: 17
Autores: John E. Rose.
The tools developed to work with an expanding number of biomedical ontologies are all directed &amp;#x201c;inward,&amp;#x201d; back toward the scientists. The Semantic Web is an effort to assign meaning to data available on the internet resulting in a universal platform of knowledge exchange. For the Open Biomedical Ontologies to become a part of the Semantic Web, a more &amp;#x201c;outward-looking&amp;#x201d; tool is required. A prototype, AmiGA, based on 21 ontologies with over 600,000 terms,&amp;#xd;&amp;#xa;has been constructed.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3527/version/1

Populous: A Tool For Populating OWL Ontologies From Templates
Provedor de dados: 17
Autores: Simon Jupp.
We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute.&amp;#xd;&amp;#xa;Populated tables are mapped to patterns that can then be used to automatically generate the ontology&amp;#x27;s content. Populous&amp;#x27;s contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5419/version/1

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species
Provedor de dados: 17
Autores: Charles Chen; Genevieve DeClerck; Terry Casstevens; Ken Youens-Clark; Jon Zhang; Doreen Ware; Pankaj Jaiswal; Susan McCouch; Edward Buckler.
The Genetic Diversity module of the Gramene database (&amp;#x22;http://www.gramene.org/diversity&amp;#x22;:http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4645/version/1

The future of annotation/biocuration
Provedor de dados: 17
Autores: Amos Bairoch.
Talk given at 3rd International Biocuration Conference. Berlin 2009
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3092/version/1

A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset; Christoph Grabm&amp;#xfc;ller; Dietrich Rebholz-Schuhmann.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/2

Relation Ontology II
Provedor de dados: 17
Autores: Cristian Cocos.
Conceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2479/version/1

PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
Provedor de dados: 17
Autores: Karthik Raman; Nagasuma Chandra.
Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as _Escherichia coli_, _Saccharomyces cerevisiae_ and _Staphylococcus aureus_ have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA. PathwayAnalyser interfaces with the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1868/version/1

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;&amp;#xd;&amp;#xa;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/2

BioPax and SBML output from Reactome: where we are, where we are heading
Provedor de dados: 17
Autores: David Croft.
Reactome is a free, open-source, open access, pathway database. Currently, Reactome has over 5000 human proteins, involved in over 4000 manually curated reactions.  Additionally, it has nearly 30,000 reactions inferred by orthology projection from human to 20 other model organisms.  Facilities exist for exporting single pathways or the entire database to either BioPax or SBML.  SBML generation now uses libSBML, ensuring syntactic correctness, and has adopted MIRIAM URIs for references to external databases.  For the future, we anticipate that users will be able to submit a list of species to Reactome and obtain as an output customized BioPax or SBML, based on reactions extracted from Reactome.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6376/version/1

Inherited mutations impair responses to environmental carcinogens:  Cancer prevention in mutation carriers
Provedor de dados: 17
Autores: Bernard Friedenson.
Some environmental carcinogens may be responsible for a modest increase in the numbers of cancers after years of exposure.  Economic or political factors weigh against widespread bans of carcinogens.  However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects. &amp;#xd;&amp;#xa;Hereditary cancer gene mutations can target specific tissues if they are exposed to a carcinogen and the hereditary deficit impairs normal protective responses.  Mutation carriers should then have higher risks for specific cancers caused by specific carcinogens.&amp;#xd;&amp;#xa;  &amp;#xd;&amp;#xa;For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6024/version/1

Identification of new leads for human IGFBP-2: a therapeutic target for cardiovascular diseases
Provedor de dados: 17
Autores: Kanipakam Hema; I Vani Priyadarshini; Amineni Umamaheswari.
IGFBP-2, the largest member of insulin-like growth factor binding proteins family, is under-expressed in hazardous cardiovascular diseases like obesity and type II diabetes mellitus, which upon aging leads to heart stroke. Therefore, IGFBP-2 has been proposed as a possible target for the development of novel leads for cardiovascular disease therapy. High-throughput virtual screening, one of the most common methods used to identify lead compounds was implemented here to identify potential IGFBP-2 activators. The NMR (nuclear magnetic resonance) structure of human IGFBP-2 was retrieved from the protein data bank. A 2D similarity search was performed for known IGFBP-2 activator TPA to acquire 383 structural analogs. The 3D structural conversion and multiple...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6570/version/1

Data Management Plan for Monogram BioSciences
Provedor de dados: 17
Autores: Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5668/version/1

eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery
Provedor de dados: 17
Autores: Erik  Segerdell; Melanie L. Wilson; Ted Bashor; Daniela Bourges-Waldegg; Karen Corday; H. Robert Frost; Tenille Johnson; Christopher J. Shaffer; Larry Stone; Carlo Torniai; Melissa A. Haendel.
The eagle-i Consortium (&amp;#x22;http://www.eagle-i.org/home&amp;#x22;:www.eagle-i.org/home) comprises nine geographically and ethnically diverse universities across America working to build a federated network of research resources. Biomedical research generates many resources that are rarely shared or published, including: reagents, protocols, instruments, expertise, organisms, training opportunities, software, human studies, and biological specimens. The goal of eagle-i is to improve biomedical research by helping researchers more easily find scientific resources that are difficult to discover, reducing time-consuming and expensive duplication of resources. Now in early development, the system will ultimately expand to include research resources at...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5176/version/1

In-silico Predictive Mutagenicity Model Generation Using Supervised Learning Approaches
Provedor de dados: 17
Autores: Anurag  Passi; Abhik Seal; OSDD  Consortium; UC Abdul  Jaleel.
With the advent of High Throughput Screening techniques, it is feasible to filter possible leads from a mammoth chemical space that can act against a particular target and inhibit its action. Virtual screening complements the in-vitro assays which are costly and time consuming. This process is used to sort biologically active molecules by utilizing the structural and chemical information of the compounds and the target proteins in order to screen potential hits. Various data mining and machine learning tools utilize Molecular Descriptors through the knowledge discovery process using classifier algorithms that classify the potentially active hits for the drug development process.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6116/version/1

Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton
Provedor de dados: 17
Autores: Jack A. Gilbert; Paul Somerfield; Ben Temperton; Susan Huse; Ian Joint; Dawn Field.
Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using 747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and nutrient...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4406/version/1

Polar Mapper: a computational tool for integrated visualization of protein interaction networks and mRNA expression data
Provedor de dados: 17
Autores: Joana P. Gon&amp;#xe7;alves; M&amp;#xe1;rio Gr&amp;#xe3;os; Andre X. C. N. Valente.
Polar Mapper is a computational application for exposing the architecture of protein interaction networks. It facilitates the system-level analysis of mRNA expression data in the context of the underlying protein interaction network. Preliminary analysis of a human protein interaction network and comparison of yeast oxidative stress and heat shock gene expression responses are addressed as case studies.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2663/version/1

A generic approach for representing complex structures in biological models
Provedor de dados: 17
Autores: Robert I. Muetzelfeldt.
Increasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in their models.   On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation, while on the other hand the &amp;#x22;Virtual X&amp;#x22; communities (where X is some organism or organ) need to represent the organisational structure within their object of study.   To date, various approaches have been proposed, such as  the SBML Level 3 &amp;#x27;comp&amp;#x27;, &amp;#x27;spatial&amp;#x27;, &amp;#x27;array&amp;#x27; and &amp;#x27;dyn&amp;#x27; extension packages, and domain-specific elements in languages such as NeuroML, but there is no generic approach intended to be adopted by the various...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5188/version/1

Automated Annotation-Based Bio-Ontology Alignment with Structural Validation
Provedor de dados: 17
Autores: Cliff Joslyn; Bob Baddeley; Judith Blake; Carol Bult; Mary Dolan; Rick Riensche; Karin Rodland; Antonio Sanfilippo; Amanda White.
We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3518/version/1

Miraculous Survival of Three Trapping Miners by Drinking High Mineral Mine Water for 25
Provedor de dados: 17
Autores: Cheng C. Liang; Deng Sheng; Wang Lin; Mu Mao.
Little is known that how long a human been can survive a complete starvation. There were dozens of miners who lost their lives in a coal mine disaster at Qinglong,Guizhou,China in June 2009, only three of them were rescued 25 days later after they had been trapped in a coal mine 600 meters underground. They maintained their lives only by drinking mineral water in the mine, which created a miracle of life. We reported here on this life miracle in relation to high mineral mine water.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5438/version/1

Computational system biology
Provedor de dados: 17
Autores: Ankit Geete.
Systems biology is a multi-disciplinary &amp;#xfb01;eld that deals with mechanisms involved in complex biological processes by considering them as integrated systems of multiple interacting components. The huge amount of data involved in this study necessitates the use of computational tools.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7104/version/1

In silico design of potent agonists for human PPAR &amp;#x3b3;
Provedor de dados: 17
Autores: Navya Pallapotu; Divya M; Kanipakam Hema; Amineni Umamaheswari.
Peroxisome proliferator-activated receptor (PPAR &amp;#x3b3;) acts as a key regulator on adipocyte differentiation and glucose homeostasis. PPAR &amp;#x3b3; has been implicated in the pathology of type 2 diabetes. As human PPAR &amp;#x3b3; activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for human PPAR &amp;#x3b3; protein. The co-crystal structure of PPAR &amp;#x3b3;, solved through X-Ray diffraction method was retrieved from the protein data bank. Four PPAR &amp;#x3b3; agonists selected from literature were submitted to subsequent 2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR &amp;#x3b3; co-crystal structure and ligand dataset were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6957/version/1

Flaw-tolerance in silk fibrils explains strength, extensibility and toughness of spider silk
Provedor de dados: 17
Autores: Melis Arslan; Markus  J. Buehler.
Silk is an ancient but remarkably strong, extensible and tough material made from simple protein building blocks. Earlier work has shown that the particular molecular geometry of silk with a composite of semi-amorphous and nanocrystalline beta-sheet protein domains provides the structural basis for its characteristic softening-stiffening behavior and remarkable strength at the nanoscale. Yet, an open question remains as to how these nanoscale properties are upscaled so effectively to create strong, extensible and tough silk fibers. Here we discover that the geometric confinement of fibrils to &amp;#x2248;50-100 nm width and arranged in bundles to form larger-scale silk fibers, is the key to explaining the upscaling of the mechanical properties of silk from...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5916/version/1

Lipid models for united-atom molecular dynamics simulations of protein
Provedor de dados: 17
Autores: Andreas Kukol.
Molecular dynamics (MD) simulations of biomolecules are performed at various levels of atomic detail from all-atom models to coarse grained models. United-atom models are at an intermediate level, in which non-polar hydrogen atoms are subsumed into their adjacent carbon-atom reducing the number of particles for a DPPC lipid molecule by 60%. United-atom models of the lipids DPPC, DMPC, POPC and POPG in the GROMOS96 53a6 force field were developed, that reproduced experimental properties of lipid bilayers without assumption of a constant surface area or inclusion of surface pressure. In the absence of experimental data a&amp;#x9;surface&amp;#x9;per lipid area for the negatively charged POPG of 0.700&amp;#xb1;0.007 nm2 was obtained&amp;#x9;that is higher than...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5977/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl.
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3543/version/1

SBGN-PD: Current status, future changes and unresolved issues
Provedor de dados: 17
Autores: Stuart L. Moodie.
SBGN PD is currently at Level 1 Version 1.2, which is a maintenance release. The next release will be L1 Version 2.0, which will incorporate changes to the state glyph, add the annotation glyph and change the semantics of complex sub-units. These issues may be discussed further as will some unresolved issues in the specification.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5997/version/1

Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types or tissues. We present DEXSeq, a statistical method to test for differential exon usage in RNA-Seq data. DEXSeq employs generalized linear models and offers reliable control of false discoveries by taking biological variation into account. DEXSeq detects genes, and in many cases specific exons, that are subject to differential exon usage with high sensitivity. We demonstrate the versatility of DEXSeq by applying it to several data sets. The method facilitates the study of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/2

Developing Ontology Support for Human Malaria Control Initiatives
Provedor de dados: 17
Autores: Daramola Olawande; Fatumo Segun.
Malaria is one of the most common infectious diseases and an enormous public health problem in Sub-Sahara Africa, Asia and parts of America. In this paper, we discuss the development of the Human Malaria Control Ontology (HMCO) which contains general information on Malaria and epidemiological information that can help in the formulation of effective malaria control policies. The HMCO is aimed at providing interoperability support for the knowledge management of malaria control initiatives, and serve as an open semantic web infrastructure for malaria research and treatment.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3591/version/1

In-silico analysis of human IGFBP-4 involved in cardiovascular diseases
Provedor de dados: 17
Autores: Manne MuniKumar; Kavali Roopesh; Amineni  Umamaheswari.
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure. IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was pursued in the present study to propose potential inhibitors of IGFBP-4. Two published inhibitors were selected to initiate high throughput virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH, Asinex Ltd and KEGG ligand....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6567/version/1

On The Dangers Of Aligning RNA Sequences Using &amp;#x201c;Conserved&amp;#x201d; Motifs
Provedor de dados: 17
Autores: Roderic Page.
Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignments. Incorporating information on RNA secondary structure can improve the alignment, but this must usually be done by hand. One approach to aligning RNA sequences uses &amp;#x22;conserved motifs&amp;#x22;, however relying on these motifs may lead to gross errors of alignment if, in fact, those motifs are not conserved.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1029/version/1

*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol*
Provedor de dados: 17
Autores: Thomas Perls; Nir Barzilai.
The &amp;#x22;Archon Genomics X PRIZE Validation Protocol&amp;#x22;:http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the scientific community. Here, we suggest 100 subjects age &amp;#x3e;=105 years as the source of DNAs for the competition.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5756/version/1

COMBINE and MIRIAM Registry
Provedor de dados: 17
Autores: Nicolas Le Novere.
N/A
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6152/version/1

In silico Gene Characterization and biological annotation of Aspergillus niger CBS 513.88
Provedor de dados: 17
Autores: Anuraj  Nayarisseri; Mukesh Yadav; Vini Lokhande; Rajesh  Patidar; Mayura  Maynal.
Genome annotation is the process of estimation of biological features from genomic data. The target of a genome annotation is to identify the key features of the genome sequence particularly, the genes and gene products. The characteristics of a gene, its products, and gene prediction programs of Aspergillus niger are discussed. Although the number of genomes in genomic databases are increasing day by day, genome-wide analyses are affected by the quality of the genome annotations. This study illustrates the importance of integrative approaches for automatic annotations of genomes of Aspergillus niger by computational methods. However, the annotation process is more complicated in Eukaryotes; we used a comparative study for gene prediction using the FgenesH...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5806/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/1

Universal fractal scaling of self-organized networks
Provedor de dados: 17
Autores: Paul J. Laurienti; Karen E. Joyce; Qawi K. Telesford; Jonathan H. Burdette; Satoru Hayasaka.
There is an abundance of literature on complex networks describing a variety of relationships among units in social, biological, and technological systems. Such networks, consisting of interconnected nodes, are often self-organized, naturally emerging without any overarching designs on topological structure yet enabling efficient interactions among nodes. Here we show that the number of nodes and the density of connections in such self-organized networks exhibit a power law relationship. We examined the size and connection density of 46 self-organizing networks of various biological, social, and technological origins, and found that the size-density relationship follows a fractal relationship spanning over 6 orders of magnitude. This finding indicates that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4894/version/2

Quadruple context-free L-System mathematical tools as origin of biological evolution
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
It is well known that A, T, G, C annealed together early in evolution and the long stretch of DNA was found which ultimately resulted into chromosomes of different organisms.  But it is unclear till date how exons, introns, conserved protein domains was formed. Using the DNA sequences of the largest known gene-family present in human genome, i.e., olfactory receptors and simplest possible quadruple context-free L-Systems, we show that conserved protein domains and intergenic regions which lies at the heart of the biological evolution started with a sixteen base-pairs stretch of DNA.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4851/version/1

JSBML: a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez; Marine Dumousseau; Alexander D&amp;#xf6;rr; Clemens Wrzodek; Roland Keller; Sebastian Fr&amp;#xf6;hlich; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java&amp;#x2122; programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6372/version/1

Strong violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Bacteria and plants are able to form population waves as a result of their consumer behaviour and propagation. A soliton-like interpenetration of colliding population waves was assumed but not proved earlier. Here we show how and why colliding population waves of trophically identical but fitness different species can interpenetrate through each other without delay. We have hypothesized and revealed here that the last mechanism provides a stable coexistence of two, three and four species, competing for the same limiting resource in the small homogeneous habitat under constant conditions and without any fitness trade-offs. We have explained the mystery of biodiversity mechanistically because (i) our models are bottom-up mechanistic, (ii) the revealed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6667/version/1

Microarray Analysis of PBMC after Plasmodium falciparum Infection: Molecular Insights into Disease Pathogenesis
Provedor de dados: 17
Autores: Wan-Chung(Wan-Jiung) Hu; Alan Scott; Nathan Wolfe; Sher Singh; Anne Jedlicka; August Louis Bourgeois.
Our laboratory&amp;#x2019;s previous microarray analysis of subjects with  Plasmodium falciparum revealed up-regulation of Toll-like receptor, NF-kB, TNF-&amp;#x3b1;, IFN-&amp;#x3b3;, IL-1&amp;#x3b2;, p38 MAPK, and MHC  molecules. We performed further time-course microarray analysis focusing on malaria pathogenesis by using peripheral leukocytes as a cellular model. We found up-regulation of coagulation-related genes (SERPINB2, thrombomodulin, thrombospondin), heat shock proteins, glycolytic enzymes, glucose transporters, and vacuolar H+-ATPases in acute febrile malaria. In early malaria, prior to detectable parasitemia, CD36 and ICAM1 were up-regulated. During acute malaria, a correlation was observed between IL-1&amp;#xdf; and  heat shock proteins,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5929/version/1

Mapping from Statistical to Biological Proximity
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We verify whether the proximity claimed by state-of-the-art statistical similarity measures are indeed biologically appropriate or not. We present some analytical results on it.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7122/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3913/version/1

Disruptive Strategies for Removing Drug Discovery Bottlenecks
Provedor de dados: 17
Autores: Sean Ekins; Chris L. Waller; Mary  P. Bradley; Antony J. Williams.
Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6961/version/1

A Systematic Approach to Identifying Protein-Ligand Binding Profiles on a Proteome Scale
Provedor de dados: 17
Autores: Li Xie; Nancy  Buchmeier; Lei Xie; Philip Bourne.
Identification of protein-ligand interaction networks on a proteome scale is crucial to address a wide range of biological problems such as correlating molecular functions to physiological processes and designing safe and efficient therapeutics. We have developed a novel computational strategy to identify ligand binding profiles of proteins across gene families and applied it to predicting protein functions, elucidating molecular mechanisms of drug adverse effects, and repositioning safe pharmaceuticals to treat different diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2207/version/1

Nationwide Study of Breast Cancer Risk Factors in Latinas
Provedor de dados: 17
Autores: Michael Dean; Latoya Silverton; Julie Sawitzke.
Breast cancer is the most common cancer among American women. Any woman can be affected by breast cancer, with risk for the disease increasing with age.  Risk for breast cancer is also exacerbated in women who have certain genetic alterations. Mutations in the BRCA1 and BRCA2 genes predispose women to breast and ovarian cancer, and are increasingly recognized in prostate and pancreatic cancers (1-3).  In Caucasian and Asian ethnicities BRCA mutations are associated with basal-type/triple-negative disease. However this association between BRCA gene mutations and basal/triple-negative disease has been understudied in other ethnicities (4-6). The incidence and mortality of breast cancer of Hispanics and Native Americans are lower than other ethnicities;...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5691/version/1

Differential Gene Expression of Human Mast cell Activation Reveals Gene profiles of Innate and Adaptive Immunity.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Reghunathan Renji; Peter Natesan Pushparaj; Alirio Jose Melendez.
High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively used in many areas of biomedical research. Immunoglobulin E (IgE) mediated allergic response (type-1 hypersensitivity) is one of the most powerful reactions of the immune system. Tissue Mast Cells (MCs) and circulating basophils are the major effector cells in these reactions. By dissecting the regulatory circuitry of mast cells by analyzing the genome wide effects of antigen stimulation triggered by Fc&amp;#x3b5;RI, offers a potential for finding novel genes as &amp;#x2018;targets&amp;#x2019; for therapeutic intervention. In this work, we tried to study the gene expression pattern in IgE sensitized and Fc&amp;#x3b5;RI cross linked cord...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1148/version/1

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from _Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and _Schizosaccharomyces pombe_), contain less...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/16/version/1

ExO: An Ontology for Exposure Science
Provedor de dados: 17
Autores: Carolyn J. Mattingly; Thomas  E. McKone; Michael Callahan; Judith  Blake; Elaine A. Cohen Hubal.
An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them.  Ontologies are critically important for specifying data of interest in a consistent manner, thereby enabling data aggregation, analysis and exchange.  An exposure ontology, consistent with those being used in toxicology and other health sciences, is required to formally represent exposure concepts, the relationships between these concepts and most important, the relationships between exposure, susceptibility, and toxicology information.  A successful exposure ontology must facilitate the semantic retrieval of exposure data in the context of environmental health science, medical...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6321/version/1

IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR
Provedor de dados: 17
Autores: G&amp;#xe9;raldine Folch; Joumana Jabado-Michaloud; Fatena Bellahcene; Laetitia Regnier; V&amp;#xe9;ronique Giudicelli; Marie-Paule Lefranc.
The cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the IMGT^&amp;#xae;^ nucleotide database IMGT/LIGM-DB^1^ and 75% of them are from human and mouse. A few cDNA are germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have been studied extensively in IMGT^&amp;#xae;^ (&amp;#x22;http://www.imgt.org&amp;#x22;:http://www.imgt.org) ^2^, which allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts^3^ are the key elements indispensable to perform the annotation of IG...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3159/version/1

2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help in resolving questions that remain unclear due to the incompleteness of the dataset.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6110/version/1

Fast and Scriptable Molecular Graphics in Web Browsers without Java3D
Provedor de dados: 17
Autores: Egon Willighagen; Miguel Howard.
Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/50/version/1

Exposing WikiPathways as Linked Open Data
Provedor de dados: 17
Autores: Andra Waagmeester; Helena Deus; Chris T. Evelo.
Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways  provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6679/version/1

An Ontology-Based Framework for Clinical Research Databases
Provedor de dados: 17
Autores: Richard H. Scheuermann; Megan Kong; Carl Dahlke; David Karp.
The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical research database in the Immunology Database and Analysis Portal (ImmPort) system.  OBX was designed around the logical structure provided by the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI).  By using the logical structure provided by these two well-formulated ontologies, we have found that a relatively simple, extensible data model could be developed to represent the relatively complex domain of clinical research.  In addition, the common framework provided by the BFO should make it straightforward to utilize OBX database data dictionaries based on reference and application ontologies from the OBO...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3482/version/1

Innovation in cardiology. A new diagnostic standard establishing criteria of quantitative &amp;#x26; qualitative evaluation of main parameters of the cardiac &amp;#x26; cardiovascular system according to ECG and Rheo based on cardiac cycle phase analysis
Provedor de dados: 17
Autores: M Rudenko; S Kolmakov; Konstantine Weber; O Voronova; V Zernov; S Rudenko; K Mamberger; D Makedonsky.
Over more than 50 years the theory of functioning of the cardiac &amp;#x26; cardiovascular system remained unchanged. As a rule, all conventional diagnostics methods are based on statistics data on changes in shapes of cardiac signals only, so that it is impossible to determine the relevant cause-effect relations with respect to their formation [1,2]. But a theory of elevated fluidity of liquid offered twenty five years ago makes it possible to develop an innovative method of the phase analysis of the cardiac cycle [3]. The successful application of the said method in researches for the last 5 years has enabled a practical implementation of an indirect measuring concept with respect to volumetric hemodynamic parameters [4]. By evaluating hemodynamic...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3667/version/1

3D model of amphioxus steroid receptor complexed with estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood.  An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates.  To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol.  This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR.  These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR....
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3316/version/1

Para-(benzoyl)-phenylalanine as a potential inhibitor against leptospirosis
Provedor de dados: 17
Autores: Dibyabhaba  Pradhan; Vani Priyadarshini; Manne Munikumar; Amineni  Umamaheswari.
Leptospirosis is a zoonotic disease of global concern caused by Leptospira interrogans. Subtractive genomic approach, metabolic pathway analysis and multi strain genome comparisons of Leptospira interrogans serovars had proposed 88 common drug targets from 5,124 genes of serovar Copenhageni and 4,727 genes of serovar Lai. Three potential drug targets (lpxC, lpxD and lpxB) were identified from Lipid A biosynthesis process of lipopolysaccharide (LPS) biosynthesis pathway. Lipid A is one of the three components of LPS that contains multiple hydrophobic fatty acid chains which anchor the LPS into the bacterial membrane. Designing inhibitory drug molecules targeting Lipid A biosynthesis would dissolve the structural integrity of membrane structure leading to...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5636/version/1

Adding automated data analysis and biological evaluation to affyanalysisQC
Provedor de dados: 17
Autores: Anwesha Dutta.
Almost every cell in the body contains a full set of chromosomes and identical genes. However, only a fraction of these genes are turned on, at any given time and it is this subset of genes that are expressed, which confers unique properties to each cell type.  Gene expression is the term used to describe the transcription of the information contained within the DNA into messenger RNA (mRNA) molecules that are then translated into proteins which perform most of the critical functions of cells. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Gene expression is a highly complex and tightly regulated process that allows a cell to respond dynamically both to environmental stimuli and to its own changing needs. This mechanism acts as both an on/off switch to control which...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5969/version/1

ESG: Extended Similarity Group method for automated protein function prediction
Provedor de dados: 17
Autores: Meghana Chitale; Troy Hawkins; Changsoon Park; Daisuke Kihara.
We present here the Extended Similarity Group (ESG) method, which annotates query sequences with Gene Ontology (GO) terms by assigning probability to each annotation computed based on iterative PSI-BLAST searches. Conventionally sequence homology based function annotation methods, such as BLAST, retrieve function information from top hits with a significant score (E-values). In contrast, the PFP method, which we have presented previously, goes one step ahead in utilizing a PSI-BLAST result by considering very weak hits even an E-value of up to 100 and also by incorporating the functional association between GO terms (FAM matrix) computed using term co-occurrence frequencies in the UniProt database. PFP is very successful which is evidenced by the top rank...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2193/version/1

Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint
Provedor de dados: 17
Autores: Helena Deus.
Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The maturation of Semantic Web technologies offers solutions to those problems by allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We address the systems challenge of The Cancer &amp;#xd;&amp;#xa;Genome Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data generated and processed at 5 academic...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6303/version/1

Logic motif of combinatorial control in transcriptional networks
Provedor de dados: 17
Autores: Xuebing Wu; Zhirong Sun; Rui Jiang.
Combinatorial control is prevalent in transcriptional regulatory networks. However, whether there are specific logic patterns over- or under-represented in real networks remains uninvestigated. Using a theoretic model and _in-silico_ simulations, we systematically study how the relative abundance of distinct regulatory logic patterns influences the network&amp;#x2019;s global dynamics. We find that global dynamic characteristics are sensitive to several specific logic patterns regardless of the detailed network topology. We show it is possible to infer logic motifs based on the sensitivity profile and the biological interpretations of these global characteristics.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2227/version/1

Using Textpresso for Information Retrieval, Fact Extraction
Provedor de dados: 17
Autores: Karen Yook; Kimberly Van Auken; Paul W. Sternberg; The WormBase Consortium.
Ten years ago WormBase^1^ started as a repository for sequence data for the model&amp;#xd;&amp;#xa;organism Caenorhabditis elegans and has since striven to include the curation of all&amp;#xd;&amp;#xa;genetic and molecular data published for this nematode. With a publication rate in the C.&amp;#xd;&amp;#xa;elegans field of approximately 800 papers per year, WormBase (WB) has the opportunity to include information from every paper published. Currently there are ~11,000 full text research papers (mid-1970&amp;#x27;s to the present) downloaded into the WB curation database, from which over 27 data types (i.e. genetic interactions, transgene objects, gene expression patterns, mutant phenotypes etc.) are extracted by curators. Textpresso^2^ is an open source...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3302/version/1

Frequency and accuracy of weight comments by others, and the association with weight misperception among Hong Kong adolescents
Provedor de dados: 17
Autores: Wing-Sze Lo; Sai-Yin Ho; Kwok-Kei Mak; Yuen-Kwan Lai; Tai-Hing Lam.
*Purpose:* To assess the frequency and accuracy of weight comments received from different sources among Chinese adolescents and the relation of weight comments to weight misperception.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methods:* In the Hong Kong Student Obesity Surveillance (HKSOS) project 2006-07, 22612 form 1 to 7 students (41.5% boys) completed a questionnaire on obesity. Students were asked if they had received serious &amp;#x22;too fat&amp;#x22; or &amp;#x22;too thin&amp;#x22; comments over the past 30 days from family members, peers and professionals, and the accuracy of the comments was assessed against the actual weight status. Weight misperception was defined as discordance between the actual and perceived weight status. Logistic regression was...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2742/version/1

From Machine Learning to Learning Machines - A Perspective toward Personalized Medicine
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We describe how to learn a network using a bottom-up approach by building networks from expression profiles. Then we can analyze these networks with different graph mining approaches and by studying topological behaviors. Finally, how we can achieve personalized medicine from the network biology.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7118/version/1

The Entropic Landscape of proteins revealing protein folding mechanism
Provedor de dados: 17
Autores: Kentaro Onizuka.
It has long since been a mystery why most proteins fold within a flash of time into particular structures out of astronomically large numbers of possible conformations. Even more confusing is that protein folding in vivo is played out in rich solution containing various organic and non-organic, big and small molecules and ions which would potentially bind the protein molecules and prevent them folding. A possible answer to these mysteries might be, &amp;#x22;Nature have favoured such proteins that quickly fold in rich solution through natural selection&amp;#x22;. Then what mechanism of folding has been favoured? Here I show how to decipher protein sequences to reveal the folding mechanism. The entropic landscape of a protein sequence tells which region of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2719/version/1

Homology Modeling of Human &amp;#x3b1;~2A~-Adrenoceptor
Provedor de dados: 17
Autores: Jignesh Patel; Gourja G; Vivek Kumar; Yogesh Narkhede; Shikhar Gupta; C. Gopi Mohan.
&amp;#x3b1;~2A~-adrenoceptor (ADA2A) is a membrane bound receptor which has been classified as the member of larger superfamily G-protein coupled receptors (GPCRs); also known as seven transmembrane (7-TM) domains receptor. Around 50% drugs currently available in the market exert their effects through GPCRs. Membrane proteins are difficult to crystallize as compared to soluble proteins. There is a need of 3D-structure of ADA2A to understand   binding modes of various agonists and antagonists and hence homology model of ADA2A was developed. Homology model of ADA2A constructed based on crystal structure of &amp;#x3b2;~2~-adrenoceptor. The crystal structure of &amp;#x3b2;~2~-adrenoceptor (PDB ID: 2RH1) was used as template, which has good sequence identity...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4106/version/1

In silico comparative analysis of conserved genes expressed in solanaceous plants under abiotic stresses
Provedor de dados: 17
Autores: sanchita gupta; sunita singh dhawan; ashok  sharma.
The gene expression data was studied in order to analyze genes involved in different abiotic stresses in solanaceous plants.  Salt, temperature (heat &amp;#x26; cold) and drought are the main abiotic stresses to the plants. Abiotic stress responses are important for sessile organisms like plants because they have to cope with environmental changes to survive. The idea was to analyze those differentially expressed genes, which show common expression in response to different abiotic stress conditions in each plant.  Mitogen activated protein kinases (MAPK) are important mediators in signal transmission, connecting the perception of external stimuli to cellular responses. In plants, MAPKs plays a major role in the signaling of abiotic stresses. The expression...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6717/version/1

STRING and STITCH: known and predicted interactions between proteins and chemicals
Provedor de dados: 17
Autores: Lars J. Jensen; Michael Kuhn; Manuel Stark; Samuel Chaffron; Christian von Mering; Peer Bork.
Information on protein-protein and protein-chemical interactions is essential for understanding cellular functions. The STRING and STITCH web resources integrate interaction evidence derived from pathways, automatic literature mining, primary experimental data, and genomic context. The resulting interaction networks cover 1.5 million proteins from 373 organisms and 68,000 chemicals.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2265/version/1

In Silico Analysis and Identification of Potent Inhibitors for Human Serine/Threonine Protein Kinase PIM-3 Involved in Hepatic Cancer
Provedor de dados: 17
Autores: Prasanna Kumar Guttala; Dibyabhaba  Pradhan; Amineni Umamaheswari.
PIM3 belongs to a family of proto oncogenes that encode serine/threonine protein kinases in human. Pim-3 is involved in cell cycle progression, suppression of apoptosis and proliferation of human hepatoma cell lines. During normal cell cycle progression, Bcl-2 associated death promoter (BAD protein) inactivates Bcl-2 and Bcl-xL there by promoting apoptosis. However, phosphorylation of BAD protein by Pim-3 leaves Bcl-2 free to inhibit Bax-triggered apoptosis. Thus, designing inhibitors against Pim-3 would stop BAD phosphorylation, hence would be highly useful for development of novel means of cancer therapeutics. Computer aided drug designing approach was followed here to explore lead molecules targeting human Pim-3. For this, proteomic nature and phylogeny...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4899/version/1

Transcriptional complex assembly represented in SBGN PD
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Peter Ghazal.
This poster shows how transcriptional complex assembly can be represented in SBGN Process Description language. Example: LPS-induced TNF-alpha enhancer complex formation.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4984/version/1

Developing a Mammalian Behaviour Ontology
Provedor de dados: 17
Autores: Tim Beck; John M. Hancock; Ann-Marie Mallon.
The use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to define the entity under observation.  A domain currently lacking a specialised ontology is mammalian behaviour, and so the Mammalian Behaviour Ontology is being constructed to address this.  Top-level class distinctions are made between behavioural activities and behavioural functions of individuals, and those between two or more individuals.  The ontology is manually developed and encourages contributions from domain experts.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3565/version/1

Developing an application ontology for annotation of experimental variables &amp;#x2013; Experimental Factor Ontology
Provedor de dados: 17
Autores: James Malone; Tomasz Adamusiak; Ele Holloway; Helen Parkinson.
The Experimental Factor Ontology (&amp;#x22;www.ebi.ac.uk/efo&amp;#x22;:http://www.ebi.ac.uk/efo) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3806/version/1

A Three dimesional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well-characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/1

Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search&amp;#x2122;
Provedor de dados: 17
Autores: Elizabeth J. Goldsmith; Saurabh Mendiratta; Radha Akella; Kathleen Dahlgren.
Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition&amp;#x2019;s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2315/version/1

Structural Analysis of Polarizing Indels Argues the Root of the Tree of Life is Near the Chloroflexi
Provedor de dados: 17
Autores: Ruben E. Valas; Philip E. Bourne.
Determining which branches of the tree of life have derived features narrows down the possible location of the root. Currently the polarization of indels done by Lake _et al_.^1-5^ and the polarizing transitions of Cavalier-Smith^6^ arrive at contradictory positions for the root of the tree.  We have analyzed the sequence based indel arguments using protein structure wherever possible. Structure strongly supports some of the polarizations, but in other indels it argues for a different conclusion. We conclude that there is no contradiction between Lake _et al_. and Cavalier-Smith; the root of the tree of life must be near the Chloroflexi.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3290/version/1

Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm
Provedor de dados: 17
Autores: S.S.  Soam; Feroz  Khan; Bharat  Bhasker; B. N.  Mishra.
The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class&amp;#x2013;II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6608/version/1

Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the ageing of constituent networks
Provedor de dados: 17
Autores: Huba J. M. Kiss; &amp;#xc1;goston Mihalik; Tibor N&amp;#xe1;n&amp;#xe1;si; B&amp;#xe1;lint &amp;#x150;ry; Zolt&amp;#xe1;n Spir&amp;#xf3;; Csaba S&amp;#x151;ti; Peter Csermely.
The analysis of network topology and dynamics is increasingly used for the description of the structure, function and evolution of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing the costs and benefits of cooperation as a necessary behaviour to build this network hierarchy, we outline the major hypothesis of the paper: the emergence of hierarchical complexity needs cooperation leading to the ageing of the constituent networks. Local cooperation in a stable environment may lead to over-optimization developing an &amp;#x2018;always-old&amp;#x2019; network, which ages slowly, and dies in an apoptosis-like process. Global cooperation...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2610/version/1

Consortium for Functional Glycomics Overview
Provedor de dados: 17
Autores: James C. Paulson.
This presentation provides an overview of the Consortium for Functional Glycomics.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/11/version/1

Identification and Evolution of Transcription Factors in Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases; in addition to TFs, other transcriptional regulators (TRs) participate in transcriptional modulation. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of TFs and TRs can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6672/version/1

Metacuration Standards and Minimum Information about a Bioinformatics Investigation
Provedor de dados: 17
Autores: Tin Wee Tan; Asif M. Khan; Shen Jean Lim; Yong Li Hu; Mark de Silva; Kuan Siong Lim.
Many bioinformatics databases published in journals are here this year and gone the next. There is generally (i) no requirement, mandatory or otherwise, by reviewers, editors or publishers for full disclosure of how databases are built and how they are maintained; (ii) no standardized requirement for data in public access databases to be kept as backup for release and access when a project ends, when funds expire and website terminates; (iii) the case of proprietary resources, there is no requirement for data to be kept in escrow for release under stated conditions such as when a published database disappears due to company closure. Consequently, much of the biological databases published in the past twenty years are easily lost, even though the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5078/version/1

WikiPathways: Community Curation of Biological Pathways
Provedor de dados: 17
Autores: Alexander Pico.
Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed &amp;#x22;WikiPathways&amp;#x22;:http://www.wikipathways.org/index.php/WikiPathways ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria....
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5359/version/1

Towards Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets
Provedor de dados: 17
Autores: Olivier Bodenreider; Anita Burgun.
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3536/version/1

Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips
Provedor de dados: 17
Autores: Donald  C. Cooper; Bryan Callahan; Phil  Callahan; Lee  Burnett.
Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. These data were then used to create standard curves to allow quantification of COC/BE in biological samples. MIR quantification of COC and BE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6827/version/1

BRIF workshop working group.
Provedor de dados: 17
Autores: Laurence Mabile.
Number of attendees, geographical origin of the group, skills and areas represented, tools developed to help the BRIF progress.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5582/version/1

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/1

Data Mining of the Coffee Rust Genome
Provedor de dados: 17
Autores: David Octavio  Botero-Rozo; William Giraldo; Alvaro Gaitan; Marco Cristancho; Diego M. Ria&amp;#xf1;o-Pachon; Silvia Restrepo.
The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the genomic data.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7034/version/1

Digital BioCuration: A Question of Balance
Provedor de dados: 17
Autores: James Ostell.
Curation of biomedical data has come to encompass a broad range of activities and considerations, which include the building of digital archives, making decisions on the relative value and longevity of one dataset vs another, editing data records manually, performing or assessing computational processes over very large sets of data, and grappling with issues of web usability and data standards. People who consider themselves biological curators may range from a single domain expert, who develops a collection which reflects their personal judgments and priorities, to groups of people supporting large, long term public resources such as GenBank, RefSeq, or PubMed, and everything in between. Finding the right balance between objective measures of quality and...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3257/version/1

Large sets of edit-metric sequence identification tags to facilitate large-scale multiplexing of reads from massively parallel sequencing
Provedor de dados: 17
Autores: Brant C. Faircloth; Travis C. Glenn.
*Background*&amp;#xd;&amp;#xa;Massively parallel DNA sequencing technologies provide exponential increases in the amount of data returned from the sequencing process, relative to traditional (Sanger-based) techniques.  Use of unique, synthetic oligonucleotides (identifying sequence tags) on each sample enables the deconvolution of samples pooled prior to massively parallel sequencing.  To counteract oligonucleotide synthesis and sequencing errors, sequence tags should be drawn from combinations with sufficient differences and with an appropriate error-correcting code over the alphabet [A,C,G,T].  This method ensures that errors within the tags do not cause sequences to be assigned to the wrong sample while also enabling correction and recovery of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5672/version/1

An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Hiroko Kou; Jun Zhou; Kouji Kozaki; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on &amp;#x22;anatomical structure of organs&amp;#x22; and &amp;#x22;abnormal states in the human body&amp;#x22;. On the basis of the investigation, we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of relations.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3498/version/1

On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis
Provedor de dados: 17
Autores: Graham Jones.
This article discusses possible reasons why posterior clade probabilities obtained from Bayesian phylogenetic analyses might be inaccurate. It attempts to list all possible sources of uncertainty and error in Bayesian phylogenetic analysis. The choice of priors on trees has been suggested by several authors as a cause of inaccurate posterior clade probabilities. I argue strongly for using priors based on biological knowledge. Two possible sources of bias which do not seem to have been published before are also discussed. One is a computational problem and the other related to majority rule consensus trees.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1494/version/1

Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin J. Lercher; Laurence D. Hurst.
For some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate.  But how is noise in gene expression modulated?  We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism.   Stochastic simulation models confirm the expectation.  The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4792/version/1

Statistical analysis of network data and evolution on GPUs: High-performance statistical computing
Provedor de dados: 17
Autores: Thomas W. Thorne; Michael P. H. Stumpf.
Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man&amp;#x27;s parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6874/version/1

bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Provedor de dados: 17
Autores: Roderic Page.
Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using  HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. bioGUID is available at &amp;#x22;http://bioguid.info/&amp;#x22;:http://bioguid.info/. Source code is...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3079/version/1

Comparison of computationally- and manually-assigned Gene Ontology annotations to improve functional characterization of gene products.
Provedor de dados: 17
Autores: Maria Costanzo; Rama Balakrishnan; Karen Christie; Eurie Hog; Julie Park; J. Michael Cherry.
The Gene Ontology (GO) describes molecular functions, biological processes, and cellular components of gene products using controlled-vocabulary terms that are related to each other in a structure that facilitates computing on GO annotations within and across species. Experimentally-based GO annotations that are manually curated from the literature are often used to predict the functions of related uncharacterized proteins. The accuracy of such annotations is thus critically important, particularly for a well-studied model organism such as _Saccharomyces cerevisiae_ which is frequently used as the source of the experimental data. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Comparison of experimentally-based annotations with those predicted by computational methods...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5095/version/1

Measuring impact in online resources with the CI&amp;#xad;number (the CitedIn Number for online impact)
Provedor de dados: 17
Autores: Andra Waagmeester; Chris Evelo.
CitedIn is a webservice that can be found at www.citedin.org. It tracks online citations in databases, blogs, wikis, and community sites to the literature covered in Pubmed. For biomedical scientific literature Pubmed is by far the most interesting resource. Pubmed is the interface to the Medline repository which covers over 1 century of publications and contains almost all relevant publications in the field. Pubmed uses very simple unique numeric identifiers. This makes it easy to cite publications using these Pubmed Identifiers (PMIDs) or to link to Pubmed itself based on those. This ease of use results in PMIDs often being used for online citations, this is often the standard in biomedical databases and for instance in Wikipedia. CitedIn uses a federate...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6037/version/1

Open Biomedical Ontologies Applied to Prostate Cancer
Provedor de dados: 17
Autores: James A. Overton; Cesare Romagnoli; Rethy Chhem.
In this presentation we survey preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the Open Biomedical Ontologies (OBO) library have been used to annotate clinical reports about prostate cancer. First we discuss why we rejected several controlled vocabularies, including SNOMED, DICOM, and RadLex, preferring instead to use the OBO library. We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked to the ontology terms. This method allows us to discover which relevant terms exist in the OBO library, and which do not. The final section of this paper discusses these...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3589/version/1

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/2

BioModels Database: curation and annotation
Provedor de dados: 17
Autores: Michael Schubert; Ishan Ajmera; Vijayalakshmi Chelliah; Lukas Endler; Nicolas Rodriguez; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In this poster we provide an overview of its capabilities, as well as the curation and annotation process with two use cases concerning blood coagulation and glucose homeostasis.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6361/version/1

Managing Bio-Models: &amp;#xb;Model Storage, Retrieval, Ranking and Versioning
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Olaf Wolkenhauer.
In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently  addressed in existing systems.&amp;#xd;&amp;#xa;To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6325/version/1

Uberon: towards a comprehensive multi-species anatomy ontology
Provedor de dados: 17
Autores: Melissa A. Haendel; Georgios G. Gkoutos; Suzanna E. Lewis; Chris Mungall.
The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies.
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3592/version/1

Word Activation Forces Map Word Networks
Provedor de dados: 17
Autores: Jun Guo; Hanliang Guo; Zhanyi Wang.
Words associate with each other in a manner of intricate clusters^1-3^. Yet the brain capably encodes the complex relations into workable networks^4-7^ such that the onset of a word in the brain automatically and selectively activates its associates, facilitating language understanding and generation^8-10^. One believes that the activation strength from one word to another forges and accounts for the latent structures of the word networks. This implies that mapping the word networks from brains to computers^11,12^, which is necessary for various purposes^1,2,13-15^, may be achieved through modeling the activation strengths. However, although a lot of investigations on word activation effects have been carried out^8-10,16-20^, modeling the activation...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5764/version/1

Models of Multifunctional Central Pattern Generators: Polyrhythmic Bursting
Provedor de dados: 17
Autores: Andrey Shilnikov.
We demonstrate a motif of three reciprocally inhibitory cells that is able to produce multiple patterns of bursting rhythms. Through the examination of the qualitative geometric structure of two-dimensional maps for phase lag between the cells we reveal the organizing centers of emergent polyrhythmic patterns and their bifurcations, as the asymmetry of the synaptic coupling is varied. The presence of multistability and the types of attractors in the network are shown to be determined by the duty cycle of bursting. This analysis does not require knowledge of the equations that model the system, and so provides a powerful new approach to studying regulatory networks. Thus, the approach is applicable to a variety of biological phenomena beyond motor control.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5800/version/1

Revolutionizing scientific communication and collaboration
Provedor de dados: 17
Autores: Konrad U. Foerstner.
This presentation introduces new web-based ways of scientific communication and collaboration. It focuses on wikis and the _First Online EMBL PhD Symposium_ as an example of an online conference.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/153/version/1

Towards more Challenging Problems for Ontology Matching Tools
Provedor de dados: 17
Autores: Ernesto Jimenez-Ruiz; Bernardo Cuenca Grau.
We motivate the need for challenging problems in the evaluation of ontology matching tools. To address this need, we propose mapping sets between well-known biomedical ontologies that are based on the UMLS Metathesaurus. These mappings could be used as a basis for a new track in future OAEI campaigns (http://oaei.ontologymatching.org/).&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6612/version/1

Biased amino acid composition in warm-blooded animals
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin  J. Lercher.
Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2974/version/1

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators
Provedor de dados: 17
Autores: Shen Lin; Stefan Haas; Tomasz Zemojtel; Peng Xiao; Martin Vingron; Renhui Li.
Background:&amp;#xd;&amp;#xa;Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported; however, the studies focusing on the diversity of transposable systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity.&amp;#xd;&amp;#xa;Results:&amp;#xd;&amp;#xa;In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4923/version/1

Dynamics of proteins and DNA in a Paul trap
Provedor de dados: 17
Autores: Kushal Shah.
Paul traps are increasingly being used in a wide variety of applications in biology including study of protein dynamics and DNA sequencing. In this paper, statistical properties of a macromolecule chain in a Paul trap are theoretically analyzed using a simple model of charged particles connected by rigid rods. It is found that the mean displacement of chain varies linearly with the chain length, showing properties of enhanced diffusion, compared to the normal diffusion relation which exists for the case of a macromolecule chain in a force-free region. The dependence of the mean displacement on the chain length and trap parameters is also found to be very different for the case of pure dc operation and pure ac operation of the Paul trap.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6297/version/1

Bioinformatics analysis of homologies between pathogen antigens, autoantigens and the CFTR cystic fibrosis protein: A role for immunoadsorption therapy?
Provedor de dados: 17
Autores: Christopher Carter.
The cystic fibrosis CFTR chloride channel is involved in pathogen entry into epithelial cells, and provides the glutathione and hypochlorous acid necessary for bactericidal and viricidal actions. CFTR mutations block these effects, diminishing pathogen defence and allowing pathogen accumulation in the extracellular space, where antibody encounter is likely. The pathogen antigens observed in cystic fibrosis (including P. Aeruginosa, S.Aureus and S.Maltophilia proteins) are homologous to the autoantigens reported in cystic fibrosis and all are homologous to the CFTR protein itself. Antibodies to pathogens and autoantigens may also target the CFTR protein, acting as antagonists, further compromising its function. The tripartite relationship between pathogen...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5352/version/1

Towards automatic classification within the ChEBI ontology
Provedor de dados: 17
Autores: Janna Hastings; Paula de Matos; Marcus Ennis; Christoph Steinbeck.
*Background*&amp;#xd;&amp;#xa;Appearing in a wide variety of contexts, biochemical &amp;#x27;small molecules&amp;#x27; are a core element of biomedical data. Chemical ontologies, which provide stable identifiers and a shared vocabulary for use in referring to such biochemical small molecules, are crucial to enable the interoperation of such data. One such chemical ontology is ChEBI (Chemical Entities of Biological Interest), a candidate member ontology of the OBO Foundry. ChEBI is a publicly available, manually annotated database of chemical entities and contains around 18000 annotated entities as of the last release (May 2009). ChEBI provides stable unique identifiers for chemical entities; a controlled vocabulary in the form of recommended names (which...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3525/version/1

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Provedor de dados: 17
Autores: Debra M. Krupke; Dale A. Begley; Steven B. Neuhauser; Joel E. Richardson; John P. Sundberg; Carol J. Bult; Janan T. Eppig.
Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, &amp;#x22;http://tumor.informatics.jax.org&amp;#x22;:http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Although primary source for the data represented in MTB is peer-reviewed scientific literature an...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3245/version/1

LibSBGN Status Update
Provedor de dados: 17
Autores: Martijn van Iersel; Tobias Czauderna; Alice C. Villeger.
LibSBGN is a library for reading, writing and validating maps that use the Systems Biology Graphical Notation (SBGN). The goals of LibSBGN are to 1) increase interoperability between pathway visualization tools, 2) increase the amount of code re-used, and 3) make it easier for tool developers to adopt the SBGN standard. This presentation is a status update of the project, presented at the COMBINE 2011 meeting.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6373/version/1

Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
Provedor de dados: 17
Autores: Dagmar Waltemath; Frank T. Bergmann; Richard Adams; Nicolas Le Novere.
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the experimental task to run, and which result to produce.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5846/version/1

Amino acid features: a missing compartment of prediction of protein function
Provedor de dados: 17
Autores: Esmaeil Ebrahimie; Mansour  Ebrahimi; Mahdi  Ebrahimi.
Enormous computational efforts have been carried out to predict structure and function of protein. However, nearly all of these efforts have been focused on prediction of function based on primary nucleic acid sequence or modeling 3D structure of protein from its nucleic acid sequence. In fact, it seems that amino acid attributes, which is an intermediate phase between DNA/RNA and advanced protein structure, has been missed.&amp;#xd;&amp;#xa;From 2010, we examined the possibility of precise prediction of structural protein function based on amino acid features by improving the following three aspects of amino acid research: (1) Increasing the number of computationally calculated amino acid features, (2) Testing different feature selection (attribute...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6693/version/1

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets
Provedor de dados: 17
Autores: Peter Midford; Paula Mabee; Todd Vision; Hilmar Lapp; Jim Balhoff; Wasila Dahdul; Cartik Kothari; John Lundberg; Monte Westerfield.
The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000 species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting via a web-based interface at &amp;#x22;http://kb.phenoscape.org&amp;#x22;:http://kb.phenoscape.org.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3594/version/1

Exchanging Experimental Kinetic Data via SabioML
Provedor de dados: 17
Autores: Martin Golebiewski.
The simulation of quantitative biochemical models not only requires qualitative information about the stoichiometry of the described networks, but also kinetic data describing their dynamics. Such kinetic data have to be experimentally measured, collected, systematically structured and stored to finally make them accessible. However, the dataflow from the experiment to the model is still a bottleneck, calling for systems that capture the data directly from the instrument, process and normalize it to agreed standards and finally transfer the data to publicly available databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SABIO-RK (http://sabio.h-its.org) is a curated database system which we have developed for bundling data referring to biochemical reactions and...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5030/version/1

Update On The Zebrafish Genome Project
Provedor de dados: 17
Autores: J P Almeida-King; S Donaldson; G K Laird; D M Lloyd; H K Sehra; J E Collins; K Howe; B Reimholz; J Torrance; S Trevanion; D Stemple; I Barroso; J G R Gilbert; E Griffiths; J E Loveland; R Storey; J L Harrow; T Hubbard.
The zebrafish genome, which consists of 25 linkage groups and is ~1.4Gb in size, is being sequenced, finished and analysed in its entirety at the Wellcome Trust Sanger Institute. The manual annotation is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group and is released at regular intervals onto the Vertebrate Genome Annotation (Vega) database (&amp;#x22;http://vega.sanger.ac.uk&amp;#x22;:http://vega.sanger.ac.uk) and may be viewed as a DAS source in Ensembl (&amp;#x22;http://www.ensembl.org/Danio_rerio&amp;#x22;:http://www.ensembl.org/Danio_rerio). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our annotation is compiled in close collaboration with the Zebrafish Information Network (ZFIN)...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3105/version/1

Evidence for gliadin antibodies as causative agents in schizophrenia.
Provedor de dados: 17
Autores: Chris J. Carter.
Antibodies to gliadin, a component of gluten, have frequently been reported in schizophrenia. Highly immunogenic B cell epitopes along its length are homologous to numerous proteins relevant to schizophrenia, including members of the DISC1 interactome, glutamate, dopamine and neuregulin signaling networks, and plasticity or myelination pathways. Antibodies to gliadin may cross react with these key proteins, as has already been observed with synapsin 1 and calreticulin. Gliadin may thus be a causative agent in schizophrenia, under certain genetic and immunological conditions, producing its effects via antibody mediated knockdown of multiple proteins relevant to the disease process. Because of such homology, an autoimmune response may be sustained by the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5351/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/3

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Provedor de dados: 17
Autores: Michael F. Lin; Irwin Jungreis; Manolis Kellis.
As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF&amp;#x27;s classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4784/version/1

Literature Triage and Indexing in the Mouse Genome Informatics (MGI) Group
Provedor de dados: 17
Autores: Randal P. Babiuk; Dale A. Begley; Susan M. Bello; Dirck W. Bradt; Donna L. Burkart; Howard Dene; Alexander D. Diehl; Harold J. Drabkin; Jacqueline H. Finger; Terry F. Hayamizu; David P. Hill; Michelle Knowlton; Debra M. Krupke; Ira Lu; Lois J. Maltais; Monica McAndrews-Hill; Terrence F. Meehan; Li Ni; Hiroaki Onda; Dmitry Sitnikov; Constance M. Smith; Cynthia L. Smith; Monika Tomczuk.
The Mouse Genome Informatics (MGI; &amp;#x22;http://www.informatics.jax.org&amp;#x22;:http://www.informatics.jax.org) group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature identification and collection is performed cooperatively amongst the groups.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In recent years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals. This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the group used to be...
Tipo: Poster
Palavras-chave: Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3246/version/1

Toward a Complete Phyloreferencing Language
Provedor de dados: 17
Autores: T. Michael Keesey.
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few &amp;#x201c;standard&amp;#x201d; forms (node&amp;#x2011;, branch&amp;#x2011;, and perhaps apomorphy&amp;#x2011;based clades) without the capacity to represent more &amp;#x201c;exotic&amp;#x201d; forms (e.g., ancestor&amp;#x2011;based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4652/version/1

Natural Environment Research Council - Data Policy
Provedor de dados: 17
Autores: Mark Thorley.
The Natural Environment Research Council (NERC) has a policy on data in order to:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(a) Ensure the continuing availability of environmental data of long-term value for research, teaching, and for wider exploitation for the public good, by individuals, government, business and other organisations;&amp;#xd;&amp;#xa;(b) Support the integrity, transparency and openness of the research it supports;&amp;#xd;&amp;#xa;(c) Help in the formal publication of data sets, as well as enabling the tracking of their usage through citation and data licences;&amp;#xd;&amp;#xa;(d) Meet relevant legislation and Government guidance on the management and distribution of environmental information.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6017/version/1

High Resolution Imaging of the Fusiform Face Area (FFA) Using Nonlinear Classifiers Shows Diagnosticity for Nonface Categories
Provedor de dados: 17
Autores: Stephen Hanson; Arielle Schmidt.
How are objects represented in the human visual pathway? This question continues to elude the neuroimaging field due to at least two kinds of problems: first, the relatively low spatial resolution of fMRI and second, the bias inherent in prevailing statistical methods for analyzing the actual diagnosticity of cortical tissue. We collected high-resolution (1mm x 1mm) imaging data of the fusiform face area (FFA) from 4 subjects while they categorized images as &amp;#x27;animal&amp;#x27;, &amp;#x27;car&amp;#x27;, &amp;#x27;face&amp;#x27;, or &amp;#x27;sculpture.&amp;#x27; We performed exploratory analysis to determine the nature of the distributions over classes and the similarity structure between classes. The FFA was visualized using nonmetric...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2235/version/1

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6115/version/1

Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/1

Maize gene review - A new on-line journal promotes community curation of phenotypes
Provedor de dados: 17
Autores: Mary L. Schaeffer.
The first formal phenotype summaries for maize can be found in early editions of the&amp;#xd;&amp;#xa;Maize Genetics Cooperation Newsletter (MNL). Prior to on-line databases, the MNL&amp;#xd;&amp;#xa;served to systematize available mutant stocks, genetic maps, and addresses for maize&amp;#xd;&amp;#xa;geneticists. In fact, the first phenotypic data entered into MaizeGDB, in 1991, was from&amp;#xd;&amp;#xa;the MNL stock center report. To support renewed, community submission of similar&amp;#xd;&amp;#xa;data, the MNL has initiated a new on-line journal, called the &amp;#x2018;maize gene review&amp;#x2019; (MGR,&amp;#xd;&amp;#xa;www.maizegenereview.org). It represents an extension of the Mutants of Maize (1997),&amp;#xd;&amp;#xa;eds MG Neuffer, EH Coe, SR...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3221/version/1

Global Network Alignment
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Natasa Przulj.
Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4505/version/1

1st INCF Workshop on Sustainability of Neuroscience Databases
Provedor de dados: 17
Autores: Jack Van Horn; Jaap van Pelt.
The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1983/version/1

Empirical predictions of an intrinsically disordered protein theory approach to glycan/lectin reaction kinetics
Provedor de dados: 17
Autores: Rodrick Wallace.
Newly-developed methods from the theory of intrinsically disordered proteins can be applied to the flexible glycan structures that coat cellular surfaces and provide rich channels for biological information transmission. Extension of a mechanistic &amp;#x27;arm-in-sleeve&amp;#x27; model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated &amp;#x27;spectral&amp;#x27; classifications in glycan/lectin interaction, parameterized by an appropriate index of glycan frond length or other index of topological complexity, possibly requiring groupoid classifications analogous to quasicrystals.
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6752/version/1

Identifying Data Sharing in Biomedical Literature
Provedor de dados: 17
Autores: Heather Piwowar; Wendy W. Chapman.
Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1721/version/1

OpenCOR
Provedor de dados: 17
Autores: Alan Garny.
A description of the OpenCOR project. What has been done so far, the choices that were made, etc., as well as the direction in which we are heading.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5898/version/1

SBGN PD: Current status, future changes and unresolved issues.
Provedor de dados: 17
Autores: Stuart L. Moodie.
The presentations reports and the current status of the SBGN-PD specification and highlights issues for further discussion.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6831/version/1

Using Ontology Fingerprints to evaluate genome-wide association study results
Provedor de dados: 17
Autores: Lam C. Tsoi; Michael Boehnke; Richard L. Klein; W. Jim Zheng.
We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block.  We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3615/version/1

Consensus virtual screening approaches to predict protein ligands
Provedor de dados: 17
Autores: Andreas Kukol.
In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database. Towards that goal consensus methods combining the results of several docking algorithms were developed and compared against the individual algorithms. Furthermore, a recently proposed rescoring method based on drug efficiency indices was evaluated. Among AutoDock Vina 1.0, AutoDock 4.2 and GemDock, AutoDock Vina was the best performing single method in predicting high affinity ligands from a database of known ligands and decoys. The rescoring of predicted binding energies with the water/butanol partition coeffcient...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5979/version/1

Designing Potent Inhibitors Of Human p38&amp;#x3b3; For Effective Breast Cancer Therapy
Provedor de dados: 17
Autores: Natarajan  Pradeep; Dibyabhaba  Pradhan; Amineni Umamaheswari.
Oncogenic constitutive enzyme human p38&amp;#x3b3; is a serine/threonine protein kinase, activated through phosphorylation by environmental stress and pro-inflammatory cytokines responses. Breast cancer, hepatoma, colon cancer, atherosclerotic lesion (coronary artery lesion / hardening of artery), hypertension and inflammations are some of the diseases caused by human p38&amp;#x3b3; due to over expression. Over expression of the protein in turn induces anti-apoptosis and inflammatory responses, increased malignant transformation and cell differentiation. Thus, designing potent inhibitors against p38&amp;#x3b3; would be highly practicable for development of novel means of breast cancer therapeutics.  Extensive preclinical data and proteomic analysis support...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4904/version/1

Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes
Provedor de dados: 17
Autores: Jung Kyoon Choi; Sohyun Hwang; Young-Joon Kim.
Phenotypic diversity and fidelity can be balanced by controlling stochastic molecular mechanisms. Epigenetic silencing is one that has a critical role in stress response. Here we show that in yeast, incomplete silencing increases stochastic noise in gene expression, probably owing to unstable chromatin structure. Telomere position effect is suggested as one mechanism. Expression diversity in a population achieved in this way may render a subset of cells to readily respond to various acute stresses. By contrast, strong silencing tends to suppress noisy expression of genes, in particular those involved in life cycle control. In this regime, chromatin may act as a noise filter for precisely regulated responses to environmental signals that induce huge...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1612/version/1

Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies
Provedor de dados: 17
Autores: Ward Blond&amp;#xe9;; Erick Antezana; Bernard De Baets; Vladimir Mironov; Martin Kuiper.
While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3562/version/1

Argudas: arguing with gene expression information
Provedor de dados: 17
Autores: Kenneth McLeod.
In situ hybridization gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This presentation examines a system, Argudas, designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of both explaining and justifying the behavior of Argudas. Throughout the discussion of Argudas a number of issues will be raised including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online biological databases.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5394/version/1

HEAT: a New Tool for Gene Set Enrichment Analysis Using Comprehensive Annotation of Human Genes in H-InvDB
Provedor de dados: 17
Autores: Tadashi Imanishi; Akiko O. Noda; Miho Sera.
H-InvDB Enrichment Analysis Tool (HEAT) is a new data-mining tool for gene set enrichment analysis based on comprehensive annotations of human genes in H-InvDB.  HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts.  The advantage of HEAT is the wide variety of annotation items used for its analysis: chromosomal bands, InterPro functional domains, Gene Ontology terms, KEGG pathways, H-InvDB gene families/groups, SCOP structural domains, subcellular localization predicted by using the Wolf-PSORT program, tissue-specific gene expression as defined in the H-ANGEL database, and transcription factor binding sites in promoter regions based on JASPAR.  HEAT...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5185/version/1

Just-in-time assembly of cell-cycle protein complexes
Provedor de dados: 17
Autores: Lars J. Jensen; Ulrik de Lichtenberg; Thomas S. Jensen; S&amp;#xf8;ren Brunak; Peer Bork.
Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs significantly between organisms and is often mirrored by changes in cell-cycle-dependent phosphorylation of the protein products. This indicates that many different solutions have evolved for just-in-time assembly of the same molecular machines.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2273/version/1

Proliferating Cell Nuclear Antigen (PCNA) allows the automatic identification of follicles in microscopic images of human ovarian tissue
Provedor de dados: 17
Autores: Tom Kelsey; Benedicta Caserta; Luis Castillo; Hamish Wallace; Francisco C&amp;#xf3;ppola Gonz&amp;#xe1;lvez.
Background: Human ovarian reserve is defined by the population of non-growing follicles (NGFs) in the ovary. Direct estimation of ovarian reserve involves the identification of NGFs in prepared ovarian tissue. Previous studies involving human tissue have used hematoxylin and eosin (HE) stain, with NGF populations estimated by human examination either of tissue under a microscopic, or of images taken of this tissue.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Methods: In this study we replace HE with Proliferating Cell Nuclear Antigen (PCNA), and automate the identification and enumeration of NGFs that appear in the resulting microscopic images. We compared the automated estimates to those obtained by human experts, with the gold standard taken to be the average of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4418/version/1

Applications Of Microspectroscopy, Hyperspectral Chemical Imaging And Fluorescence Microscopy In Chemistry, Biochemistry, Biotechnology, Molecular And Cell Biology
Provedor de dados: 17
Autores: I. C. Baianu.
Chemical imaging is a technique for the simultaneous measurement of spectra (chemical information) and images or pictures (spatial information)^1,2^. The technique is most often applied to either solid or gel samples, and has applications in chemistry, biology^3-8^, medicine^9,10^, pharmacy^11^ (see also for example: Chemical Imaging Without Dyeing), food science, Food Physical Chemistry, Biotechnology^12,13^, Agriculture and industry. NIR, IR and Raman chemical imaging is also referred to as hyperspectral, spectroscopic, spectral or multi-spectral imaging (also see micro-spectroscopy). However, other ultra-sensitive and selective, chemical imaging techniques are also in use that involve either UV-visible or fluorescence microspectroscopy.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6593/version/1

Suggested actions from the Melbourne HVP Information Seminar
Provedor de dados: 17
Autores: Richard Cotton; Myles Axton; Agnes Bankier; Bernard Brais; Lawrence Cavedon; Desir&amp;#xe9;e du Sart; Peter George; David Goldgar; Terence Harrison; Marienne Hibbert; John Hopper; Finlay Macrae; Christine M. O&amp;#x2019;Keefe; David Ravine; Ravi Savarirayan; Les Sheffield; Tim Smith; Nicola Stokes; Vijaya Sundararajan; David Thorburn; Ingrid Winship.
The Human Variome Project (HVP; www.humanvariomeproject.org) was initiated at a meeting in June 2006 and addressed the problems of collecting genetic information and generated 96 recommendations (http://www.nature.com/ng/journal/v39/n4/full/ng0407-423.html) to overcome these, with the focus on Mendelian disease. A considerable number of projects have been added, to those that have been ongoing for a number of years, since that meeting. Also, a planning meeting is to be held May 25-29, 2008 in Spain (http://www.humanvariomeproject.org/HVP2008/).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A dramatic boost has been given to the HVP by the preparedness and action of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org), to,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1784/version/2

Universality of a mesenchymal transition signature in invasive solid cancers
Provedor de dados: 17
Autores: Dimitris Anastassiou.
In this brief communication, additional computational validation is provided consistent with the unifying hypothesis that a shared biological mechanism of mesenchymal transition, reflected by a precise gene expression signature, may be present in all types of solid cancers when they reach a particular stage of invasiveness.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6862/version/1

The CALBC RDF Triple store: retrieval over large literature content
Provedor de dados: 17
Autores: Samuel Croset.
Integration of the scientific literature into a biomedical research infrastructure requires the processing of the literature, identification of the contained named entities (NEs) and concepts, and to represent the content in a standardised way.&amp;#xd;&amp;#xa;The CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions (Silver Standard Corpus, SSC). The four semantic groups were chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). The content of the SSC has been fully integrated into RDF Triple Store (4,568,678 triples) and has been aligned with content...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5383/version/1

Integration of the scientific literature into the Semantic Web: Facts from biomedical data resources
Provedor de dados: 17
Autores: Dietrich Rebholz; Samuel Croset; Christoph Grabmueller.
Scientific literature is the primary resource for relevant and innovative information. The integration of the literature with other data resources in the biomedical research community generates overhead that can be avoided through the used of Semantic Web Technology generating openly accessible data. Projects such as SESL and CALBC have producted significant amount of data that that are ready for exploitation.&amp;#xd;&amp;#xa;The tutorial will teach different approaches on how to integrate the scientific literature with the content from biomedical databases, and will discuss the inferences that can be achieved. Furthermore, the tutorial will point to the resources that are ready for use and enable integration of the literature at your discretion. A good...
Tipo: Presentation
Palavras-chave: Biotechnology; Immunology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7011/version/1

Biological resource catalog: NIF and NeuroLex
Provedor de dados: 17
Autores: Anita E. Bandrowski.
In the digital age one can find data and teaching materials on the web, however data and materials of a high quality are not always ranked very high on commercial search engines that look at the number of other sites that link to a page rather than the quality of the information. Additionally, many such materials are maintained within databases that are inaccessible to search technology. To solve these problems, the Neuroscience Information Framework (NIF: http://www.neuinfo.org) was created to aid the neuroscience community to discover useful digital resources, such as academic databases, and it has also developed a large digital catalog of resources that are related to neuroscience.&amp;#xd;&amp;#xa;NIF has developed a &amp;#x201c;resource...
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6238/version/1

Accurate telemonitoring of Parkinson&amp;#x2019;s disease progression by non-invasive speech tests
Provedor de dados: 17
Autores: Athanasios Tsanas; Max A. Little; Patrick E. McSharry; Lorraine O. Ramig.
Tracking Parkinson&amp;#x27;s disease (PD) symptom progression often uses the Unified Parkinson&amp;#x2019;s Disease Rating Scale (UPDRS), which requires the patient&amp;#x27;s presence in clinic, and time-consuming physical examinations by trained medical staff. Thus, symptom monitoring is costly and logistically inconvenient for patient and clinical staff alike, also hindering recruitment for future large-scale clinical trials. Here, for the first time, we demonstrate rapid, remote replication of UPDRS assessment with clinically useful accuracy (about 7.5 UPDRS points difference from the clinicians&amp;#x2019; estimates), using only simple, self-administered, and non-invasive speech tests. We characterize speech with signal processing algorithms,...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3920/version/1

Bio::Phylo - Phyloinformatic Analysis Using Perl
Provedor de dados: 17
Autores: Rutger Vos.
Recent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps often need to be redone by the researcher multiple times anyway  and are too error-prone, tedious and time-consuming to do by hand. Hence, phyloinformatic analyses benefit from increased automation. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from a variety of...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4601/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3543/version/2

Conceptual model of E. coli transcriptional machinery
Provedor de dados: 17
Autores: Anatoly Sorokin; Timur Dzhelyadin; Svetlana G. Kamzolova.
At the moment one type of analysis of transcription regulatory networks (TRNs) in prokaryotes is topological analysis of graph structure of possible regulatory interaction links (see for example [1]). That type of analysis takes into account possibility links that designate the fact that one gene product in some conditions can modulate transcription of the other. The benefit of such approach is that it is allow analyzing TRN at the whole cell level. At the same type it is known that at least some responses are regulated by abundance of elements of transcription machinery [2-3]. We have developed conceptual model of whole cell E. coli TRN with SBGN ER, SBGN PD and SBGN AF languages [4]. That model is the first step towards incorporation of some quantitative...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6341/version/1

A Simple Nested Simulation for SED-ML
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a simple nested Simulation Experiment for SED-ML [1] that is easy to implement and will help to broaden what SED-ML is able to encode.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4257/version/1

Modularity maps reveal community structure in the resting human brain
Provedor de dados: 17
Autores: Paul Laurienti; Christina Hugenschmidt; Satoru Hayasaka.
The brain is a complex network of interconnecting neurons that combines regional specificity with distributed processing. Recent advances in the field of network theory have facilitated ground-breaking analyses demonstrating that brain connectivity exhibits small-world properties similar to other self-organized networks such as the internet, the genome, or even social organizations. Brain connectivity supports local and global processing through high clustering and short connectivity paths, respectively. While these comprehensive network indices highlight the global organization of the network, the regional specificity is related to the interconnectivity of local neighborhoods within the global system. The work presented here evaluated the community...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3069/version/1

Ontology-based Trial Management System (ObTiMA)
Provedor de dados: 17
Autores: Mathias Brochhausen; Gabriele Weiler; Fatima Schera; Jochen Rauch; Norbert Graf; Stephan Kiefer.
The ACGT project which aims to foster the sharing of research result from both, clinical and molecular research for the benefit of cancer patients uses ontology-driven semantic services. One novelty ACGT provides is a tool named ObTiMA which allows to build questionnaires directly from the ACGT Master Ontology. This will facilitate the process of creating Case Report Forms. Furthermore, the clinical data collected is already annotated in the terms of the ontology.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3753/version/1

Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research
Provedor de dados: 17
Autores: Matthias Samwald.
Key assertions are extracted from &amp;#x201c;conclusions&amp;#x201d; sections of PubMed abstracts and&amp;#xd;&amp;#xa;converted into Semantic Web / Linked Data format. The results are made accessible via&amp;#xd;&amp;#xa;files, a SPARQL endpoint, and a faceted search interface. Conclusion sections are&amp;#xd;&amp;#xa;identified as valuable resources for machine-augmented key assertion identification and&amp;#xd;&amp;#xa;integration in the biomedical domain. Results are discussed and opportunities for future&amp;#xd;&amp;#xa;work and cooperation are highlighted.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3775/version/1

The Future of the Journal? Integrating research data with scientific discourse
Provedor de dados: 17
Autores: Anita de Waard.
To advance the pace of scientific discovery we propose a conceptual format that forms the basis of a truly new way of publishing science. In our proposal, all scientific communication objects (including experimental workflows, direct results, email conversations, and all drafted and published information artifacts) are labeled and stored in a great, big, distributed data store (or many distributed data stores that are all connected). Each item has a set of metadata attached to it, which includes (at least) the person and time it was created, the type of object it is, and the status of the object including intellectual property rights and ownership. Every researcher can (and must) deposit every knowledge item that is produced in the lab into this...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4742/version/1

Immunogenetic sequence annotation based on IMGT-ONTOLOGY
Provedor de dados: 17
Autores: Joumana  Jabado-Michaloud; G&amp;#xe9;raldine Folch; Fatena Bellahcene; Fran&amp;#xe7;ois Ehrenmann; Patrice Duroux; V&amp;#xe9;ronique Giudicelli; Marie-Paule Lefranc.
IMGT/LIGM-DB^1^ is the first and the largest IMGT^&amp;#xae;^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3165/version/1

16S rRNA based identification of _Aeromonas sp. kumar_ by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar
Provedor de dados: 17
Autores: P. Kumar; C. M. Ramakritinan; A. K. Kumaraguru.
A bacterial strain, designated _Aeromonas sp. kumar_, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3898/version/1

Report on trial of SatScan tray scanner system by SmartDrive Ltd.
Provedor de dados: 17
Autores: Vladimir  Blagoderov; Ian Kitching; Thomas Simonsen; Vincent Smith.
Smartdrive Ltd.  has developed a prototype imaging system, SatScan, that captures digitised images of large areas while keeping smaller objects in focus at very high resolution. The system was set up in the Sackler Biodiversity Imaging laboratory of Natural History Museum on March 8, 2010 for a one-month trial. A series of projects imaging parts of the entomological, botanical and palaeoentomological collection were conducted to assess the systems utility for museum collection management and biodiversity research. The technical and practical limitations of the system were investigated as part of this process.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4486/version/1

Folding pathway of the B1 domain of protein G explored by a multiscale modeling
Provedor de dados: 17
Autores: Andrzej Kolinski; Sebastian Kmiecik.
The understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, _ab initio_ simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/129/version/1

Novel approaches, including systems biology, to HIV vaccine research and development: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Bali  Pulendran; Rino Rappuoli; Alan Aderem; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a two-day workshop on August 10-11 2009, at the Fred Hutchison Cancer Research Center offices in Seattle, WA, to discuss the application of novel approaches,including systems biology, to HIV vaccine research and development. The goals of this Working Group were to identify key scientific issues and opportunities that have emerged since the Enterprise Scientific Strategic Plan1 was published in 2005, and to make recommendations to Enterprise stakeholders.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4798/version/1

SABIO-RK: Access to Biochemical Reaction Kinetics Data
Provedor de dados: 17
Autores: Martin Golebiewski.
SABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. New RESTful web services, as well as a new browser...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6506/version/1

Searching the World-Wide-Web using nucleotide and peptide sequences
Provedor de dados: 17
Autores: Natarajan Ganesan; Nicholas F. Bennett; Bala Kalyanasundaram; Mahe Velauthapillai; Richard Squier.
*Background:* No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept &amp;#x2018;processed&amp;#x2019; queries, the burden of preparing such &amp;#x2018;search strings&amp;#x2019; simply defeats the purpose of quickly locating highly relevant information. Unlike &amp;#x2018;sequence similarity&amp;#x2019; searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct &amp;#x2018;sequence based&amp;#x2019; search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2492/version/1

GenColors: Annotation and comparative genomics made easy
Provedor de dados: 17
Autores: Marius Felder; Alessandro Romualdi; Gernot Gloeckner; Matthias Platzer; Juergen Suehnel.
GenColors is a web-based software/database system initially aimed at an improved and accelerated annotation of prokaryotic genomes making extensive use of genome comparison (Romualdi et al., _Bioinformatics_ 2005; Romualdi et al., _Methods Mol. Biol._ 2007). It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and maintained. The tool has been efficiently used for sequenceing and annotating the Borrelia garinii genome and is currently applied to a number of other ongoing genome projects on _Legionella_, _Pseudomonas_ and _E. coli_ genomes. Examples for freely accessible...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3111/version/1

Using open access literature to guide full-text query formulation
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background*&amp;#xd;&amp;#xa;Much scientific knowledge is contained in the details of the full-text biomedical literature.  Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume.  Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar.  However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users.  We propose improving the formulation of full-text queries...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4267/version/1

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher  J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/1

Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Availability:* A free...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/2

Genome activity profiling of monomeric-IgE and Fc-epsilon-RI-aggregation on human mast cells reveals a complex network of genes involved in inflammatory responses.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Alirio Jose P. N. Melendez; Peter Natesan A. J. Pushparaj.
Mast cell activation, mediates type-1 allergic responses, one of the most powerful reactions of the immune system. However, mast cells activation is becoming increasingly linked to inflammatory, autoimmunity, and to adaptive immunity by regulating T-cell activation.&amp;#xd;&amp;#xa;Here we analyzed the gene expression pattern in IgE-sensitized and Fc&amp;#x3b5;RI aggregation on human mast cells. Our data revealed coordinated changes in gene expression. We observed increased expression of gene-transcripts involved in allergic, innate and adaptive&amp;#xd;&amp;#xa;immune responses. Among the most prominent findings is the increased expression of transcripts encoding for MIP3a, SPARCL1, AREG, IL18, CCL1, TNFRSF9, IL1b, CX3CR1, PTGER3, MIF, MMP12, ADORA3,...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1150/version/1

Plasmodium falciparum has rare correlation properties
Provedor de dados: 17
Autores: Kushal Shah.
A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6817/version/1

Expert Assertions Through Community Annotation Jamborees
Provedor de dados: 17
Autores: Lauren Brinkac; Ramana Madupu; Elisabet Caler; Derek Harkins; Hernan Lorenzi; Mathangi Thiagarajan; Granger Sutton.
Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI&amp;#x2019;s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI&amp;#x2019;s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3170/version/1

Developments in CFG glycan and pathogen polysaccharide arrays
Provedor de dados: 17
Autores: Ola Blixt.
This presentation summarizes developments in glycan and pathogen polysaccharide arrays at the Consortium for Functional Glycomics (CFG).
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/12/version/1

Building conceptual spaces for exploring and linking biomedical resources
Provedor de dados: 17
Autores: Rafael Berlanga; Voctoria Nebot; Ernesto Jimenez-Ruiz.
The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based prototype tool which integrates the proposed infrastructure.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5381/version/1

A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements-  (v.4)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/4

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Anatoly  Sorokin; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3721/version/1

Modularization for the Cell Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl.
One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6685/version/1

INCF Lithuanian Workshop on Neuroscience and Information Technology
Provedor de dados: 17
Autores: Au&amp;#x161;ra Saudargiene.
The aim of this workshop was to give a current overview of neuroscience and informatics research in Lithuania, and to discuss the strategies for forming the Lithuanian Neuroinformatics Node and becoming a member of INCF. The workshop was organized by Dr. Au&amp;#x161;ra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF.&amp;#xd;&amp;#xa;The workshop was attended by 15 invited speakers, among them 4 guests and 11 Lithuanian neuroscientists, and over 20 participants. The workshop was organized into three main sessions: overview of the INCF activities including the Swedish and UK nodes of INCF; presentations on Neuroscience research carried out in Lithuania;...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6931/version/1

Wellcome Trust Policy on Data Management and Sharing
Provedor de dados: 17
Autores: David Carr.
The Wellcome Trust&amp;#x27;s policy statement on data management and sharing, which was originally published in January 2007 and revised in August 2010.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6007/version/1

Improvement of PubMed Literature Searching using Biomedical Ontology
Provedor de dados: 17
Autores: Zuoshuang Xiang; Yongqun He.
PubMed articles are annotated using the Medical Subject Headings (MeSH) to increase search efficiency. However, MeSH contains limited information on many biomedical domains (e.g., vaccine). Biomedical ontologies may be used to improve PubMed searching capability. This study demonstrates that Vaccine Ontology (VO) can be used to significantly improve PubMed searching efficacy in the vaccine domain. The recall and precision of the ontology-based literature mining approach are analyzed and discussed.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3491/version/1

CellML 1.1 modularity
Provedor de dados: 17
Autores: Poul Nielsen.
CellML 1.1 is an open XML-based language designed  to store and exchange computer-based mathematical models. It has a simple facility to import existing models in order to create new models. The import facility encourages the development of hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5005/version/1

The Molecular In Silico Dissection of Cancer using TCLASS and its Application in the Identification of the Tissue of Origin of &amp;#xb;Cancers of Unknown Primary Site&amp;#xb;
Provedor de dados: 17
Autores: Torik Ayoubi.
Traditional cancer diagnosis relies on a combination of clinical and histo-pathological data. In many cases, however, the morphology of in particular metastatic cancer is not discriminative enough for correct diagnosis. In addition, the morphology of tumor cells do not provide information on aberrant molecular pathways that may be used to specifically target the tumor like the application of Herceptin to breast cancers with amplification in the ERBB2 gene. With the completion of the human genome project, molecular pathology has dramatically increased its arsenal of novel molecular biomarkers that can be used to determine the phenotype of tumors. Gene expression profiling using high-density microarray technology is an extremely powerful tool to...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5300/version/1

mRNA diffusion explains protein gradients in Drosophila early development
Provedor de dados: 17
Autores: Rui Dilao; Daniele Murro.
We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of _Drosophila_. In this model, we consider that _bicoid_ mRNA diffuses along the antero-posterior axis of the embryo and the protein is produced in the ribosomes localized near the syncytial nuclei. Bicoid protein stays localized near the syncytial nuclei as observed in experiments.We calibrate the parameters of the mathematical model with experimental data taken during the cleavage stages 11 to 14 of the developing embryo of _Drosophila_. We obtain good agreement between the experimental and the model gradients, with relative errors in the range 5-8%. The inferred diffusion coefficient of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3402/version/1

Evaluation of the cutaneous microbiome in psoriasis
Provedor de dados: 17
Autores: Martin  J. Blaser; Barbara Methe; Bruce  Strober; Guillermo I. Perez Perez; Stuart Brown; Alexander  Alekseyenko.
Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contributes to the pathogenesis of...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5276/version/1

Apellicon: a web-based tool for constructing and curating Textpresso databases.
Provedor de dados: 17
Autores: William M. Urbanski; Brian  G. Condie.
As more research literature in the biological sciences is made available in electronic format, text mining systems are increasingly being used to improve the ability of investigators to retrieve relevant information. Through the use of advanced indexing techniques that utilize biological ontologies, semantic databases, and other formal representations of biological concepts text mining systems have been able to effectively parse biological literature. While text mining systems are increasingly effective at creating the linkages required to provide context-specific search results, the systems themselves are difficult to set up and use by novice computer users due to the highly technical nature of the applications. Because most researchers in the biological...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4927/version/1

A Latent Variable Approach to Multivariate Quantitative Trait Loci
Provedor de dados: 17
Autores: Bob O&amp;#x27;Hara; P&amp;#xe4;ivi  Komulainen; Outi  Savolainen; Mikko J. Sillanp&amp;#xe4;&amp;#xe4;.
A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci.  Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4137/version/1

Developing ontologies in decentralised settings
Provedor de dados: 17
Autores: Alexander  Garcia; Kieran O&amp;#x2019;Neill; Leyla J. Garcia; Phillip Lord; Robert Stevens; Oscar Corcho; Frank Gibson.
This paper addresses two research questions: &amp;#x201c;How should a well-engineered methodology facilitate the development of ontologies within communities of practice?&amp;#x201d; and &amp;#x201c;What methodology should be used?&amp;#x201d; If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3231/version/1

Memristive model of amoeba&amp;#x27;s learning
Provedor de dados: 17
Autores: Yuriy V. Pershin; Steven La Fontaine; Massimiliano  Di Ventra.
Recently, behavioural intelligence of the plasmodia of the true slime mold has been demonstrated. It was shown that a large amoeba-like cell Physarum polycephalum subject to a pattern of periodic environmental changes learns and changes its behaviour in anticipation of the next stimulus to come. Currently, it is not known what specific mechanisms are responsible for such behaviour. Here, we show that such behaviour can be mapped into the response of a simple electronic circuit consisting of an LC contour and a memory-resistor (a memristor) to a train of voltage pulses that mimic environment changes. We identify a possible microscopic origin of the memristive behaviour in the Physarum polycephalum, which together with the naturally occurring biological...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2431/version/1

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set
Provedor de dados: 17
Autores: Zhaoming Wang; Kevin Jacobs; Meredith Yeager; Amy  Hutchinson; Joshua Sampson; Nilanjan Chatterjee; Demetrius Albanes; Sonja I. Berndt; Charles C. Chung; W. Ryan Diver; Susan M. Gabstur; Lauren R. Teras; Christopher M. Haiman; Brian E. Henderson; Daniel Stram; Xiang Deng; Ann W. Hsing; Jarmo Virtamo; Michael A. Eberle; Jennifer L. Stone; Mark P. Purdue; Phil Taylor; Margaret Tucker; Stephen Chanock.
Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals.  Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^&amp;#x3e;0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6576/version/1

Functional annotation of human parvovirus b19 proteome and Molecular docking of VP1 protein with Teniposide
Provedor de dados: 17
Autores: Amburu Praneetha; Dibyabhaba Pradhan; Vani Priyadarshini; Amineni Umamaheswari.
Parvovirus B19 is a common source of infection with a seroprevalence of 60-70% in the adult population. Human parvovirus causes several distinct clinical syndromes such as erythema, polyarthritis resembling rheumatoid arthritis, vasculitis, hydrops fetalis, myocarditis etc. Recent years have witnessed manifest increase in clinical knowledge of parvovirus B19-associated complications, diagnosis and treatment. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation of human parvoviral proteome may provide insights into role of viral proteome in its survival and pathogenic mechanisms. Availability of whole proteome in the open source aided functional annotation of protein using...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5170/version/1

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/3

Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)
Provedor de dados: 17
Autores: Nicolas Le Novere; Emek Demir; Huaiyu Mi; Stuart Moodie; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5902/version/1

Laparoscopy Pneumoperitoneum Fuzzy Modeling
Provedor de dados: 17
Autores: Otavio M. Becker Jr.; Jose E. Araujo Jr.; Joao L. M. C. Azevedo.
Abstract: Gas volume to intra-peritoneal pressure fuzzy modeling for evaluating pneumoperitoneum in videolaparoscopic surgery is proposed in this paper. The proposed approach innovates in using fuzzy logic and fuzzy set theory for evaluating the accuracy of the prognosis value in order to minimize or avoid iatrogenic injuries due to the blind needle puncture. In so doing, it demonstrates the feasibility of fuzzy analysis to contribute to medicine and health care. Fuzzy systems is employed here in synergy with artificial neural network based on backpropaga tion, multilayer perceptron architecture for building up numerical functions. Experimental data employed for analysis were collected in the accomplishment of the pneumoperitoneum in a random population of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6060/version/1

Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
Withdrawn&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Incomplete data
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/2

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/2

Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program
Provedor de dados: 17
Autores: Yunfeng Y. S. Shan; Robin Gras.
The origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the Bayesian method under the coalescence model with the latest program (BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear genes encoding amino acid residues with the jackknife method for taxon sub-sampling. The results, combined with those of other three genome-scale approaches, successfully prove the hypothesis that lungfishes and coelacanths form a monophyletic sister group and are equally related to tetrapods supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3865/version/1

User Centered and Ontology Based Information&amp;#xb;Retrieval System for Life Sciences
Provedor de dados: 17
Autores: Sylvie Ranwez; Vincent  Ranwez; Mohameth Fran&amp;#xe7;ois Sy; Jacky  Montmain; Michel  Crampes.
Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of retrieved documents and no explanation for their adequacy to the query. Users may thus be confused by the selection and have no idea how to adapt their query so that the results match their expectations. &amp;#xd;&amp;#xa;This talk describes a request method and an environment based on aggregating models to assess the relevance of documents annotated by concepts of ontology. The selection of documents is then displayed in a semantic map to provide graphical indications that make explicit to what extent they match the...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5408/version/1

Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Larry Kedes; Granger Sutton; Edison  Liu; Victor Jongeneel.
This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5731/version/1

The MEROPS Database
Provedor de dados: 17
Autores: Neil D. Rawlings; Alan J. Barrett.
Many proteins undergo important post-translational proteolytic processing to remove targeting signals and activation peptides, and most proteins undergo proteolytic inactivation and catabolism.  The enzymes that hydrolyse the peptide bonds in proteins and peptides are known as peptidases, proteases or proteolytic enzymes.  The MEROPS database (&amp;#x22;http://merops.sanger.ac.uk&amp;#x22;:http://merops.sanger.ac.uk) presents the classification and nomenclature of peptidases, their inhibitors and substrates.  In 1993 we proposed the scheme for the classification of peptidases that has been internationally accepted, and in 1996 we established the MEROPS database.  Protein inhibitors have been included in the database since 2004.  About 2% of the genes in a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3103/version/1

HGNC: The Why and How of Standardised Gene Nomenclature
Provedor de dados: 17
Autores: Ruth Seal; Susan Gordon; Michael Lush; Mathew Wright; Elspeth Bruford.
The HUGO Gene Nomenclature Committee (HGNC) aims to approve a unique gene symbol and gene name for every human gene.  Standardisation of gene symbols is necessary to allow researchers and curators to refer to the same gene without ambiguity.  Consistent use of gene symbols in publications and across different websites makes it easy for researchers to find all relevant information for a particular gene and facilitates data mining and retrieval.  For each gene that we name we curate relevant information including symbol aliases, chromosomal location, locus type, sequence accessions and links to relevant databases.  Therefore, our website is a central resource for human genetics. &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;We endeavour to approve gene symbols that...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3182/version/1

Sequential Allocation and Balancing Prognostic Factors in a Psychiatric Clinical Trial
Provedor de dados: 17
Autores: Victor Fossaluza; Juliana B. Diniz; Basilio B. Pereira; Euripedes C. Miguel; Carlos  A. B. Pereira.
In controlled clinical trials, each of several prognostic factors should be balanced across the trial arms. Traditional restricted randomization may be proved inadequate especially with small sample sizes. In psychiatric disorders such as obsessive compulsive disorder (OCD), small trials prevail. Therefore, procedures to minimize the chance of imbalance between treatment arms are advisable. This paper describes a minimization procedure specifically designed for a clinical trial that evaluates treatment efficacy for OCD patients. Aitchison&amp;#x27;s compositional distance was used to calculate vectors for each possibility of allocation in a covariate adaptive method. Two different procedures were designed to allocate patients in small blocks or...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2102/version/1

Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era
Provedor de dados: 17
Autores: Andrea Califano; Atul Butte; Stephen Friend; Trey Ideker; Eric E. Schadt.
After completion of a number of large scale Genome-Wide Association Studies (GWAS), there is still a significant amount of trait and disease variance that cannot be explained by existing genetic variability. This review introduces new, Integrative Network-based Association Study (INAS) approaches that aim to minimize the impact from multiple hypothesis testing statistics, thus allowing the identification of rare variants/alterations and epistatic interactions. In particular we discuss methods that rely on the de novo computational, experimental, and integrative dissection of context specific molecular interaction networks (or interactomes, for short). We provide several examples of how these approaches may be used to tackle discovery of genetic variants...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5732/version/1

Curation at the NCBI: Genomes, Genes, &amp;#x26; Sequence Standards
Provedor de dados: 17
Autores: Garth Brown; Catherine Farrell; Jennifer Hart; Melissa Landrum; Donna Maglott; Bonnie Maidak; Michael Murphy; Terence Murphy; Bhanu Rajput; Kim D. Pruitt; Lillian Riddick; David Webb; Janet Weber; Wendy Wu.
The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and  disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC).  These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3287/version/1

Genetically modified Cotton species detection by LISS-III satellite data
Provedor de dados: 17
Autores: Saumitra Mukherjee; Satyanarayan Shashtri; Chander Kumar  Singh; Bindu  Kumari; Reena Kumari; Ram  Avatar; Amit  Singh; Anita  Mukherjee; Bhoop  Singh.
It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showing R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton has reasonably acceptable correlation...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2659/version/2

The CombiUgi Project and Closing the Open Science Loop
Provedor de dados: 17
Autores: Jean-Claude Bradley; Rikesh Parikh; Dan Zaharevitz; Rajarshi Guha.
This presentation combines 2 blog posts explaining the CombiUgi project and the predicted anti-tumor activity of a virtual library of 68,000 compounds.
Tipo: Presentation
Palavras-chave: Cancer; Chemistry; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/104/version/1

The Normal Fetal Heart Rate Study: Analysis Plan
Provedor de dados: 17
Autores: Martin Daumer; Michael Scholz; Anne-Laure Boulesteix; Stephanie Pildner von Steinburg; Sven Schiermeier; Wolfgang Hatzmann; K T M Schneider.
Recording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/980/version/2

Tendril, adhesive disc and super adhesive effect of climbing plant
Provedor de dados: 17
Autores: Wenli Deng.
Understanding the super adhesion mechanism of biological system is of great scientific interest and a prerequisite for bioinspired design of adhesive systems. To investigate the versatile climbing plant requires the development of new methods. Here I present strategies to fully study the super adhesive effect of climbing plant _Parthenocissus tricuspidata_ by the first time measuring the mass and the attached area of single adhesive disc, by further determining the microscopic structure and the adhesive strength of single adhesive disc and by finally elucidating the adhesion mechanism in cellular and molecular level using the classical theories and the proposed new hypothesis and model. I have measured that a single mature adhesive disc has an average mass...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1513/version/2

Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Peter D&amp;#x27;Eustachio; David Croft; Bernard de Bono; Gopal Gopinath; Marc Gillespie; Bijay Jassal; Lisa Matthews; Esther Schmidt; Imre Vastrik; Guanming Wu; Suzanna Lewis; Ewan Birney; Lincoln Stein.
Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1281/version/1

Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials
Provedor de dados: 17
Autores: Gwen A. Frishkoff; Paea LePendu; Robert M. Frank; Haishan Liu; Dejing Dou.
We describe a first-generation ontology for&amp;#xd;&amp;#xa;representation and integration of event-related brain potentials (ERPs). The ontology is designed following OBO &amp;#x201c;best practices&amp;#x201d; and is augmented with tools to perform ontology-based labeling and annotation of ERP data, and a database that enables semantically based reasoning over these data. Because certain high-level concepts in the ERP domain are illdefined, we have developed methods to support coordinated updates to each of these three components. This approach consists of &amp;#x201c;top-down&amp;#x201d; (knowledge-driven) design and implementation, followed by &amp;#x201c;bottom-up&amp;#x201d; (data-driven) validation and refinement. Our goal is to build an ERP...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3458/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/1

Characterization of a pig skeletal muscle microarray to study pork quality: the GenmascqChip 15K
Provedor de dados: 17
Autores: Marie Damon; Fr&amp;#xe9;d&amp;#xe9;ric Herault; Annie Vincent; Pascale Le Roy; Pierre Cherel.
Pork quality is highly variable and availability of relevant predictors of fresh meat quality at slaughter is critical to optimize carcass use and improve its valuation. High throughput gene expression studies have been widely used to describe biological mechanisms underlying variation of several traits but data are scarce regarding their use as tools for development of biomarkers. The GENMASCQ (GENomics enabled Marker Assisted Selection and Certification of Quality in Pork products ) research program was set up to select, using high-throughput gene expression screening, markers of the biological variation mostly appropriate to describe, and ultimately forecast, the sensory quality of an important meat product, accounting for nearly 40 % of meat protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5730/version/1

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Provedor de dados: 17
Autores: Mark Wilkinson; Benjamin Vandervalk; Luke McCarthy.
Background.  &amp;#xd;&amp;#xa;The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration.  There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics  community.  Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Description. &amp;#xd;&amp;#xa;SADI &amp;#x2013; Semantic Automated Discovery and Integration &amp;#x2013; is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6550/version/1

Using MicroPET Imaging in Quantitative Verification of Acupuncture Effect in Ischemia Stroke Treatment
Provedor de dados: 17
Autores: Xiaoyan  Shen; Hongtu Tang; Jia Li; Ting Xiang; Huafeng Liu; Weichuan  Yu.
While acupuncture has survived several thousand years&amp;#x2019; evolution of medical practice, its function still remains as a myth from the view point of modern medicine. Our goal in this paper is to quantitatively understand the function of acupuncture in ischemia stroke treatment. We carried out a comparative study using the Sprague Dawley rat animal model. We induced the focal cerebral ischemia in the rats using the middle cerebral artery occlusion (MCAO) procedure. For each rat from the real acupuncture group (n = 40), sham acupoint treatment group (n = 54), and blank control group (n = 16), we acquired 3-D FDG-microPET images at baseline, after MCAO, and after treatment (i.e., real acupuncture, sham acupoint treatment, or resting according to the...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4128/version/1

Topological Characterization of Protein-Protein Interaction Networks in Human and Mouse
Provedor de dados: 17
Autores: Bipin Singh.
The elucidation of the cell&amp;#x27;s large-scale organization is a primary challenge for post-genomic biology, and understanding the structure and topological properties of protein-protein interaction networks offers an important starting point for such studies. We compare the protein-protein interaction network of the human and mouse, aiming to uncover the network&amp;#x27;s generic large-scale properties and the impact of the protein&amp;#x27;s function and cellular localization on the network topology. We show that both human and mouse protein-protein interaction supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6126/version/1

BioCatalogue: A Curated Web Service Registry For The Life Science Community
Provedor de dados: 17
Autores: Carole A. Goble; Khalid Belhajjame; Franck  Tanoh; Jiten Bhagat; Katy Wolstencroft; Robert Stevens; Eric Nzuobontane; Hamish McWilliam; Thomas Laurent; Rodrigo Lopez.
Web Services have gained a momentum as a means for packaging existing data and computational resources in a form that is amenable for use and composition by third party applications. The life science community is certainly among the first adopters of Web Services. For example, &amp;#x22;Taverna&amp;#x22;:http://www.mygrid.org.uk, a workflow workbench that is popular within the life science community, provides access to over 3500 thousands web services that can be composed by scientists for constructing and enacting their _in silico_ experiments. However, one of the main issues that hinders the wide adoption and use of Web Services is the difficulty in locating the &amp;#x201c;appropriate&amp;#x201d; Web Service, i.e., the Web Service that performs the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3132/version/1

PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network
Provedor de dados: 17
Autores: Xun Huang.
A variety of methods are developed to integrating diverse biological data to predict novel interaction relationship between proteins. However, traditional integration can only generate protein interaction pairs within existing relationships. Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships between proteins. Our method is more powerful than a na&amp;#xef;ve Bayesian-network-based integration in PPI prediction, and could generate more reliable candidate PPIs. Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4107/version/1

Modeling of ARS-interacting multifunctional proteins p18 and p38.
Provedor de dados: 17
Autores: Viktor V. Deineko.
ARS-interacting multifunctional proteins (auxiliary components) &amp;#x2013; are nonezymatic proteins, associated with aminoacyl-tRNA synthetases &amp;#x2013; enzymes that catalyse the joining of amino acids with their corresponding tRNAs. All these proteins are complexed into large macromolecular multisynthetase complex in eukaryotes. It includes nine different ARSs and three auxiliary components. Their spatial structures precisely defined by X-ray analysis are still not known. Nevertheless, it very useful to have this structure while making biochemical studies. Bioinformatical tools were used to create structural models of two auxiliary components of multisynthetase complex &amp;#x2013; p18 and p38.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1047/version/1

A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/1

Simulations of Antigenic Variability in Influenza A
Provedor de dados: 17
Autores: Nuno Fachada; Vitor V. Lopes; Agostinho C. Rosa.
Computational models of the immune system (IS) and pathogenic agents have several applications, such as theory testing and validation, or as a complement to first stages of drug trials. One possible application is the prediction of the lethality of new Influenza A strains, which are constantly created due to antigenic drift and shift. Here, we present several simulations of antigenic variability in Influenza A using an agent-based approach, where low level molecular antigen-antibody interactions are explicitly described. Antigenic drift and shift events are analyzed regarding the virulence of emergent strains against the IS. Results are discussed from a qualitative point of view taking into account recent and generally recognized immunology and influenza...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2303/version/1

Biomedical Resource Ontology
Provedor de dados: 17
Autores: Trish  Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6354/version/1

SBML Editor&amp;#x2019;s Report: Principles for Package Development
Provedor de dados: 17
Autores: Lucian Smith.
In the last six months, the SBML Editors have developed several principles to guide the development of SBML Level 3 packages.  An update on what those principles are, and some controversies that have arisen as a result.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6403/version/1

Kinetic Simulation Algorithm Ontology
Provedor de dados: 17
Autores: Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6330/version/1

The SOL Genomics Network Model: Making Community Annotation Work
Provedor de dados: 17
Autores: Naama Menda; Isaak Tecle; Anuradha Pujar; Aureliano Bombarely; Tom York; Adri Mills; Joseph Gosselin; Robert Buels; Lukas Mueller.
The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up&amp;#x2010;to&amp;#x2010;date knowledge in biological databases.&amp;#xd;&amp;#xa;The Solanaceae Genomics Network (&amp;#x22;SGN&amp;#x22;:http://sgn.cornell.edu/) is a clade&amp;#x2010;oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3134/version/1

What&amp;#x27;s in an &amp;#x27;is a&amp;#x27; link?
Provedor de dados: 17
Autores: William R. Hogan.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Several researchers have demonstrated that current medical terminologies and ontologies use relations in inconsistent and ambiguous ways,[1] despite Woods&amp;#x2019; seminal work that first illustrated the problem.[2] The goal of the present work is to catalog the different ways in which SNOMED CT uses the _is a_ relation.  The rationale for creating the catalog is to serve as a basis for systematically improving the semantics of terminologies and ontologies so as to improve their accessibility to machine inference.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;I reviewed the literature to find ontological mistakes that change the interpretation of the _is a_ relation, without...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3462/version/1

Terminizer - Assisting Mark-Up of Text Using Ontological Terms
Provedor de dados: 17
Autores: David Hancock; Norman Morrison; Giles Velarde; Dawn Field.
We present a tool that automatically detects ontological terms in free text. Once candidate terms have been identified the results are displayed either overlaid on the original text or in a list organised by the ontology and frequency.  The user can interactively accept or reject each match, or try to find a more appropriate match by exploring the network of ontology concepts themselves. In typical ontological resources, the parent(s) of a term represent broader concepts whilst the children of a term represent more specific concepts. In this way, the suggested match can used as a starting point for the user to find a more suitable term. The ontology browser interface incorporates a graphical visualisation which uses Flash to present an interactive view of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3128/version/1

Mining SOM expression portraits: Feature selection and integrating concepts of molecular function
Provedor de dados: 17
Autores: Henry Wirth; Martin von Bergen; Hans Binder.
Background: &amp;#xd;&amp;#xa;Self organizing maps (SOM) enable the straightforward portraying of high-dimensional data of large sample collections in terms of sample-specific images. The analysis of their texture provides so-called spot-clusters of co-expressed genes which require subsequent significance filtering and functional interpretation. We address feature selection in terms of the gene ranking problem and the interpretation of the obtained spot-related lists using concepts of molecular function.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: &amp;#xd;&amp;#xa;Different expression scores based either on simple fold change-measures or on regularized Students t-statistics are applied to spot-related gene lists and compared with special emphasis on the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6666/version/1

Incorporating Community Annotation Interfaces into the CIPRO2.5 Database with Comprehensible Sketches to Support Quick Annotations of Proteome Data.
Provedor de dados: 17
Autores: Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Toshinori Endo.
User annotation or comment interfaces are now widely used in several web sites such as journals, news, weblogs and Wikipedia. However, there are only a few biological databases with annotation interfaces. The _Ciona_ _intestinalis_ protein database (CIPRO) was created in order to provide integrated proteome data especially for experimental biologists. The current database contains 89,673 unique sequences covering all the known and predicted gene models. Typical tasks include which gene models are reliable and which function is plausible. The human-curated annotation is most important for the meaningful database.&amp;#xd;&amp;#xa;Here we incorporate three new functions into the CIPRO2.5 database (http://cipro.ibio.jp/2.5/), providing enriched resources for...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5064/version/1

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur &amp;#x2013; a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B) The Ribosomal Database (RDP) nai&amp;#x308;ve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/2

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle
Provedor de dados: 17
Autores: Silvia  Vilasi; Raffaele Ragone.
The potent immunomodulatory, anti-inflammatory and procoagulant properties of the&amp;#xd;&amp;#xa;protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have been&amp;#xd;&amp;#xa;previously found to be modulated by a supramolecular monomer-trimer equilibrium.&amp;#xd;&amp;#xa;More structural details that integrate experimental data into a predictive framework&amp;#xd;&amp;#xa;have recently been reported. Unfortunately, homology modelling and fold-recognition&amp;#xd;&amp;#xa;strategies were not successful in creating a theoretical model of the structural&amp;#xd;&amp;#xa;organization of SV-IV. It was inferred that the global structure of SV-IV is not similar&amp;#xd;&amp;#xa;to any protein of known three-dimensional structure. Reversing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1394/version/1

Homology modeling and docking studies to explore the novel drug for monocyte differentiation antigen CD14
Provedor de dados: 17
Autores: Bhimisetty Reshma; Sandeep Swaragam; Amineni Umamaheswari.
Monocyte differentiation antigen CD14 belongs to the leucine rich family. Elevated levels of monocyte differentiation antigen CD14 and toll-like receptor 4 (TLR4) play a major role in inflammatory response and cause ischemic heart diseases, neuropathic pain and LPS (endotoxin) induced septic shock. IAXO compounds (IAXO-101, IAXO-102 and IAXO-103) inhibit the CD14-dependent and TLR4-independent signaling pathways but they have severe side effects.  Due to unavailability of human monocyte differentiation antigen CD14 crystal structure, 3D structure was constructed based on template structure (1WWL) using Modeler 9v9. The modeled structure was refined, energy minimized and validated. Binding site residues of human monocyte differentiation antigen CD14 were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6580/version/1

Online Training of New Curators
Provedor de dados: 17
Autores: Marc E. Gillespie; Bijay Jassal.
The basic information in Reactome is provided by bench biologists who are experts on a particular pathway, the Reactome Team is always working hard to drive engagement. This engagement between experts, curators, editors and reviewers requires maintenance and improvement, and in this sense Reactome is itself a model for large biocuration projects that are driven by community engagement.  &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;This tutorial will highlight issues from the perspective of online training participants, the trainer&amp;#x27;s and the audience&amp;#x27;s. From the audience perspective the tutorial will introduce the concepts that drive the Reactome data model, cover the basic steps that a researcher would have to follow in order to breakdown a...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3420/version/1

Genetically modified Cotton species detection by LISS-III satellite data
Provedor de dados: 17
Autores: Saumitra Mukherjee; Satyanarayan Shashtri; Chander Kumar  Singh; Bindu  Kumari; Reena Kumari; Ram  Avatar; Amit  Singh; Anita  Mukherjee; Bhoop  Singh.
It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showed R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton also has reasonably acceptable...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/2659/version/3

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value.   With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial.  While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains.  In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/2

Benchmarking triple stores with biological data
Provedor de dados: 17
Autores: Vladimir Mironov.
We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query specific. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second, and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5417/version/1

PAL:  A Perl Script for Rapidly Identifying the Active Site of Large Protein Families
Provedor de dados: 17
Autores: Andres A. Larrea; Pablo A. Larrea.
In the post-genomic era, with an ever-increasing amount of sequence information, it is critical to develop tools that assist in sifting through all the data to identify information amidst the noise.  The two main steps in determining the functional sites in proteins are aligning a large set of homologous sequences and analyzing this large file to identify highly conserved residues.  Although a number of tools exist for generating high quality alignments rapidly there are much fewer tools available for rapidly identifying conserved cores within that multiple sequence alignment. PAL, is a Perl script that rapidly identifies conserved residues present in a large alignment file.  The strengths of PAL are: speed, flexibility and ease of use.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/917/version/1

Building and Using Geospatial Ontology in the BioCaster Surveillance System
Provedor de dados: 17
Autores: Son Doan; Quoc-Hung Ngo; Ai Kawazoe; Nigel Collier.
This abstract presents an approach to building a geospatial ontology from Wikipedia and using it in BioCaster, a system for detecting and tracking infectious disease outbreaks from online news. Motivated by the need to interpret the geospatial dynamics of events we built a database containing the names of countries and major cities from Wikipedia. We started by automatically extracting country and dependent territory names and sub-country (subdivision and dependent area) names in the form of ISO 3166-1 and ISO 3166-2, respectively. Then, we re-created the part-whole relation between countries and sub-countries by verifying links from countries to their sub-countries. Verification was done by manual checking. The building process is semi-automatically...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2110/version/1

Management and provision of computational models
Provedor de dados: 17
Autores: Camille Laibe.
Quantitative models of biological systems provide an understanding of chemical and biological phenomena based on their underlying mechanisms. Moreover, they can be used for example, to predict the behaviour of a system under given conditions or direct future experiments. This has made quantitative models the perfect tools to answer a variety of questions in the biological sciences and has lead to a steady growth of the number of published models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. BioModels Database(http://www.ebi.ac.uk/biomodels/) has been developed to exactly fulfil those needs....
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7013/version/1

Insights from the Structure of Estrogen Receptor into the Evolution of Estrogens: Implications for Endocrine Disruption
Provedor de dados: 17
Autores: Michael E. Baker.
In the last decade, there has been important progress in understanding the origins and evolution of receptors for adrenal steroids (aldosterone, cortisol) and sex steroids (estradiol, progesterone, testosterone) due to the sequencing of genomes from animals that are at key sites in vertebrate evolution.  Although the estrogen receptor [ER] appears to be the ancestral vertebrate steroid receptor and estradiol [E2] is the physiological ligand for vertebrate ERs, the identity of the ancestral ligand(s) for the ER remains unknown.  Here, using an analysis of crystal structures of human ER[alpha] with E2 and other chemicals and 3D models of human ER[alpha] with 27-hydroxycholesterol and 5-androsten-3[beta],17[beta]-diol, we propose that one or more [DELTA]5...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5777/version/1

MIREOT: the Minimum Information to Reference an External Ontology Term
Provedor de dados: 17
Autores: M&amp;#xe9;lanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan R. Brinkman; Alan Ruttenberg.
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3576/version/1

Mining PubMed for Biomarker-Disease Associations to Guide Discovery
Provedor de dados: 17
Autores: Walter J. Jessen; Katherine T. Landschulz; Thomas G. Turi; Rachel Y. Reams.
Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6941/version/1

Searching BioModels Database
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Andre Peters; Lukas Endler; Nicolas le Nov&amp;#xe8;re.
*Aim*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The increasing number of computational models of biological systems demands a better support for search facilities. One possible improvement is to enable ranked retrieval of models based on existing model annotation. &amp;#xd;&amp;#xa;&amp;#xa0;&amp;#xd;&amp;#xa;Applying existing Information Retrieval (IR) techniques to computational models, we have implemented a new search strategy in BioModels Database. In this search strategy the index of search terms contains not only the model descriptions in the database, but is expanded by including ontological and textual information about a model and its constituents retrieved from external sources. To add more background knowledge, we additionally index the abstracts of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4985/version/1

Hacking the JPEG/PDF tree format
Provedor de dados: 17
Autores: Joseph Hughes.
We have been illustrating the relationships between species and genes as trees for over a century. Whilst in the early years of morphological and molecular phylogenetics, embedding illustrations into manuscripts might have been the most appropriate way to disseminate knowledge, this has resulted in the locking up of phylogenetic hypotheses into the pages of journals and books without an easy way to access this information. As a result, most phylogenetic knowledge is lost upon publication. I will explain the reasons for re-using published trees, discuss ways to liberate this information and avoid these problems in the future.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6556/version/1

Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy
Provedor de dados: 17
Autores: C&amp;#xe9;cile An&amp;#xe9;; Colin N. Dewey; Satish K. Kotha; Bret R. Larget.
When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4625/version/1

Intracellular Regulatory Networks are close to Monotone Systems
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan; Ravi Iyengar; Eduardo D. Sontag.
Several meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/25/version/1

The Vaginal Microbiome: Disease, Genetics and the Environment
Provedor de dados: 17
Autores: Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James  P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael  D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico A. Puma; Mark A. Reimers; Maria C. Rivera; Seth B. Roberts; Myrna G. Serrano; Nihar Sheth; Judy L. Silberg; Logan Voegtly; Elizabeth C. Prom-Wormley; Bin Xie; Timothy  P. York; Cynthia N. Cornelissen; Jerome F. Strauss III; Lindon J. Eaves; Gregory A. Buck.
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5150/version/2

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/3

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/1

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/4967/version/2

Generalised and abdominal adiposity are important risk factors for chronic disease in older people: results from a nationally representative survey
Provedor de dados: 17
Autores: Vasant Hirani.
Objective: To look at the trends in prevalence of generalised (body mass index (BMI)&amp;#x2265; 25 kg/m2) and abdominal obesity (waist circumference (WC) &amp;#x3e;102cm, men; &amp;#x3e;88cm, women) among older people from 1993 to 2008, prevalence of chronic disease by overweight/obesity and waist circumference categories in England 2005 and evaluate the association of these measures with chronic diseases. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: Analyses of nationally representative cross-sectional population surveys, the Health Survey for England (HSE), including non-institutionalised men and women aged &amp;#x2265;65years.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: Generalised obesity and abdominal obesity increased among men and women from 1993...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4515/version/1

jlibSEDML - a Java library for working with SED-ML
Provedor de dados: 17
Autores: Richard Adams; Ion Moraru; Anuradha Lakshminaryana.
jlibSEDML is an open-source  Java library to support the emerging SED-ML standard to record the operations needed to run simulations and other operations on biochemical models. It is compatible with level 1 version 1 of the specification and is available from http://sourceforge.net/projects/jlibsedml
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4965/version/1

Coincidence between transcriptome analyses on different microarray platforms using a parametric framework
Provedor de dados: 17
Autores: Tomokazu Konishi; Fumikazu Konishi; Shigeru Takasaki; Kohei Inoue; Kouji Nakayama; Akihiko Konagaya.
A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1746/version/1

Internal conformation of the &amp;#x27;protein folding code&amp;#x27; inferred from empirical tertiary structural classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying &amp;#x27;protein folding code network&amp;#x27; is found to have one major, highly dominant &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4640/version/1

Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.  Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner.  A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/1

Worm Annotation in the UniProt Knowledgebase (UniProtKB)
Provedor de dados: 17
Autores: Duncan J. Legge; UniProt Consortium.
The nematode worm, _Caenorhabditis elegans_, was the first multicellular organism to be sequenced. Its genome was published in 1998, providing an impetus for gene and protein annotation. Recently, the genome of _C. briggsae_ has been sequenced. This has given bioinformaticans the opportunity to study comparative genomics between two highly similar organisms. Currently, there are 12 species of _Caenorhabditis_ in UniProtKB and over 700 nematode species, including some of interest to parasitology. Functional and sequence annotation from literature and sequence analysis tools are included in each curated record. _C. elegans_ has a relatively small genome size, short life span and a transparent body, making it ideal for knock-out/RNAi studies. Thus many _C....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3157/version/1

Inhibiton of NF&amp;#x3ba;B activation and aromatase activity by vanilloids: An in vitro and in silico study
Provedor de dados: 17
Autores: Suaib  Luqman; Abha  Meena; Laura  E. Marler; Tamara  P. Kondratyuk; John  M. Pezzuto.
Target-specific drugs, including natural products, offer promise for the amelioration of cancer and other human ailments with reduced side-effects. Capsaicin, the pungent ingredient present in chillies (Capsicum annuum L.), and capsazepine, a synthetic analogue of capsaicin (collectively referred to as vanilloids), are known to possess a variety of pharmacological and physiological properties. In our continuous effort to discover cancer chemopreventive agents from natural products, we investigated the effect of vanilloids on NF&amp;#x3ba;B activation with stably transfected 293/NF&amp;#x3ba;B-Luc human embryonic kidney cells induced by treatment with tumor necrosis factor (TNF&amp;#x3b1;), and aromatase activity. Capsaicin and capsazepine blocked...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6913/version/1

GUDMAP - An Online GenitoUrinary Resource
Provedor de dados: 17
Autores: Chris Armit; Simon Harding; Jamie A. Davies; Jane Armstrong; Jane Brennan; Sue Lloyd-MacGilp; Derek Houghton; Mehran Sharghi; Xingjun Pi; Y. Cheng; Bruce Aronow; Kevin Gaido; Sean Grimmond; Peter Koopman; Jim Lessard; Melissa Little; Andy McMahon; Cathy Mendelsohn; Steve Potter; Michelle Southard-Smith; Duncan Davidson.
The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with gene expression data and tools to facilitate research (see &amp;#x22;www.gudmap.org&amp;#x22;:http://www.gudmap.org). The data provided by GUDMAP includes large _in situ_ hybridization screens (wholemount and section) and expression microarray analysis of components of the developing mouse urogenital system (including laser-captured material and FACS-isolated cells from transgenic reporter mice). In addition, a high-resolution anatomy ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3297/version/1

An evolutionary approach to Function
Provedor de dados: 17
Autores: Phillip Lord.
The distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for applying these definitions in practice.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3228/version/1

JSBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Andreas Dr&amp;#xe4;ger.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML&amp;#x27;s clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use&amp;#xd;&amp;#xa;library.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4986/version/1

A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7052/version/1

Novel developments in SBGN-ED and applications
Provedor de dados: 17
Autores: Tobias Czauderna; Eva Grafahrend-Belau; Astrid Junker; Anja Hartmann; Matthias Klapperst&amp;#xfc;ck; Falk Schreiber.
Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.&amp;#xd;&amp;#xa;We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6415/version/1

The Systems Biology Markup Language (SBML) Level 2 Version 2
Provedor de dados: 17
Autores: Michael Hucka; Sarah M. Keating.
The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. SBML is by no means a perfect format, but it has achieved widespread acceptance as a de facto standard. It is supported worldwide by over 100 software systems (both open-source and commercial). The broad acceptance of a common, open format for exchanging models between software tools is a crucial step towards wider use of quantitative modeling in biology, because it allows...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/19/version/1

General updates about SBML and SBML Team activities
Provedor de dados: 17
Autores: Michael Hucka.
In this presentation, I summarize very briefly some recent updates to SBML.org, SBML development, and software from the SBML Team.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6345/version/1

An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Provedor de dados: 17
Autores: Todd A. Castoe*; A.P. Jason de Koning*; Hyun-Min Kim; Wanjun Gu; Brice P. Noonan; Zhi J. Jiang; Christopher L. Parkinson; David D. Pollock.
Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2123/version/1

Wormbase Curation Interfaces and Tools
Provedor de dados: 17
Autores: Xiaodong Wang.
Curating biological information from the published literature can be time- and labor-intensive  especially without automated tools. WormBase1 has adopted several curation interfaces and tools, most of which were built in-house, to help curators recognize and extract data more efficiently from the literature.  These tools range from simple computer interfaces for data entry to employing scripts that take advantage of complex text extraction algorithms, which automatically identify specific objects in a paper and presents them to the curator for curation. By using these in-house tools, we are also able to tailor the tool to the individual needs and preferences of the curator. For example, Gene Ontology Cellular Component and gene-gene interaction curators...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5112/version/1

Open Source Drug Discovery
Provedor de dados: 17
Autores: Jyoti Yadav; OSDD  Consortium.
Tuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected with TB bacilli every second. Overall, one-third of the world&amp;#x27;s population is currently infected with the TB bacillus. Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome sequence of the causative pathogen _Mycobacterium tuberculosis_ was published about a decade ago and many years of painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting protection....
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2537/version/1

1st INCF Workshop on Global Portal Services for Neuroscience
Provedor de dados: 17
Autores: Jaap van Pelt; Gordon  Shepherd.
The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated portal services.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1779/version/1

Phyloinformatics in the age of Wikipedia
Provedor de dados: 17
Autores: Roderic Page.
This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon&amp;#x27;s scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4583/version/1

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/3

Origin and diversification of steroids: Co-evolution of enzymes and nuclear receptors
Provedor de dados: 17
Autores: Michael E. Baker.
Recent sequencing of amphioxus and sea urchin genomes has provided important data for understanding the origins of enzymes that synthesize adrenal and sex steroids and the receptors that mediate physiological response to these vertebrate steroids.  Phylogenetic analyses reveal that CYP11A and CYP19, which are involved in the synthesis of adrenal and sex steroids, first appear in the common ancestor of amphioxus and vertebrates.  This correlates with recent evidence for the first appearance in amphioxus of receptors with close similarity to vertebrate steroid receptors.  Other CYP450 enzymes involved in steroid synthesis can be traced back to invertebrates, in which they have at least two functions: detoxifying xenobiotics and catalyzing the synthesis of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4674/version/1

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification.   The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure.   Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4372/version/1

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Provedor de dados: 17
Autores: Jonathan M. J. Derry; Lara M. Mangravite; Christine Suver; Matt Furia; David  Henderson; Xavier  Schildwachter; Jonathan Izant; Solveig K. Sieberts; Michael R. Kellen; Stephen H. Friend.
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5883/version/1

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;&amp;#xd;&amp;#xa;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/3

Constraint-Guided Workflow Composition Based on the EDAM Ontology
Provedor de dados: 17
Autores: Anna-Lena Lamprecht; Stefan Naujokat; Bernhard Steffen; Tiziana Margaria.
Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain, in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how the ability to flexibly formulate domain-specific and problem-specific constraints supports the workflow development process.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5397/version/1

UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web
Provedor de dados: 17
Autores: Nicole Redaschi; UniProt Consortium.
The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework (&amp;#x22;http://www.w3.org/RDF/&amp;#x22;:http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium&amp;#x27;s Semantic Web activities...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3193/version/1

Estimation of the Multiple Testing Burden for Genomewide Association Studies of Common Variants
Provedor de dados: 17
Autores: Itsik Pe&amp;#x27;er; Roman Yelensky; David Altshuler; Mark J. Daly.
Genomewide association studies are an exciting strategy in genetics, recently becoming feasible. While pioneering studies are being underway, it is already clear that the analytic issue of determining the significance of results presents a challenge to the wide community of researchers. Rather than each study engaging in independent evaluation, there is need in the community to have standards set for whole-genome significance. &amp;#xd;&amp;#xa;We have therefore undertaken the task of developing such standards, based on data collected with collaborators in the International Haplotype Map Consortium. We report an estimated burden of a million independent tests genomewide in Europeans, and twice that number in Africans. We further identify the sensitivity of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/359/version/1

Identification of potent inhibitors for p38&amp;#x3b4; MAPkinase of human through in silico analysis
Provedor de dados: 17
Autores: Naga Lakshmi M; Manne Munikumar; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
P38&amp;#x3b4; Mitogen activated protein kinase is a serine/threonine protein kinase that participates in signaling cascades, mediating cellular responses to cytokinines, UV radiation, hyperosmotic stress, inducing keratinocyte differentiation and regulating apoptosis. Over expression of p38&amp;#x3b4; leads to tumor development by impairing the ERK1/2 &amp;#x2013;AP1 pathway that is critically linked to the control of cell proliferation and tumorigenesis on skin which was experimentally proven in knockout mice. Therefore, herein, a computational approach was undertaken to design novel inhibitors against p38delta for effective cancer therapy. The tertiary structure of p38&amp;#x3b4; was retrieved from a protein databank and active sites were predicted from...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5459/version/1

Role of cardiac resynchronization therapy in the development of new-onset atrial fibrillation:  A single-center prospective study.
Provedor de dados: 17
Autores: Gaetano Santulli; Massimo Chiariello; Cristofaro d&amp;#x27;Ascia; Salvatore d&amp;#x27;Ascia.
Albeit several studies examined the association between cardiac resynchronization therapy (CRT) and atrial fibrillation (AF) in heart failure (HF), results are still unclear and quite conflicting. We thereby designed a single-center prospective study to determine whether CRT has a favorable effect on the incidence of new-onset AF in a homogeneous population of patients with non-ischemic idiopathic dilated cardiomyopathy and severe heart failure HF. We enrolled 58 patients, AF na&amp;#xef;ve when received CRT. After 1 year of follow-up our population was subdivided into responders (72.4%) and non (27.6%), so to compare the incidence of AF after 1, 2 and 3 years of follow-up in these two groups. Already after 1 year, there is a significant (p&amp;#x3c;0.05)...
Tipo: Manuscript
Palavras-chave: Ecology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7137/version/1

Studies on Utilizing the Three Famous International Index Systems to Evaluate Scientific Research Level of Higher Learning Institutions
Provedor de dados: 17
Autores: Xun Liu; Changyu  Huang; Wei-Liang Qian; Yong-Chang  Huang.
Science Citation Index (SCI), The Engineering Index (EI) and Index to Scientific &amp;#x26; Technical Proceeding (ISTP) are widely accepted and used to evaluate the scientific research level of higher learning institutions by many country&amp;#x27;s science and technology field currently. After research, we point out the blemishes in this method and put forward the problems that need to be noticed, and then, under current conditions, bring forward brand-new standard and method to estimate research level, efficiency, fund exploitation and so on. One shouldn&amp;#x27;t over-emphasize the total amount of papers collected in SCI, EI &amp;#x26; ISTP when evaluating the scientific research level of higher learning institutions, whereas using...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4835/version/1

Development of an Ontology of Microbial Phenotypes (OMP)
Provedor de dados: 17
Autores: Michelle Giglio; Chris Mungall; Peter Uetz; Lanlan Yin; Johannes Goll; Deborah Siegele; Marcus Chibucos; James Hu.
*Abstract*&amp;#xd;&amp;#xa;Phenotypic data are routinely used to elucidate gene and protein function in most organisms amenable to experimental manipulation. However, although phenotype ontologies exist for many eukaryotic model organisms, no standardized system exists for the capture of phenotypic information in bacteria. We propose to build an Ontology of Microbial Phenotypes and use it to annotate the prokaryotic model organism _Escherichia coli_.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;Phenotypes are the observable characteristics of an organism that result from the combination of a particular genotype and a particular environment, and thus are a basic and fundamental aspect of the biology of all organisms. The awesome power...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3639/version/1

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Provedor de dados: 17
Autores: I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable &amp;#x27;next-state functions&amp;#x27; is extended to a &amp;#x141;ukasiewicz Topos with an n-valued &amp;#x141;ukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6206/version/1

CellML + [CMISS | OpenCMISS]
Provedor de dados: 17
Autores: David P. Nickerson.
A brief introduction and comparison to the usage of CellML models in CMISS and OpenCMISS.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5896/version/1

Composition of Biochemical Networks using Domain Knowledge
Provedor de dados: 17
Autores: Martin Goodfellow; John Wilson; Ela  Hunt.
Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4966/version/1

The spread of antimalarial drug resistance: A mathematical model with practical implications for ACT drug policies
Provedor de dados: 17
Autores: Wirichada Pongtavornpinyo; Shunmay Yeung; Ian Hastings; Arjen Dondorp; Nicholas Day; Nicholas White.
Most malaria-endemic countries are implementing a change in antimalarial drug policy to artemisinin combination therapy (ACT). The impact of different drug choices and implementation strategies is uncertain. A comprehensive model was constructed incorporating important epidemiological and biological factors and used to illustrate the spread of resistance in low and high transmission settings. The model predicts robustly that in low transmission settings drug resistance spreads faster than in high transmission settings, and that in low transmission areas ACTs slows the spread of drug resistance to a partner drug, especially at high coverage rates. This effect decreases exponentially with increasing delay in deploying the ACT and decreasing rates of...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1539/version/1

FieldML &amp;#x2013; a meta-language for field interchange
Provedor de dados: 17
Autores: Richard Christie; Poul M. F. Nielsen; Chris P. Bradley; Caton Little; Randall Britten; Peter J. Hunter.
FieldML is being developed as an XML standard for communicating computational field descriptions and data. Important principles in its design include building models from as few and as fundamental a set of concepts as necessary, supporting maximum reuse, and allowing the functional derivation of fields to be of unlimited complexity.&amp;#xd;&amp;#xa;This talk introduces concepts from the FieldML data model (at version 0.3), and demonstrates how they combine to describe rich field representations.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5901/version/1

ANN Based Virtual Classification Model for Discriminating Active and Inactive Withanolide E Analogs against  Human Breast Cancer Cell Line MCF-7
Provedor de dados: 17
Autores: Om Prakash; Feroz Khan; R.S. Sangwan.
Withanolides are a group of natural C-28 steroids built on an ergostane skeleton and classified into two major groups according to their structural skeleton: (a) compounds with a beta-oriented side chain and (b) compounds with an alpha-oriented side chain. Withanolide E represents one of the members of the latter group. Classification of active compounds on the basis of pharmacophore against specific cancer cell line poses a serious concern at the primary stage of virtual screening. To overcome this problem we have developed an artificial neural network based virtual screening model for discriminating active and non-active Withanolide-E-like derivatives or analogs against human breast cancer cell line MCF-7. In the present work, a 2D chemical descriptors...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6616/version/1

Waveomics: bringing experimental data to online collaboration
Provedor de dados: 17
Autores: Neil Swainston.
Systems biology offers an interdisciplinary approach to scientific research that typically involves the collaboration of teams of experimentalists and mathematical modellers. While the importance of data standards has been recognised in facilitating exchange of data between the parties, challenges still remain regarding the practicalities of disseminating experimental data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The introduction of novel web-based tools aimed at promoting collaborative work has provided a platform upon which scientific applications can be built. The recently released Google Wave protocol provides a facility for real-time collaboration between teams of researchers.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This work introduces a customized Robot that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4795/version/1

A Formal Ontology of Sequences
Provedor de dados: 17
Autores: Robert Hoehndorf; Janet Kelso; Heinrich Herre.
The Sequence Ontology is an OBO Foundry ontology that provides categories of sequences and sequence features that are applied to the annotation of genomes.  To facilitate interoperability with other domain ontologies and to provide a foundation for automated inference, we provide here an axiom system for the Sequence and Junction categories in first- and second-order predicate logics.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3537/version/1

Rice Genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Yuka Takahashi; Takao Asanuma; Yo  Shidahara; Shingo Sakaniwa.
In addition to maintaining a rice gene list, Oryzabase, a database of rice science, has also been hosting a website to submit newly identified genes. The current rice gene dictionary is based on a traditional rice trait gene dictionary and extended through time with new genes which are manually retrieved from journal articles. Currently over 4000 genes are listed. However it is still insufficient in both quantity and quality. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;   Recently we started to apply automated extraction before manual annotation to enhance the efficiency of gene extraction. To improve the quality of information, we started collecting relevant DNA accessions and LOCUS-ID. In Oryzabase, we try to employ the help of users to overcome this information...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5069/version/1

LipidMaps Core Update
Provedor de dados: 17
Autores: Shankar Subramaniam; Eoin Fahy.
LipidMaps (http://www.lipidmaps.org) is a multidisciplinary project involving multiple institutions. The goal of this project is to identify lipid metabolites and reconstruct pathways associated with lipids in mammalian cells using quantitative measurements of lipids in macrophage cells.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/23/version/1

Biopax and Semantics
Provedor de dados: 17
Autores: Ismael Navas-Delgado; Maria Jes&amp;#xfa;s Garc&amp;#xed;a-Godoy; Maria del Mar Rold&amp;#xe1;n-Garc&amp;#xed;a; Jos&amp;#xe9; F. Aldana-Montes.
Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in many cases. The use of large scale reasoners is a need to take advantage of these data sets.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6320/version/1

Designing Novel Lead Molecules For Human Ribosomal Protein S6 Kinase Beta-1 Involved In Cancers: Ligand Based Virtual Screening Approach
Provedor de dados: 17
Autores: Nainaru Ganesh; Dibyabhaba Pradhan; Amineni Umamaheswari.
Protein kinases are clinically relevant and attractive drug targets for most of the cancerous diseases. Ribosomal protein s6 kinase (P70s6 kinase) is a mitogen activated Ser/Thr protein kinase, essential for cell growth, G1 cell cycle progression and cell survival. Human P70s6 kinase is involved in different signaling pathways and phosphorylates the downstream S6 protein of the 40S ribosomal subunit there by controlling the translational activity. Over expression of human P70s6 or rapid amplification of gene (RPS6KB1) leads to rapid cell proliferation causing cancer in various organs of humans like colon, breast, ovary, etc. The over expression is principally due to activation of some phosphorylating sites or ATP binding sites in the domain regions. In the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4906/version/1

JSBML:  a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Marine Dumousseau; Andreas Dr&amp;#xe4;ger; Clemens Wrzodek; Alexander D&amp;#xf6;rr; Sarah M. Keating; Akiya Jouraku; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to its clearly defined specifications and the availability of libSBML, a portable, robust, and easy-to-use library.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API).  Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6718/version/1

Generating Homology Relationships by Alignment of Anatomical Ontologies
Provedor de dados: 17
Autores: Frederic Bastian; Gilles Parmentier; Marc Robinson-Rechavi.
The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at &amp;#x22;http://bgee.unil.ch/&amp;#x22;:http://bgee.unil.ch/
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3546/version/1

Human Cancer Cells Express Slug-based Epithelial-Mesenchymal Transition Gene Signature Obtained in Vivo
Provedor de dados: 17
Autores: Dimitris Anastassiou; Viktoria Rumjantseva; Wei-yi Cheng; Jianzhong Huang; Peter D. Canoll; Darrell J. Yamashiro; Jessica J. Kandel.
The biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT). Here we show that human cancer cells express in vivo a precise multi-cancer invasion-associated gene expression signature characterized by the prominent presence of collagen COL11A1 and thrombospondin THBS2. The signature is present in the expression of all solid tumor datasets that we analyzed and includes numerous EMT markers, among them the transcription factor Slug, fibronectin, and &amp;#x3b1; SMA. Using xenograft models of human cancer cells in immunocompromised mice and profiling the harvested tumors separately with species specific probes, we found that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6243/version/1

Taking shortcuts with OWL using safe macros
Provedor de dados: 17
Autores: Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland.
Accurate representation of complex domains such as biology demands powerful and expressive ontology languages such as OWL. However, the complex nested class expressions required for modeling can be a hindrance to ontology authoring and adoption. These class expressions can appear opaque to domain experts, and even users proficient in OWL can benefit from some kind of syntactic sugar or &amp;#x22;short-cut&amp;#x22; strategy, especially when authoring large ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;One solution is to have domain experts fill in simple templates (for example, in Excel) and translate the results into more complex axioms, but this has the disadvantage of being disconnected from full ontology authoring and reasoning...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5292/version/2

Unlocking biomarker discovery: Large scale application of aptamer proteomic technology for early detection of lung cancer
Provedor de dados: 17
Autores: Rachel M. Ostroff; William L. Bigbee; Wilbur Franklin; Larry Gold; Mike Mehan; York E. Miller; Harvey I. Pass; William N. Rom; Jill M. Siegfried; Alex Stewart; Jeffrey J. Walker; Joel L. Weissfeld; Stephen Williams; Dom Zichi; Edward N. Brody.
Lung cancer is the leading cause of cancer deaths, because ~84% of cases are diagnosed at an advanced stage. Worldwide in 2008, ~1.5 million people were diagnosed and ~1.3 million died &amp;#x2013; a survival rate unchanged since 1960. However, patients diagnosed at an early stage and have surgery experience an 86% overall 5-year survival. New diagnostics are therefore needed to identify lung cancer at this stage. Here we present the first large scale clinical use of aptamers to discover blood protein biomarkers in disease with our breakthrough proteomic technology. This multi-center case-control study was conducted in archived samples from 1,326 subjects from four independent studies of non-small cell lung cancer (NSCLC) in long-term tobacco-exposed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4537/version/1

Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system
Provedor de dados: 17
Autores: Marina Manrique; Pablo Pareja-Tobes; Eduardo Pareja-Tobes; Eduardo Pareja; Raquel Tobes.
We have annotated the  European outbreak E. coli EHEC genome sequenced by BGI (6-2-2011) and assembled with MIRA by Nick Loman (6-2-2011 ). Our system BG7, Bacterial Genome annotation of Era7 Bioinformatics, predicts ORFs and annotates them based on fragments of similarity with Uniprot proteins. We have predicted 6327 genes, 6156 encoding proteins y 171 corresponding to ribosomal and tRNA. Based on the preliminary results of our semi-automated method of annotation we have selected some predicted proteins with potential implications in pathogenicity and virulence.&amp;#xd;&amp;#xa;There are 33 predicted genes annotated as toxins and we have found three putative hemolysins: Hemolysin E, a putative hemolysin expression modulating protein and a channel...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6001/version/1

DNALinux Virtual Desktop Edition
Provedor de dados: 17
Autores: Sebastian Bassi; Virginia V. C. Gonzalez.
The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn&amp;#x27;t affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/670/version/1

Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems
Provedor de dados: 17
Autores: Bradly J. Alicea.
In this paper, a method for decoupling the neuromuscular function of a set of limbs from the role morphology plays in regulating the performance of an activity is introduced. This method is based on two previous methods: the rescaled range analysis specific to time series data, and the use of scaling laws. A review of the literature suggests that limb geometry can either facilitate or constrain performance as measured experimentally. Whether limb geometry is facilitatory or acts as a constraint depends on the size differential between arm morphology and the underlying muscle. &amp;#x22;Changes in size and shape&amp;#x22; are theoretically extrapolations of morphological geometry to other members of a population or species, to other species, or to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2845/version/2

ChEBI &amp;#x2013; an Open-access Chemistry Resource for the Life Sciences:&amp;#xb;Facilities for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis; Nico Adams; Adriano Dekker; Paula de Matos; Janna Hastings; Kenneth Haug; Duncan Hull; Zara Josephs; Gareth Owen; Steve Turner; Christoph Steinbeck.
ChEBI (Chemical Entities of Biological Interest) is a database of &amp;#x2018;small&amp;#x2019; molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5089/version/1

The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases
Provedor de dados: 17
Autores: Yasmin Alam-Faruque.
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submission and all experimental information relating to binary protein-protein&amp;#xd;&amp;#xa;interactions is entered into the IntAct database by curators, via a web-based editor. Interaction information is added to the SUBUNIT comment and the RP line of the relevant publication within the UniProtKB entry. There may be a single INTERACTION comment present within a UniProtKB entry, which conveys information relevant to binary protein-protein interactions. This is automatically derived from the IntAct database and is updated on a triweekly basis. Interactions can be derived by...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3936/version/1

Aligning the top-level of SNOMED-CT with Basic Formal Ontology
Provedor de dados: 17
Autores: William Hogan.
Effective translational research requires automated analysis of large datasets collected by multiple researchers working at multiple locations.  Reliable, machine interpretation of-&amp;#x2014;and reasoning with&amp;#x2014;-large datasets assembled at different times and places by different researchers requires standard representations of data.  These representations are controlled, structured vocabularies also known as ontologies.  By far, the most successful ontology is the Gene Ontology (GO), used by bioinformatics researchers to annotate genomics data.  However, to address the phenotype side of translational research will require annotation of electronic medical record data and clinical research data with a clinical-phenotype ontology analogous to GO....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2373/version/1

Using Ontology Fingerprints to Evaluate Genome-wide Association Results
Provedor de dados: 17
Autores: Lam Tsoi; Michael Boehnke; Richard Klein; Jim Zheng.
We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block.  We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3513/version/1

Binding Pattern Determination Of Class of Antifungal Drugs
Provedor de dados: 17
Autores: Arpit Tandon; A Naqvi; Nitin Chitranshi; Siddharth Sinha.
Crystal Structure of cytochrome p450 2B4 has 476 amino acids, through docking approach we have attempted to explain the specificity of CYP2B4, total 28 imidazole drug were used for the studies as antifungal drugs in which bound bifonazole (reference) shows the binding energy of -8.67 kcal/mol .Compound Miconazole shows the minimum binding energy of -10.45 kcal/mol. The 2B4-bifonazole structure identified 10 residues (ALA 298, GLY 299, GLU 301, THR 302, ILE 363, VAL 292) within 6.5 &amp;#xc5; of the active site of bifonazole. GLU 301, THR 302 are also located in 6.5 &amp;#xc5; of the bound ligand in 2B4 structure. Due to the presence of the multiple binding substrates in cytochrome p450, it acts as the major target of many drugs in xenobiotic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4314/version/1

Creating and improving detoxification pathways for interpretation of toxicogenomics data
Provedor de dados: 17
Autores: Pieter Giesbertz; Jonas Hummel; Stan Gaj; Danyel Jennen; Thomas Kelder; Chris Evelo; Joost van Delft; Jos Kleinjans.
Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4575/version/1

In Silico Docking Analysis of Peptide Deformylase (PDF) - A Novel Target for Prophylaxis of Leptospirosis
Provedor de dados: 17
Autores: Virupaksha A. Bastikar; Shweta R. Fulsundar; Jagdish S. Nair.
Peptide deformylase (PDF) is a metalloproteinase and executes an essential step in the maturation of proteins in eubacteria, by removing the formyl group from the N-terminal methionine residue of ribosome-synthesized polypeptides. This process is crucial for bacterial survival because mature proteins do not retain N-formyl-methionine, and all known N-terminal peptidases cannot utilize formylated peptides as substrate. Thus, inhibition of PDF is essential to obstruct the bacterial protein maturation process. Antibiotics based on PDF inhibition have the potential to provide the much needed antibacterial activity against most of the major drug-resistant pathogens. This study comprises an implementation of _in-silico_ techniques to validate and map the...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1520/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3913/version/2

Persistent BioPerl
Provedor de dados: 17
Autores: Hilmar Lapp.
I present BioSQL, a generic and highly extensible relational model for storing biological sequences, sequence clusters, genes, sequence features, sequence and feature annotation, and ontology terms. BioSQL also represents the interoperable persistence API among the Bio* life science programming toolkits (BioPerl, Biojava, Biopython, BioRuby), each of which has a language-binding to the BioSQL schema. I specifically present the Bioperl-db software, which in a transparent manner makes BioPerl objects persistent using BioSQL.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1233/version/1

Safe Functional Inference for Uncharacterized Viral Proteins
Provedor de dados: 17
Autores: Yaniv Loewenstein; Michal Linial.
The explosive growth in the number of sequenced genomes has created a flood of protein sequences with unknown structure and function. A routine protocol for functional inference on an input query sequence is based on a database search for homologues. Searching a query against a non-redundant database using BLAST (or more advanced methods, e.g. PSI-BLAST) suffers from several drawbacks: (i) a local alignment often dominates the results; (ii) the reported statistical score (i.e. E-value) is often misleading; (iii) incorrect annotations may be falsely propagated. &amp;#xd;&amp;#xa;Several systematic methods are commonly used to assign sequences with functions on a genomic scale. In Pfam (1) and resources alike, statistical profiles (HMMs) are built from...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2187/version/1

Using Biotic Interaction Networks for Prediction in Biodiversity and Emerging Diseases
Provedor de dados: 17
Autores: Christopher R. Stephens; Joaquin Gim&amp;#xe9;nez Heau; Camila Gonz&amp;#xe1;lez-Rosas; Carlos N. Ibarra-Cerde&amp;#xf1;a; Victor S&amp;#xe1;nchez-Cordero.
Networks offer a powerful tool for understanding and visualizing inter-species interactions within an ecology. Previously considered examples, such as trophic networks, are just representations of experimentally observed direct interactions. However, species interactions are so rich and complex it is not feasible to directly observe more than a small fraction. In this paper, using data mining techniques, we show how potential interactions can be inferred from geographic data, rather than by direct observation. An important application area for such a methodology is that of emerging diseases, where, often, little is known about inter-species interactions, such as between vectors and reservoirs. Here, we show how using geographic data, biotic interaction...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1495/version/1

Food Physical Chemistry and Biophysical Chemistry (v2)
Provedor de dados: 17
Autores: I. C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/2

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology
Provedor de dados: 17
Autores: Frank Gibson; Paul  G. Overton; Tom V. Smulders; Simon R. Schultz; Stephen  J. Eglen; Colin D. Ingram; Stefano  Panzeri; Phil Bream; Evelyne  Sernagor; Mark Cunningham; Christopher Adams; Christoph Echtermeyer; Jennifer Simonotto; Marcus Kaiser; Daniel C. Swan; Marty Fletcher; Phillip Lord.
This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1720/version/1

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description and analysis of protein-protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over- or underpredict the interface itself and cannot discriminate active from less relevant parts.&amp;#xd;&amp;#xa;We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom&amp;#x27;s depth inside the nterface. Our analysis of 54 protein-protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Order coincides with residues that were found shielded from bulk water fluctuations in a...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/version/2

2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/2

The development of a simple basal area increment model
Provedor de dados: 17
Autores: Georg Erich Kindermann.
In most cases forest practice in Austria use yield tables to predict the growth of their forests. Common yield tables show the increment of pure even-aged stands which are treated in a way the table developer recommends. The usage of these tables in stands which are either uneven-aged, mixed or treated in another way, may lead to inaccurate predictions. To avoid these problems, forest growth models have been developed. Until now they are not widely used in Austria. One reason may be, that most of the models need some input parameters which are usually not gathered by companies. In this work a basal area increment per hectare model has been developed which is based on the input parameters: diameter at breast height, height to diameter ratio, top height at...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6301/version/1

Transcriptional memory emerges from cooperative histone modifications
Provedor de dados: 17
Autores: Hans Binder; Lydia Steiner; Thimo Rohlf; Sonja Prohaska; Joerg Galle.
Background&amp;#xd;&amp;#xa;Transcriptional regulation in cells makes use of diverse mechanisms to ensure that functional states can be maintained and adapted to variable environments; among them are chromatin-related mechanisms. While mathematical models of transcription factor networks controlling development are well established, models of transcriptional regulation by chromatin states are rather rare despite they appear to be a powerful regulatory mechanism.&amp;#xd;&amp;#xa;Results&amp;#xd;&amp;#xa;We here introduce a mathematical model of transcriptional regulation governed by histone modifications. This model describes binding of protein complexes to chromatin which are capable of reading and writing histone marks. Molecular interactions between...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6507/version/1

A Systems Biology Approach to the Evolution of Codon Use Pattern
Provedor de dados: 17
Autores: Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson.
The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6312/version/1

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
Introduction: MR techniques have delivered images of a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007). In order to address one of the potential reasons behind this, we tested various automated segmentation streams (using CARET, FSL and lab-written code) that have been mainly designed for applications in humans, with the aim of optimizing them for comparisons across multiple species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: T1-weighted MR images from individuals representing 11 primate species have been acquired by Rilling and Insel...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/1

Ontology-Based Queries over Cancer Data
Provedor de dados: 17
Autores: Alejandra Gonzalez-Beltran.
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such as caGrid, support access to distributed information annotated with a domain ontology. However, caGrid&amp;#x27;s current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources&amp;#x2019; metadata and a query rewriting and translation process based on reasoning, which converts a query at the...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5406/version/1

H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Bruce R. Boynton; Jeffery Tjaden; Kenneth C. Earhart; Moustafa M. Mansour; Nasr M. ElSayed; A I. Nayei; A A. Abdelghani; Hala M. Essmat; Elassai M. Labib; E Ayoub; Mona M. Aly; A-SA Arafa; Marshall R. Monteville.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/553/version/1

Comparative Enumeration Gene Expression
Provedor de dados: 17
Autores: Leonardo Varuzza; Carlos A. D. E. B. Pereira.
This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS.  It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/1

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Does your research area re-use shared datasets?&amp;#xd;&amp;#xa;*   Re-using data has many benefits, including research synergy and efficient resource use&amp;#xd;&amp;#xa;*   Some research areas have tools, communities, and practices which facilitate re-use&amp;#xd;&amp;#xa;*   Identifying these areas will allow us to learn from them, and apply the lessons to areas which underutilize the sharing and re-purposing of scientific data between investigators&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Which datasets?&amp;#xd;&amp;#xa;This preliminary analysis examines the re-use of microarray gene expression datasets. Thousands of microarray gene expression datasets have been deposited in publicly available databases. &amp;#xd;&amp;#xa;Many studies reuse this data,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/3

SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database
Provedor de dados: 17
Autores: Maxwell L. Neal; Herbert M. Sauro.
Summary: The SBML Reaction Finder (SRF) application leverages the deep semantic annotations in the BioModels database to provide efficient retrieval and extraction of individual reactions from SBML models. We hope that the SRF will be useful to quantitative modelers who seek to accelerate their modeling efforts by reusing previously published representations of specific chemical reactions.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Availability and Implementation: The SRF is open source, coded in Java, and distributed under the Mozilla Pubic License Version 1.1. Windows, Macintosh and Linux distributions are available for download at &amp;#xd;&amp;#xa;http://sourceforge.net/projects/sbmlrxnfinder.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7028/version/1

Bogoch Replikins Pandemic Prevention: Increase of Strain-Specific Influenza Genomic Replikin Counts, Having Predicted Outbreaks and their Location Seven Times Consecutively, Up to Two Years in Advance, Provides Time for Prevention of Pandemics
Provedor de dados: 17
Autores: Samuel     Bogoch; Elenore S. Bogoch.
Earlier studies have shown that the increased concentration of a new class of virus genomic peptides, Replikins, precedes and predicts virus outbreaks. We now find that the area in the genome of the highest concentration of Replikins, and the country in which this peak exists in scout viruses, have permitted in the past five years seven consecutive accurate predictions of the geographic localization of coming outbreaks, including those now realized in Mexico for H1N1, and in Cambodia for H5N1. Real-time Replikin analysis of the evolution of the virus genome identified both mutations and structural reorganization of the hemagglutinin and p B1 genes over several years before each outbreak. This information, together with the specific Replikin sequences so...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6952/version/1

The Data Sharing Challenge. Learning Community From Consortia
Provedor de dados: 17
Autores: Winston Hide; Gabriel Altshuler; Oliver Hofmann; Kimberly Begley.
Today&amp;#x2019;s data generation and analysis environment is changing rapidly as the lure of technologies provide new opportunities to laboratory scientists. From physicians seeking rapid translation to the bedside, to environmentalists seeking new paradigms to understand the biome - large scale data generation is everywhere. How do we overcome the challenges of curation, management, interpretation and sharing of these data in the new multidisciplinary environment? One key approach is to leverage the expertise inherent in existing systems - bringing together tools and paradigms that work in subfields, and making them work together for the consortium. We will discuss the stem cell discovery engine. The approach brings together leading experts in stem cell...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5090/version/1

Quest for the descent of the Escherichia coli outbreak strain TY2482 &amp;#x2013; out of Germany?
Provedor de dados: 17
Autores: Tiruvayipati S. Avasthi; Narender Kumar; Ramani Baddam; Singamaneni H. Devi; Lothar H. Wieler; Niyaz Ahmed.
The recent outbreak of the Escherichia coli infection in north Germany reportedly has killed 35 people and sickened about 4000. Infections were reported in 2001 and 2002 in Germany and Central Africa respectively. In order to dissect all possible connections among the three infection/outbreak strains and to extract the most virulent genes responsible for the augmented  pathogenicity of the present German strain (2011), whole genome sequence data of the two isolates (E. coli TY_2482 &amp;#x26; LB226692) were analyzed. We report that the German outbreak strain isolated in 2011 is a seasoned clone of the 2002 isolate sequenced from Central Africa (55989) and perhaps a direct descendent of the German EAEC strain reported in 2001 infection cases.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6034/version/1

Simple reverse genetics approach to elucidating the biosynthetic pathway of complex thiopeptide nocathiacin
Provedor de dados: 17
Autores: Maochen Wei; Jing Deng; Shuzhen Wang; Nan Liu; Yijun Chen.
Biothythetic pathway of the most drugable thiopeptide nocathiacin has been elucidated by applying reverse genetics method based on its structural features. The present study provides an efficient approach for an easy access to the biosynthetic gene clusters of complex bioactive peptides that are ribosomally synthesized with extensive posttranslational modifications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4740/version/1

Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The evolution of H5N1 has attracted significant interest 1-4 due to linkages with avian 5,6 and human infections 7,8.  The basic tenets of influenza genetics 9 attribute genetic drift to replication errors caused by a polymerase complex that lacks a proof reading function.  However, recent analysis 10 of swine influenza genes identifies regions copied with absolute fidelity for more than 25 years.  In addition, polymorphism tracing of clade 2.2 H5N1 single nucleotide polymorphisms identify concurrent acquisition 11 of the same polymorphism onto multiple genetic backgrounds in widely dispersed geographical locations.  Here we show the aggregation of regional clade 2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa onto a human Nigerian H5N1...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/1

Extracting Functional Modules from Biological Pathways
Provedor de dados: 17
Autores: Sihai D. Zhao; Yong Li.
It has been proposed that functional modules are the fundamental units of cellular function. Methods to identify these modules have thus far relied on gene expression data or protein-protein interaction (PPI) data, but have a few limitations. We propose a new method, using biological pathway data to identify functional modules, that can potentially overcome these limitations. We also construct a network of these modules using functionally relevant PPI data. This network displays the flow and integration of information between modules and can be used to map cellular function.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1457/version/1

Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function
Provedor de dados: 17
Autores: Makoto Shimada; Tsutomu Kanasashi.
Modern human populations are known to contain &amp;#x22;ancient haplotypes&amp;#x22; that originated from archaic humans by hybridization.  Some of them had been reported before the development of human genomic diversity databases, such as HapMap.  Consequently, some of them have no information about linkage disequilibrium (LD) regions.  Because genetic information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes.  One of these ancient haplotypes, haplotype X (_hX_) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low diversity within the cluster in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6737/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry Niman; Mona M. Aly; Abdel-Satar  Arafa; Nasr El-Sayed; Ahmed  E. Nayel; Ahmed  S. Abdelghani; Hala  M. Esmat; Gregory  A. Raczniak; Mensah  Agyen-Frempong; William  K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, Kuwait, and Ghana. These changes are not easily...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/459/version/4

Many in vivo  &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous &amp;#x27;protein folding codes&amp;#x27; can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the &amp;#x27;protein folding code&amp;#x27; is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/2

A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel Ega&amp;#xf1;a Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies  has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies&amp;#x27; Cell Type Ontology, is included as an illustration.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3479/version/1

In Silico Analysis To Explore Novel Inhibitors For Human Proto-oncogene Tyrosine Protein Kinase Src
Provedor de dados: 17
Autores: Nagapriya Mahanandi; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
The first oncogene and the first non receptor tyrosine kinase, Src, plays a key role in cell morphology, motility, proliferation and survival. Over expression of Src kinase activity disrupts the RAS pathway in signaling pathway, where it loses its ability to hydrolyse GTP and thus, leads to cancer. A wide range of evidences indicated that Src-signaling was important in the oncogenesis of prostate cancer and other tumours. Src-signaling is involved in androgen-induced proliferation of prostate cancer in cancer tissue of patients having castration-refractory prostate cancer. Once prostate cancer becomes castration-resistant, bone metastases become significant problem for which treatment options are limited. As Src is involved in multiple signaling pathways,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4905/version/1

Inference of population splits and mixtures from genome-wide allele frequency data
Provedor de dados: 17
Autores: Joseph K. Pickrell; Jonathan K. Pritchard.
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6956/version/1

BioSharing - standards, policies and communication in bioscience
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends exist in both the regulatory arena and commercial science.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioSharing catalogue (www.biosharing.org)...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6153/version/1

LabelHash: A Flexible and Extensible Method for Matching Structural Motifs
Provedor de dados: 17
Autores: Mark Moll; Lydia E. Kavraki.
There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Below, we will briefly describe LabelHash, a new method for partial structure comparison. In partial structure comparison, the goal is to find the best geometric and chemical similarity between a set of 3D points called a _motif_ and a subset of a set of 3D points called the _target_. Both the motif and targets are represented as sets of labeled 3D points. A motif is ideally composed of the functionally most-relevant residues...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2199/version/1

Using a data triangle to understand molecular nutrition
Provedor de dados: 17
Autores: Chris T. Evelo.
Until recently nutrigenomics was mainly about transcriptomics related data. That already confronted us with overwhelming analytical problems. We learned to mathematically and statistically treat genome wide expression studies and studies directed to gene expression regulation. Nutrigenomics researchers had to become bilingual speaking: English and R1 and learned to think about co-expression, clusters and false discovery rates. The latter in fact proofed to be a trap. Removing all the false positives made us loose the information we were really interested in. To understand the results of our genomics experiments we often had to confront what we were measuring with what we already knew. After all false positives are not likely to all be related to the same...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5689/version/1

Towards an Open Taxonomy
Provedor de dados: 17
Autores: Roderic Page.
Taxonomy is in many ways still predigital. Most taxonomic databases are little more than digitized index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitizing efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an &amp;#x22;Open Taxonomy.&amp;#x22; The first step towards this goal is digitally linking scientific names to the primary...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6560/version/1

Marked Rise in Replikin Counts in H5N1 Influenza Virus Localized to Lethality Gene p B1.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Abstract: Virus outbreaks have been found to be related to the concentration of a new class of genomic peptides, Replikins^1^. The eight genes of H5N1 influenza virus were analyzed for the distribution of Replikin Counts (number Replikins /100 amino acids) in 2,441 sequences from birds and humans. An increase (p&amp;#x3c;0.001) occurred from 2004 to August 2011 in one gene, pB1.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6420/version/1

AntEpiSeeker2.0: extending epistasis detection to epistasis-associated pathway inference using ant colony optimization
Provedor de dados: 17
Autores: Yupeng Wang; Xinyu Liu; Romdhane Rekaya.
Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6994/version/1

Bioinformatics for Human Proteomics: Current State and Future Status
Provedor de dados: 17
Autores: Amos Bairoch.
We are entering a new era in the exploration of the human proteome.&amp;#xd;&amp;#xa;Advances in technologies are allowing researchers to map with a much&amp;#xd;&amp;#xa;better resolution and improved accuracy this very complex universe. Such&amp;#xd;&amp;#xa;an exploration also requires a compendium of adequate bioinformatics&amp;#xd;&amp;#xa;tools, data repositories and knowledge resources. We are going to describe&amp;#xd;&amp;#xa;what are the state of the art in term of data and knowledge resources for&amp;#xd;&amp;#xa;human proteins: from repositories of proteomics data such as PRIDE,&amp;#xd;&amp;#xa;PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and&amp;#xd;&amp;#xa;knowledgebase such as UniProtKB/Swiss-Prot....
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5050/version/1

Nuisance Signal in Resting-State fMRI Study
Provedor de dados: 17
Autores: Xi-Nian Zuo; Michael P. Milham.
We systematically presented various nuisance signals in resting-state fMRI (R-fMRI) dataset. First, we examined the impact of different extraction methods on the default-mode pattern seeded by posterior cingulate cortex (PCC). Second, we compared their differences in test-retest reliability. Finally, we speculated the equivalence of removing global mean signal to removing gray matter mean signal.
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4352/version/1

In silico Protein Structural Modeling and Active binding site Evaluation of Streptococcus pneumoniae
Provedor de dados: 17
Autores: M. Balakrishnan; R.C. Srivastava; M. Ramachandran.
Structure function relation of glucose kinese in Streptococcus pneumoniae. However, a solved structure for _Streptococcus pneumoniae_ glucose kinese is not available at the protein data bank. Glucose kinase is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression system. So, we created a model of glucose kinese from _Streptococcus pnemoniae_ using the X-ray crystallography structure of glucose kinese enzymes from _Enterobacteria faecalis_ as template with Molsoft ICM v3.5 software. The model was validated using protein structure checking tools such as PROCHECK, WHAT IF: for reliability. The active site amino acid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3207/version/1

Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7002/version/1

Metagenomic study of the human skin microbiome associated with acne
Provedor de dados: 17
Autores: Huiying Li.
The human microbiota contributes to our normal postnatal development and plays a significant role in defining our physiology. To understand the role of microbiota in human health and disease, we study the skin microbiome in pilosebaceous units (hair follicles) and its association with acne.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Acne is one of the most common skin diseases. Although its etiology still needs to be defined, a bacterial factor has been suggested in the development of the disease. In fact, antibiotic therapy targeting _Propionibacterium acnes_ has been a mainstay treatment for more than 30 years.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our preliminary study shows that the microcomedone, a specialized skin compartment where acne arises, has a tractable...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5305/version/1

Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take into account their natural variability throughout the dynamic range. When the number of replicates is small, error  modeling is needed to achieve statistical power. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Availability: A free open-source...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/1

Interoperable Semantic Web services (Tutorials)
Provedor de dados: 17
Autores: Mat&amp;#xfa;&amp;#x161; Kala&amp;#x161;; Jon Ison.
Life-scientific Web services are increasingly available and diverse. Their semantic interoperability is crucial to enable automated workflow construction and efficient searching for the right service. At the same time, smooth programmatic access must be possible with all the main programming, scripting, or workflow languages.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This tutorial gave an introduction to the &amp;#x22;SAWSDL&amp;#x22;:http://www.w3.org/standards/techs/sawsdl#w3c_all standard for semantic annotation of Web services and XML Schemas; the &amp;#x22;EDAM&amp;#x22;:http://edamontology.sourceforge.net ontology for describing bioinformatics tools; and &amp;#x22;BioXSD&amp;#x22;:http://bioxsd.org as a canonical data model for bioinformatics Web services....
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5565/version/1

Curation of NISEED, an integrative framework for the digital representation of embryonic development
Provedor de dados: 17
Autores: Delphine Dauga; Olivier Tassy; Fabrice Daian; Daniel Sobral; Patrick Lemaire.
NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution.  In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its...
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3168/version/1

The Normal Fetal Heart Rate Study: Analysis Plan
Provedor de dados: 17
Autores: Martin Daumer; Michael Scholz; Anne-Laure Boulesteix; Stephanie Pildner von Steinburg; Sven Schiermeier; Wolfgang Hatzmann; K T M Schneider.
Recording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/980/version/1

Data, Databases, and Communities
Provedor de dados: 17
Autores: Matthew Day.
Overview&amp;#xd;&amp;#xa;* Publishing landscape and challenges&amp;#xd;&amp;#xa;* Nature gateways and databases&amp;#xd;&amp;#xa;* NCI-Nature Pathway Interaction Database&amp;#xd;&amp;#xa;* A few other communication tools
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2884/version/1

Network-based analyses of Huntington&amp;#x2019;s Disease
Provedor de dados: 17
Autores: Ravi K. Kalathur; Matthias  E. Futschik.
The use of high-throughput technologies has provided us with large amounts of data for _Huntington&amp;#x27;s disease_ (HD), especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a network-based approach.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: To analyse and visualise protein interaction networks through a dedicated database to HD, we have established &amp;#x22;HDNetDB&amp;#x22;: http://hdnetdb.sysbiolab.eu. This platform will not only help to understand molecular mechanisms better, but also assist in identifying potential molecular markers...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7090/version/1

Fundamentals of Molecular Biology
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present some basic concepts of molecular biology and the related open problems.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7121/version/1

MitoWheel, visualizing the  human mitochondrial genome
Provedor de dados: 17
Autores: G&amp;#xe1;bor  Zsurka; Attila Csord&amp;#xe1;s.
So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at &amp;#x22;http://mitowheel.org&amp;#x22;:http://mitowheel.org.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3167/version/1

Genome Replikin Count Predicts Increased Lethality of Cancer
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Those cancers, like thyroid and pancreatic cancer, with the lowest 5-year mortality rates, have Replikin Counts of about 20; lung and brain cancers, with the highest 5-year mortality rates, have Replikin Counts of 275 and 325 respectively; the others fall in between with approximate linearity. This is the first quantitative relationship of a genomic structure, Replikins, to 5-year mortality rates.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7143/version/1

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Samuel V. Angiuoli; W. Florian  Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR-Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/1

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu Mi; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/3721/version/4

Autism-associated SNPs in the clock genes _npas2_, _per1_ and the homeobox gene _en2_ alter DNA sequences that show characteristics of microRNA genes.
Provedor de dados: 17
Autores: Brad Nicholas; Michael J. Owen; Dawn C. Wimpory; Thomas Caspari.
Intronic single nucleotide polymorphisms (SNPs) in the clock genes _npas2_ and _per1_ and the homeobox gene _en2_ are reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated SNPs rs1861972 and rs1861973 in _en2_, rs1811399 in _npas2_, and rs885747 in _per1_, shows that these regions encode RNA transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted _in silico_ by the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated in autism...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2366/version/1

A novel predicted calcium-regulated kinase family  implicated in neurological disorders
Provedor de dados: 17
Autores: Ma&amp;#x142;gorzata Dudkiewicz; Anna Lenart; Krzysztof Paw&amp;#x142;owski.
Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7015/version/1

A Database for TSSs of Human MicroRNAs
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3&amp;#x27;-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6832/version/1

Entropic Landscape: the method to predict folding patterns and regional stability of proteins
Provedor de dados: 17
Autores: Kentaro Onizuka.
I propose a new method to calculate the entropy of a given protein sequence fragment. The set of fragment entropies over all possible fragments of the given sequence shows which region of the sequence is statistically stable and which region has a strong desire to fold into particular conformations. Here are three methods to calculate fragment entropy, the results from each of which represent entropies of different stage of protein folding.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2972/version/1

PrOCoil - Advances in predicting two- and three-stranded coiled coils
Provedor de dados: 17
Autores: Carsten C. Mahrenholz*; Ingrid G. Abfalter*; Ulrich Bodenhofer; Rudolf Volkmer; Sepp Hochreiter.
*Overview* | Coiled coils are usually described as consisting of two up to seven &amp;#x3b1;-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.&amp;#xd;&amp;#xa;Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4677/version/1

A prelude report on molecular docking of HER2 protein towards comprehending anti-cancer properties of saponins from Solanum tuberosum
Provedor de dados: 17
Autores: Puneet  K. Singh; Pratyoosh Shukla.
Saponins are extensively known for many biological activities e.g. antimicrobial, anti-palatability, anti-cancer and hemolytic. As cancer cells have a more cholesterol-like compound in their membrane structure the saponins bind cholesterol due to their natural affinity to bind cancer cell membrane. This prevents them from entering the body through the intestinal tract, where they have the ability to attach themselves to vital organs and grow. This study reports the effective use of lower dose saponins like immunotoxin so that they can inhibit the proliferation of cancerous pancreatic cells. The investigation of pancreatic cancer metabolic pathway it was found that proteins 3H3B produced by genes HER-2 are involved in the enhancement of this type of cancer....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7147/version/1

1st INCF Workshop on NeuroImaging Database Integration
Provedor de dados: 17
Autores: Lars  Forsberg; Per Roland.
The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of database federations. The report includes several recommendations for future developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1781/version/1

Toxicity prediction of anti tuberculosis active molecules
Provedor de dados: 17
Autores: Sajeev  R; Abdul  Jaleel.U.C.
Abstract&amp;#xd;&amp;#xa;The aim of the work was to understand the toxicity, physically significant descriptors and pharmaceutically relevant properties of some imidazoles obtained from the open sources that may found to be active against tuberculosis. At present five azoles were modeled for the prediction and calculation of descriptors that were carried out by means of computational approach [1].&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6236/version/1

Envelope protein as molecular target for YFV (Yellow fever virus) drug discovery
Provedor de dados: 17
Autores: Manne  Munikumar; Dibyabhaba Pradhan; I. Vani Priyadarshini; Amineni Umamaheswari.
Yellow fever (YF), a mosquito-borne viral haemorrhagic fever, is one of the most lethal viral diseases. Despite the availability of vaccines, yellow fever virus (YFV) strikes an estimated 2, 00,000 persons world-wide each year and causes 30,000 deaths approximately. There are no approved antiviral therapies for the treatment of YFV disease in humans. YFV 17D strain RNA genome is of 10,862 nucleotides, which encodes three structural proteins (C, PrM, and E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Identification of different protein functions facilitates a mechanistic understanding of YFV infection and opens novel means for drug development. Functional assignment of complete YFV proteome was done through support Vector...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5151/version/1

ProbCD: enrichment analysis accounting for categorization uncertainty
Provedor de dados: 17
Autores: Ricardo V&amp;#xea;ncio; Ilya Shmulevich.
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for&amp;#xd;&amp;#xa;the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/369/version/1

The Importance of Modularity in Bioinformatics Tools
Provedor de dados: 17
Autores: Martina Kutmon; Martijn P. van Iersel; Thomas Kelder; Chris T. Evelo.
In the last decade the amount of Bioinformatics tools has increased enormously. There are tools to store, analyse, visualize, edit or generate biological data and there are still more in development. Still, the demand for increased functionality in a single piece of software must be balanced by the need for modularity to keep the software maintainable. In complex systems, the con&amp;#xfb02;icting demands of features and maintainability are often solved by plug-in systems.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For example Cytoscape, an open source platform for Complex-Network Analysis and Visualization, is using a plug-in system to allow the extension of the application without changing the core. This not only allows the integration of new functionality...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6113/version/1

Simple SVM based whole-genome segmentation
Provedor de dados: 17
Autores: Justin Bedo; Geoff Macintyre; Izhak Haviv; Adam Kowalczyk.
We present a support vector machine (SVM) based framework for DNA segmentation into binary classes. Two applications are explored: transcription start site prediction and transcription factor binding prediction. Experiments demonstrate our approach has significantly better performance than other methods on both tasks.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3811/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/2

First steps towards WikiPathways RDF
Provedor de dados: 17
Autores: Andra Waagmeester.
This presentation presents the first steps in modeling WikiPathways content in RDF. WikiPathways is stored in a proprietary GPML format. By modeling this data in RDF, semantic web features become available to WikiPathways content.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6300/version/1

The Systems Biology Markup Language (SBML): Where It&amp;#x27;s Been and Where It&amp;#x27;s Going
Provedor de dados: 17
Autores: Michael Hucka.
A cornerstone of systems biology is the use of computational modeling, by which hypotheses can be cast into a quantitative form that can be tested systematically.  The use of computational modeling by biologists promises to pave the way for more rigorous analyses of biological functions, and ultimately will lead to new and better treatments for disease.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A crucial enabler for more widespread use of computational modeling in biology is reaching agreement on how to represent, store, and communicate models between software tools. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models in biology.  By supporting SBML as an input and output...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/21/version/1

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, changes in the input should equal changes in the output within any specific period of time. What I...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6741/version/2

A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/2

Omics Data Sharing - BioSharing: on Data Policies&amp;#x2019;s Plans and Reporting Standards
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Several data preservation, management and sharing policies have emerged in response to increased funding for high-throughput approaches in major genomics and functional genomics bioscience domain; and nowadays, several funding agencies also require inclusion of data-sharing plans in grant applications. But despite some commonalities, the policies are heterogeneous by nature, given the different types of communities served and the data types they generate. In parallel, an escalating number of community-driven standardization efforts (including biocurators, database developers and experimentalists, vendors etc), operate to develop minimal requirements checklists, ontologies, and file-formats to support the harmonization of the reporting process, so that...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5049/version/1

HTself2: Combining p-values to Improve Classification of Differential Gene Expression in HTself
Provedor de dados: 17
Autores: Daniel A. Cortez; Angela P. Tonon; Pio Colepicolo; Ricardo Z. N. V&amp;#xea;ncio.
HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression for low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. The method was previously described in V&amp;#xea;ncio et al, (DNA Res. 12: 211- e 214, 2005). In this work we consider an extension of HTself by calculating p-values instead of using a fixed credibility level &amp;#x3b1;. As before, the statistic used to compute single spots p-values is obtained from the gaussian Kernel Density Estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent p-values which can be...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4855/version/1

ArrayMining.net: a  web-server for integrative microarray and gene set analysis
Provedor de dados: 17
Autores: Enrico Glaab; Jonathan M. Garibaldi; Natalio Krasnogor.
DNA microarray experiments provide a means to understand cancer and genetic diseases on a molecular level, improve diagnosis and identify new drug targets. However, choosing appropriate data processing methods and parameters is a difficult and time-consuming task, particularly for researchers without prior experience in this field. &amp;#xd;&amp;#xa;We present *ArrayMining.net*, a free web-service for automatic microarray analysis to address these issues. ArrayMining.net covers several major areas in statistical microarray analysis - Feature Selection, Clustering, Prediction, Gene Set and Network Analysis - providing access to several algorithms for each of these tasks based on a single, easy-to-use interface.
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5552/version/1

The Gene Ontology Annotation (GOA) Database
Provedor de dados: 17
Autores: Rachael Huntley; Emily Dimmer; Daniel Barrell; David Binns; Rolf Apweiler.
The Gene Ontology (GO) is a well-established, structured vocabulary that has been successfully used for 10 years in the annotation of proteins. GO terms, created in consultation with the biology community, are used to replace the multiple nomenclatures used by scientific databases that can hamper data integration. Currently GO consists of more than 26,500 terms distributed over three ontologies that describe the molecular function, biological process and subcellular location of a protein in a generic cell.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The Gene Ontology Annotation (GOA) database (&amp;#x22;http://www.ebi.ac.uk/GOA&amp;#x22;:http://www.ebi.ac.uk/GOA) aims to provide high-quality manual and electronic GO annotations to proteins within the UniProt...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3154/version/1

Community content building for evolutionary biology: Lessons learned from LepTree and Encyclopedia of Life
Provedor de dados: 17
Autores: Cynthia Parr; Dana Campbell; John Park.
Online resources to aid large-scale ecological and evolutionary biology are beginning to take root, only a decade behind fields such as genomics and molecular biology. One barrier has been a long tradition, in evolutionary biology at least, of work by individuals on the order of a few hundred of species rather than the thousands or hundreds of thousands necessary to understand the general evolutionary or ecological processes that explain species characteristics and distributions. Advances in collaborative and semantic software offer promise &amp;#x2013; it should be possible to develop high quality online species-level datasets for comparative analyses and even to integrate, via machine reasoning, across highly customized datasets. In this talk we will...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4603/version/1

Envisioning a data reuse registry
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Repurposing research data holds many benefits for the advancement of biomedicine, yet is very difficult to measure and evaluate. We propose a data reuse registry to maintain links between primary research datasets and studies that reuse this data. Such a resource could help recognize investigators whose work is reused, illuminate aspects of reusability, and evaluate policies designed to encourage data sharing and reuse.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2152/version/1

Astrobiological Perspectives on Consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5286/version/1

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I. C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related pathways referred to as networks.&amp;#xd;&amp;#xa;The variable biotopology of such dynamic networks is highly complex, and has a number of interesting properties that can be formally characterized at one level of organization by mathematical structures called &amp;#x27;biogroupoids&amp;#x27;. &amp;#xd;&amp;#xa;One such family of pathways contains the cell cyclins. Cyclins are proteins that link several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6205/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6271/version/1

Metarel: An Ontology to Support the Inferencing of Semantic Web Relations within Biomedical Ontologies
Provedor de dados: 17
Autores: Ward Blond&amp;#xe9;.
Metarel allows the creation of millions of relational inferences in the RDF Knowledge Base BioGateway, by using five types of SPARUL closure queries. Metarel can be found at &amp;#x22;http://www.metarel.org&amp;#x22;:http://www.metarel.org.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3463/version/1

Computer aided drug design studies to explore novel antagonist of human myotrophin
Provedor de dados: 17
Autores: Sandeep Swargam; K Mahesh; Amineni Umamaheswari.
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy.  Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmalogical properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was persuaded in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schr&amp;#xf6;dinger software suite 2010 (maestro v9.1), docked...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6562/version/1

Signi&amp;#xfb01;cance tests for comparing digital gene  expression pro&amp;#xfb01;les
Provedor de dados: 17
Autores: Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira.
Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/3

Diffusion Approximations for Demographic Inference: DaDi
Provedor de dados: 17
Autores: Ryan N. Gutenkunst; Ryan D. Hernandez; Scott H. Williamson; Carlos D. Bustamante.
Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4594/version/1

Systems Biology Graphical Notation: Entity Relationship language Level 1
Provedor de dados: 17
Autores: Nicolas Le Nov&amp;#xe8;re; Stuart Moodie; Anatoly Sorokin; Falk Schreiber; Huaiyu Mi.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3719/version/1

Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the &amp;#x27;logic gate&amp;#x27; spectrum
Provedor de dados: 17
Autores: Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological &amp;#x27;logic gates&amp;#x27; having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6413/version/1

Nasal Bacterial Microbiome: Probing a Healthy Porcine Family
Provedor de dados: 17
Autores: Min Yue; Weicheng Bei; Huanchun Chen.
Upper respiratory tract (URT) infection caused the leading and devastating diseases in pigs. It was believed that the normal microbiome of URT plays a vital role in health and disease development. As the entry point of the URT, little knowledge of bacterial microbiome in porcine nasal was known. A cultivation-independent approach directly to 16s ribosomal RNA genes enabled us to reveal the nasal bacterial community, structure and diversity. Here, we found that an unprecedented 207 phylotypes were characterized from 933 qualified clones, indicating the variable, species richness but particularly dominant bacterial microbiome. The dominant species were from genus Comamonas and Acinetobacter, which constitute core normal bacterial microbiome in porcine nasal....
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6699/version/1

3DScape: three dimensional visualization plug-in for Cytoscape
Provedor de dados: 17
Autores: Qi Wang.
3DScape is the first plug-in which enables three-&amp;#xd;&amp;#xa;dimensional network visualization in Cytoscape. The extra dimension is useful in accommodating, visualizing, and distinguishing larger networks with multiple crossing connections.&amp;#xd;&amp;#xa;Special features in 3DScape include 3D layout algorithms, mapping onto 3D models and animation effects on a series of expression data. 3DScape is available at  http://www.rendware.com
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6094/version/1

Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences: Application to Estimation of Selection Bias in Protein (Human TP53) Evolution
Provedor de dados: 17
Autores: Wei Zhang.
Understanding of the mechanism of DNA mutation process is critical for studying the functional consequences of genetic variation in clinical medicine (eg. drug response) as well as other complex traits (eg. gene expression and cause of common diseases). During the last several decades, many probabilistic models of DNA nucleotide substitution have been proposed for studying this process. A common feature of these mutation models is that they assume the nucleotides evolve independently at each site. In other words, they are sequence context-independent models. However, based on various biochemical studies, it is now recognized that the DNA mutation process resulting in substitutions in both coding and non-coding regions may depend on sequence context. We...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1243/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Jeremy I. Posner; Seth Berger; Avi M. Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/2

MIRIAM Resources: next steps
Provedor de dados: 17
Autores: Camille Laibe.
This presentation gives a short introduction of MIRIAM Resources (&amp;#x22;http://www.ebi.ac.uk/miriam/&amp;#x22;:http://www.ebi.ac.uk/miriam/), a robust annotation and cross referencing framework, based on URNs.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The presentation also explains some potential issues with the current system and presents a possible solution.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Finally, the presentation introduces some forthcoming and suggested updates and extensions to the current infrastructure.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5130/version/1

NCBO Overview and Biositemaps
Provedor de dados: 17
Autores: Patricia L. Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6355/version/1

MMsPred: a bioactivity and toxicology predictive system
Provedor de dados: 17
Autores: Joel Masciocchi; Luca Pireddu; Ricardo Medda; Piergiorgio Palla; Matteo Floris; Luca Pani; Patricia Rodriguez-Tome.
In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption, distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could provide solutions to this problem.&amp;#xd;&amp;#xa;The goal of my research is to develop classifiers that accurately discriminate between active and inactive...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4188/version/1

The NCBO OBOF to OWL Mapping
Provedor de dados: 17
Autores: Dilvan A. Moreira; Christopher J. Mungall; Nigam H. Shah; Stuart Aitken; John-Day Richter; Timothy Redmond; Mark A. Musen.
Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3938/version/1

Development and application of molecular and bioinformatic tools for the genetic monitoring of wild beets
Provedor de dados: 17
Autores: Matthias Enders; Lothar  Frese; Marion Nachtigall.
Crop Wild Relatives (CWR) are an economically important plant genetic resource (PGR) for plant breeding. One strategy to conserve PGR in the natural habitat (in situ) is the genetic reserve technique. This approach protects the existing intraspecific diversity and allows, in contrast to the ex situ approaches, the emergence of new diversity. &amp;#xd;&amp;#xa;The genetic reserve conservation technique will be tested in practice with the Genus _Beta_ within the framework of the EU Project &amp;#x201c;AEGRO&amp;#x201d;. _Beta patula_ (Ait.) (BP) and _Beta vulgaris_ (L.) _maritima_ (Arcang.) (BVM) are used as models. Both species are important resources for sugar beet breeding. BP is a rare and endangered species with a very limited habitat. In contrast BVM...
Tipo: Presentation
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5742/version/1

A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Bruce E. Wilson; Jake F. Weltzin; the rest of the USA-NPN Protocol Development Team.
The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise&amp;#x2014;from backyard naturalists to professional scientists&amp;#x2014;to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify speci&amp;#xfb01;c single dates at which individual phenological events are observed, but the scienti&amp;#xfb01;c usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3695/version/2

Novel network pharmacology methods for drug mechanism of action identification, pre-clinical drug screening and drug repositioning
Provedor de dados: 17
Autores: Jianghui Xiong.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Here we present two methodology innovations on network pharmacology modeling. (1) We hypothesize that the gene network associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. We proposed a novel in vivo genetic interaction between genes as &amp;#x2018;synergistic outcome determination&amp;#x2019;, in a similar way to &amp;#x2018;synthetic lethality&amp;#x2019;. We scanned above genetic interactions based on microarray profiling for cancer prognosis, and identified a cluster of important yet epigenetically regulated gene modules. By...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6455/version/1

Direct submission system and literature annotation of rice genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Takao Asanuma; Yo Shidahara; Shingo Sakaniwa.
Oryzabase (&amp;#x22;http://www.shigen.nig.ac.jp/rice/oryzabase/&amp;#x22;:http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date, literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown genes...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3164/version/1

Annotation and Curation of the Protein Data Bank
Provedor de dados: 17
Autores: Jasmine Young; RCSB PDBj PDBe  Protein Data Bank.
The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological macromolecules. Established in 1971 with just seven structures, it presently includes more than 56,000 entries. To maintain the highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data annotation and the development of procedures, tools, and resources. Annotation-related issues, particularly those impacted by new developments&amp;#xd;&amp;#xa;in structural biology, are critically reviewed at in-person and virtual meetings regularly and frequently. Comprehensive documentation of the procedures, formats, and related data dictionaries used in data annotation are available at the wwPDB...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3379/version/1

The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein
Provedor de dados: 17
Autores: Burak Erman; Nazan Walpoth.
Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6678/version/1

1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy
Provedor de dados: 17
Autores: Mihail Bota; Larry Swanson.
The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1780/version/1

Analysis of binding properties of VP2 protein of Human parvovirus B19 through in silico molecular docking
Provedor de dados: 17
Autores: Praneetha Amburu; Dibyabhaba  Pradhan; Vani  Priyadarshini; Munikumar Manne; Umamaheswari  Amineni.
Human parvovirus B19, a member of the Parvoviridae family, is a pathogen associated with a wide variety of diseases. Most commonly, it causes childhood rash erythema infectiosum, but in some cases more serious symptoms such as persistent arthropathy, critical failures of red cell production causing transient aplastic crisis, this infection in pregnancy causes hydrops fetalis and myocarditis. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation would provide role of viral proteome in its survival and pathogenic mechanisms. SVMProt functional family annotations of VP2 protein had deciphered its zinc-binding, coat protein, outer membrane, chlorophyll biosynthesis, DNA repair and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5289/version/1

Conservation Pakage for Modal Ecorace
Provedor de dados: 17
Autores: Ajit Kumar Sinha.
Conserving biodiversity is about genetic variety, species, habitats and ecosystems. All are important, but it is often most appropriate, practical and effective to focus on species. With modern conservation awareness, there is a welcome and popular commitment to maintaining the diversity of species in India. Nevertheless, over the last 50 years, we have witnessed the severe decline of many once widespread and familiar species, such as tropical Tasar silkworm Antherea mylitta D. Conservation is not just about avoiding extinctions, but about restoring or recovering species populations to secure levels and preventing other species from reaching such a perilous situation in the first place. Species, by their very nature, have specific ecological requirements....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6162/version/1

Charting the NF-kB pathway interactome map
Provedor de dados: 17
Autores: Paolo Tieri; Alberto Termanini; Elena Bellavista; Stefano Salvioli; Claudio Franceschi.
One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as &amp;#x201c;inflammaging&amp;#x201d;, negatively correlated with longevity. The five components of the Nuclear Factor kB (NF-kB) family are prominent mediators of inflammation. Several different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of this analysis is to provide a wider, systemic picture of such...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5266/version/1

Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
Provedor de dados: 17
Autores: Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth&amp;#x2019;s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2146/version/1

Experimental demonstration of associative memory with memristive neural networks
Provedor de dados: 17
Autores: Yuriy Pershin; Massimiliano Di Ventra.
When someone mentions the name of a known person we immediately recall her face and possibly many other traits. This is because we possess the so-called associative memory - the ability to correlate different memories to the same fact or event. Associative memory is such a fundamental and encompassing human ability (and not just human) that the network of neurons in our brain must perform it quite easily. The question is then whether electronic neural networks - electronic schemes that act somewhat similarly to human brains - can be built to perform this type of function. Although the field of neural networks has developed for many years, a key element, namely the synapses between adjacent neurons, has been lacking a satisfactory electronic representation....
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3258/version/1

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies
Provedor de dados: 17
Autores: Jennifer Hoyal Cuthill; Michael Charleston.
The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic M&amp;#xfc;llerian mimicry, thought &amp;#x2013; but rarely demonstrated &amp;#x2013; to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence)...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6829/version/1

RDF Curator: A Novel Workflow that Generates Semantic Graph from Literature for Curation Using Text Mining
Provedor de dados: 17
Autores: Yusuke Komiyama; Osamu Gotoh.
There exist few databases that enable cross-reference among various research fields related to bioenergy. Cross-reference is highly desired among bioinformatics databases related to environment, energy, and agriculture for better mutual cooperation. By uniting Semantic Graph, we can economically construct a distributed database, regardless of the size of research laboratories and research endeavors.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our purpose is to design and develop a workflow based on RDF (Resource Description Framework) that generates Semantic Graph for a set of technical terms extracted from documents of various formats, such as PDF, HTML, and plain text. Our attempt is to generate Semantics Graph as a result of text mining including morphological...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5072/version/1

Human Immune Responses to Plasmodium falciparum infection: Molecular Evidence for a Suboptimal TH&amp;#x3b1;&amp;#x3b2;(TH9) and TH17 Bias over Ideal and Effective Traditional TH1 Immunity
Provedor de dados: 17
Autores: Wan-Chung(Wan-Jiung) Hu; August Louis Bourgeois; Nathan Wolfe; Sher Singh; Anne Jedlicka; Alan Scott.
Using microarray analysis, we showed up-regulation of  Toll-like receptors 1,2,4,7,8, NF-[kappa][BETA], TNF-[alpha], p38-MAPK and MHC molecules in human peripheral blood mononuclear cells following infection with Plasmodium falciparum. We report herein further studies based on time-course microarray analysis with a focus on malaria-induced host immunity.  Results show that in early malaria; selected immunity-related genes were up-regulated including alpha, beta, and gamma interferon related genes, as well as genes of IL-15, CD36, chemokines (CXCL10, CCL2, S100A8/9, CXCL9, and CXCL11), TRAIL and IgG Fc receptors.  During acute febrile malaria, up-regulated genes included alpha, beta, and gamma interferon related genes, IL-8, IL-1[beta], IL-10 downstream...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5930/version/1

Best practices for building interoperable systems for translational research
Provedor de dados: 17
Autores: Warren Kibbe.
Research databases, clinical systems, and lab systems all have different standards, formats and drivers for data capture, operation, analysis and integration. For interdisciplinary nutritional researchers, however, there is a dependence on all of these areas and technologies. While building and integrating these systems can be difficult, using agile practices including short iterations, testing and continuous integration methods, and close engagement with all stakeholders to create useful systems for translational research. Interoperability also requires good data standards, including the use of structured data dictionaries and existing data standards such as HL7, UMLS, LOINC, ICD, and OBO foundry ontologies.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5197/version/1

Dys-regulated Gene Expression Networks by Meta-Analysis of Microarray Data on Oral Squamous Cell Carcinoma
Provedor de dados: 17
Autores: Zhongyu Liu; Yulong Niu; Chao Li; Yang Zhou; Yi Yang; Chunfang Gao.
Background: Oral squamous cell carcinoma (OSCC) is the sixth most common type of carcinoma worldwide. Development of OSCC is a multi-step process involving genes related to cell cycle, growth control, apoptosis, DNA damage response and other cellular regulators. The pathogenic pathways involved in this tumor are mostly unknown and therefore a better characterization of OSCC gene expression profile would represent a considerable advance. The availability of publicly available gene expression datasets has opened up new challenges especially for the integration of data generated by different research groups and different array platforms with the purpose of obtaining new insights on the biological process...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4269/version/1

Unique for human centromeric regions of interphase chromatin homing (CENTRICH) govern dynamic features of chromatin fractal globules
Provedor de dados: 17
Autores: Gennadi Glinsky.
We report the results of the genome-wide alignment of inter- and intra-chromosomal chromatin interactions within the context of interphase chromatin binding to nuclear lamina and nucleolus. For all human chromosomes, a significant correlation exists between binding of chromosomal loci to nuclear lamina and segregation into spatially-defined distinct compartments of genome-wide chromatin interactions identified by Hi-C method. We report identification of near-centromeric intergenic regions on human chromosomes (chr2; chr10; chr17; chr1), which are highly enriched for interphase chromatin homing sites and function as attractors of long-range physical interactions (Centromeric Regions of Interphase Chromatin Homing, CENTRICH). CENTRICH are engaged in 397-1526...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6756/version/1

SBML Level 3 Hierarchical Model Composition
Provedor de dados: 17
Autores: Lucian P. Smith; Michael Hucka.
A new proposal for incorporating modularity (or &amp;#x27;model composition&amp;#x27;) into SBML Level 3.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5133/version/1

BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6015/version/1

A stable backbone for the fungi
Provedor de dados: 17
Autores: Ingo Ebersberger; Matthias Gube; Sascha Strauss; Anne Kupczok; Martin Eckart; Kerstin Voigt; Erika Kothe; Arndt von Haeseler.
Fungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2901/version/1

LexOWL: A Bridge from LexGrid to OWL
Provedor de dados: 17
Autores: Cui Tao; Jyotishman Pathak; Harold Solbrig; Christopher  Chute.
The Lexical Grid project is an on-going community driven initiative that provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. In order to add more powerful functionalities to the existing infrastructure and align LexGrid more closely with various Semantic Web technologies, we introduce the LexOWL project for representing the ontologies modeled within the LexGrid environment in OWL (Web Ontology Language). The crux of this effort is to create a &amp;#x201c;bridge&amp;#x201d; that functionally connects the LexBIG (a LexGrid API) and the OWL API (an interface that implements OWL) seamlessly. In this paper, we discuss the key aspects of designing and...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3469/version/1

A Bayesian Framework for Parameter Estimation in Dynamical Models with Applications to Forecasting
Provedor de dados: 17
Autores: Fl&amp;#xe1;vio Code&amp;#xe7;o Coelho; Claudia T. Code&amp;#xe7;o.
Mathematical models in Biology are powerful tools for the study and exploration of complex dynamics. Nevertheless, bringing theoretical results to an agreement with experimental observations involves acknowledging a great deal of uncertainty intrinsic to our theoretical representation of a real system.&amp;#xd;&amp;#xa;Proper handling of such uncertainties, is key to the successful usage of models to predict experimental or &amp;#xfb01;eld observations. This problem has been addressed over the years by many tools for model calibration an parameter estimation. In this article we present a general framework for uncertainty analysis and parameter estimation which is designed to handle uncertainties associated with the modeling of dynamic biological systems...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4044/version/1

Bio-resources for sharing: which communities and what specific needs
Provedor de dados: 17
Autores: Andres Metspalu.
Biobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact, sharing of bio-resources and data is an integral part of a biobank&amp;#x27;s role. For an effective partnership a list of requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general. Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the &amp;#x22;impact&amp;#x22; a biobank has to the field. As an example, the practice of the Estonian Genome Center of the University of Tartu is presented.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5659/version/1

Higher Efficiency In Prediction Of TIBO Activity By Evolutionary Neural Network
Provedor de dados: 17
Autores: Abhik Seal.
The treatment of acquired immunodeficiency syndrome (AIDS) is a challenging medical problem. TIBO is a nonnucleoside reverse transcriptase inhibitor, which binds non-competitively to the hydrophobic pocket on the p66 subunit of RT enzyme. We used a dataset consisting of physicochemical properties and reverse transcriptase inhibitor activities of 88 set of 4,5,6,7-tetrahydro-y-imidazo-[4,5,1-jk][1,4]-x-benzodiazepin-2-(1h)one derivatives that are variously substituted by halogens, alkyl groups. The dataset was taken from the BIOBYTE database at (www.davidhoekman.com). The concentration of the compound leading to 50% effect has been measured and expressed as IC50. The logarithm of the inverse of this parameter has been used as biological end points (log 1/C)...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5585/version/1

Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
A detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves,  near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and  application examples for several related areas.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7079/version/1

GO-WORDS: An Entropic Approach to Semantic Decomposition of Gene Ontology Terms
Provedor de dados: 17
Autores: Tuanjie Tong; Yugyung Lee; Deendayal Dinakarpandian.
The Gene Ontology (GO) has a large and growing number of terms that constitute its vocabulary. An entropy-based approach is presented to automate the characterization of the compositional semantics of GO terms. The motivation is to extend the machine-readability of GO and to offer insights for the continued maintenance and growth of GO. A proto-type implementation illustrates the benefits of the approach.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1933/version/1

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I C. Baianu; V. I. Prisecaru.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/1

Context-based generation of kinetic equations with SBMLsqueezer 1.3
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Sandra Nitschmann; Alexander D&amp;#xf6;rr; Johannes Eichner; Michael J. Ziller; Andreas Zell.
The development of predictive, quantitative models constitutes a common task in today&amp;#x2018;s systems biology. To obtain a mathematical model description for the simulation of gene-regulatory, signaling, and metabolic networks, kinetic equations are required for each reaction within the network. Deriving and assembling these formulas is a complicated, time-consuming, and error-prone process that requires knowledge about the structure of interactions, consistently choosing a rate law for each type of reaction, and assignment of appropriate units to all parameters. In many cases, thermodynamic dependencies between the parameters have to be taken into account. For multi compartment models, the concentration units of reacting species have to be converted...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4983/version/1

Functional annotation of bacterial sugars
Provedor de dados: 17
Autores: Frederique Lisacek.
Glyco-bioinformatics means different things to different people. It ranges, for example, from the mining of the genome for glycosylation pathway enzymes, through to analysis of microarray expression of glycosyltransferases, to glycoprotein identification data, to the development of tools that facilitate the interpretation of mass spectra and to the construction of structural glycan databases. Lastly, these data need to be mined so that the function of the glycan structures attached to the range of glycoconjugates in nature can be determined. The quality of the data in these databases needs to be maintained for this work to be meaningful.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For easier analysis, glycan structures are often characterised independent of the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5107/version/1

Weight matrix based identification of terpene synthases conserved motifs in Arabidopsis thaliana proteome
Provedor de dados: 17
Autores: Suchita  Srivastava; Suaib  Luqman; Feroz  Khan.
Terpenes comprise the most diverse collection of natural products. Out of more than 30,000 individual terpenoids identified, at least half are synthesized by plants. A relatively small, but quantitatively significant, number of terpenoids are involved in primary plant metabolism. However, the vast majorities are classified as secondary metabolites; compounds not required for plant growth and development but presumed to have an ecological function in communication or defense and are widely used in industrial applications. Terpene hydrocarbon scaffolds are generated by the action of the mechanistically intriguing family of mono-, sesqui-, and diterpene synthases collectively termed as terpene synthases, that catalyze multistep reactions with diphosphorylated...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6909/version/1

Towards reproducible MSMS data preprocessing, quality control and quantification
Provedor de dados: 17
Autores: Laurent Gatto; Kathryn S. Lilley.
The development of MSnbase aims at providing researchers dealing with labelled quantitative proteomics data with a transparent, portable, extensible and open-source collaborative framework to easily manipulate and analyse MS2-level raw tandem mass spectrometry data. The implementation in R gives users and developers a great variety of powerful tools to be used in a controlled and reproducible way. Furthermore, MSnbase has been developed following an object-oriented programming paradigm: all information that is manipulated by the user is encapsulated in ad hoc data containers to hide it&amp;#x27;s underlying complexity. We illustrate the usage and achievements of our software using a published spiked-in data set in which varying quantities of test proteins...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5010/version/1

MRI and MRSI Application in Neurodegeneration
Provedor de dados: 17
Autores: Rakesh Sharma.
MRI combined with MR spectroscopy generates better information of both brain tissue composition and mesurement of metabolites or neurochemicals in multiple sclerosis(MS), Alzheimer&amp;#x27;s disease and epilepsy. New fast imaging techniques are technical advance in visualizing accurate anatomy and measurement of absolute neurochemicals in brain. Gray metter seated MS lesions is a new form of disease and lesion may appear normal on MRI but show spectroscopy peaks. High magnetic field scanners are available for fast imaging.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4317/version/1

Standards and infrastructure for managing experimental metadata
Provedor de dados: 17
Autores: Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Manon Delahaye; Richard Evans; Susanna-Assunta Sansone.
*See also the &amp;#x22;related presentation&amp;#x22;:http://precedings.nature.com/documents/3145/version/1*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5^ to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The infrastructure&amp;#x2019;s components include: a data capture and editing tool (_ISAcreator_); validator (_ISAvalidator_); database (_BioInvestigation Index_); and converter (_ISAconverter_); and a BioConductor analysis package...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3144/version/1

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/3721/version/2

Category of Metabolic-Replication Systems in Biology and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x27;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7045/version/1

Development of cost-effective SNP assays for chickpea genome analysis and breeding
Provedor de dados: 30
Autores: Varshney, R.K.,( Rajeev K. Varshney ).
Palavras-chave: Genomes; Polymorphism; Genotypes; Enzymes; Nucleotides; Chickpeas; DNA; Bioinformatics; Genetic structures; Genes.
Ano: 2007
URL: http://agropedia.iitk.ac.in/openaccess/?q=node/3282

Nurturing the seeds of success in the semi-arid tropics
Provedor de dados: 30
Palavras-chave: Bioinformatics; Chickpeas; Pigeonpeas; Sorghum; Mycotoxins; Millets; Hybrids; Groundnuts; Biotechnology; Transgenics.
Ano: 2007
URL: http://agropedia.iitk.ac.in/openaccess/?q=node/3270

Cloning, expression, and analysis of the group 2 allergen from Dermatophagoides farinae from China
Provedor de dados: 42
Autores: Yu-bao,Cui; Zhou,Ying; Weihong,Shi; Guifang,Ma; Yang,Li; Yungang,Wang.
To obtain the recombinant group 2 allergen product of Dermatophagoides farinae (Der f 2), the Der f 2 gene was synthesized by RT-PCR. The full-length cDNA comprised 441 nucleotides and was 99.3% identical to the reference sequence (GenBank AB195580). The cDNA was bound to vector pET28a to construct plasmid pET28a(+)-Der f 2, which was transformed into E. coli BL21 and induced by IPTG. SDS-PAGE showed a specific band of about 14kDa in the hole cell lysate. s estiated by chroatography, about 3.86 g of the recobinant product as obtained, which conjugated with serum IgE from asthmatic children. The protein had a signal peptide of 17 amino acids. Its secondary structure comprised an alpha helix (19.86%), an extended strand (30.82%), and a random coil (49.32%)....
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Dermatophagoides farinae; House-dust-mite allergy; Mite allergens; Der f 2; Allergen engineering; Immunotherapy; Bioinformatics.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652010000400017

A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle
Provedor de dados: 48
Autores: Shen,Wenlong; Wang,Dong; Ye,Bingyu; Shi,Minglei; Zhang,Yan; Zhao,Zhihu.
BACKGROUND: The CCCTC-binding factor (CTCF) is a highly conserved insulator protein that plays various roles in many cellular processes. CTCF is one of the main architecture proteins in higher eukaryotes, and in combination with other architecture proteins and regulators, also shapes the three-dimensional organization of a genome. Experiments show CTCF partially remains associated with chromatin during mitosis. However, the role of CTCF in the maintenance and propagation of genome architectures throughout the cell cycle remains elusive. RESULTS: We performed a comprehensive bioinformatics analysis on public datasets of Drosophila CTCF (dCTCF). We characterized dCTCF-binding sites according to their occupancy status during the cell cycle, and identified...
Tipo: Journal article
Palavras-chave: DCTCF; Cell cycle; Chromatin domains; Mitotic bookmarking; Bioinformatics.
Ano: 2015
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100027

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology
Provedor de dados: 48
Autores: González-Nilo,Fernando; Pérez-Acle,Tomás; Guínez-Molinos,Sergio; Geraldo,Daniela A; Sandoval,Claudia; Yévenes,Alejandro; Santos,Leonardo S; Laurie,V. Felipe; Mendoza,Hegaly; Cachau,Raúl E.
After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different...
Tipo: Journal article
Palavras-chave: Bioinformatics; Molecular simulation; Nanobiotechnology; Nanoinformatics; Nanomedicine.
Ano: 2011
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602011000100006

Application of Next-generation Sequencing in Clinical Molecular Diagnostics
Provedor de dados: 52
Autores: Seifi,Morteza; Ghasemi,Asghar; Raeisi,Sina; Heidarzadeh,Siamak.
ABSTRACT Next-generation sequencing (NGS) is the catch all terms that used to explain several different modern sequencing technologies which let us to sequence nucleic acids much more rapidly and cheaply than the formerly used Sanger sequencing, and as such have revolutionized the study of molecular biology and genomics with excellent resolution and accuracy. Over the past years, many academic companies and institutions have continued technological advances to expand NGS applications from research to the clinic. In this review, the performance and technical features of current NGS platforms were described. Furthermore, advances in the applying of NGS technologies towards the progress of clinical molecular diagnostics were emphasized. General advantages and...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Clinical molecular applications; Ethical aspects; Next generation sequencing.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132017000100303

In Silico Characterization of Meloidogyne Genus Nematode Cellulose Binding Proteins
Provedor de dados: 52
Autores: Menezes,Alana Manoela Fraga; Cavalcanti Junior,Edilton de Albuquerque; Martins,Luiza Suely Semen; Moraes Filho,Rômulo Maciel de.
Abstract Root-knot nematodes are a group of endoparasites species that induce the formation of giant cells in the hosts, by which they guarantee their feeding and development. Meloidogyne species infect over 2000 plant species, and are highly destructive, causing damage to many crops around the world. M. enterolobii is considered the most aggressive species in tropical regions, such as Africa and South America. Phytonematodes are able to penetrate and migrate within plant tissues, establishing a sophisticated interaction with their hosts through parasitism factors, which include a series of cell wall degradation enzymes and plant cell modification. Among the parasitism factors documented in the M. enterolobii species, cellulose binding protein (CBP), a...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Phytonematodes; Parasitism Factors; Cell wall degrading enzymes; Homology modeling; Protein function prediction.
Ano: 2019
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132019000100201

Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in Escherichia coli
Provedor de dados: 56
Autores: Cui,Y.; Zhou,P.; Peng,J.; Peng,M.; Zhou,Y.; Lin,Y.; Liu,L.
Our objective was to clone, express and characterize adult Dermatophagoides farinae group 1 (Der f 1) allergens to further produce recombinant allergens for future clinical applications in order to eliminate side reactions from crude extracts of mites. Based on GenBank data, we designed primers and amplified the cDNA fragment coding for Der f 1 by nested-PCR. After purification and recovery, the cDNA fragment was cloned into the pMD19-T vector. The fragment was then sequenced, subcloned into the plasmid pET28a(+), expressed in Escherichia coli BL21 and identified by Western blotting. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Sequence analysis showed the presence of an open reading frame containing 966 bp that encodes a...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Dermatophagoides farinae; Der f 1; Recombinant allergens; Cloning; Expression; Bioinformatics.
Ano: 2008
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2008000500006

The GATO gene annotation tool for research laboratories
Provedor de dados: 56
Autores: Fujita,A.; Massirer,K.B.; Durham,A.M.; Ferreira,C.E.; Sogayar,M.C.
Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous...
Tipo: Info:eu-repo/semantics/other
Palavras-chave: Gene annotation tool; (GATO); Automatic annotation; Pipeline; Bioinformatics.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005001100002

Cloning, bioinformatics analysis, and expression of the dust mite allergen Der f 5 of Dermatophagoides farinae
Provedor de dados: 56
Autores: Cui,Yubao; Zhou,Ying; Ma,Guifang; Yang,Li; Wang,Yungang; Shi,Weihong.
Crude extracts of house dust mites are used clinically for diagnosis and immunotherapy of allergic diseases, including bronchial asthma, perennial rhinitis, and atopic dermatitis. However, crude extracts are complexes with non-allergenic antigens and lack effective concentrations of important allergens, resulting in several side effects. Dermatophagoides farinae (Hughes; Acari: Pyroglyphidae) is one of the predominant sources of dust mite allergens, which has more than 30 groups of allergen. The cDNA coding for the group 5 allergen of D. farinae from China was cloned, sequenced and expressed. According to alignment using the VECTOR NTI 9.0 software, there were eight mismatched nucleotides in five cDNA clones resulting in seven incompatible amino acid...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Dermatophagoides farinae (Hughes); Der f 5; Cloning; Expression; Bioinformatics.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012000800009

Pseudorabies virus can be classified into five genotypes using partial sequences of UL44
Provedor de dados: 58
Autores: Fonseca Jr.,A. A.; Camargos,M. F.; Sales,M. L.; Heinemann,M. B.; Leite,R.C.; Reis,J. K. P.
Suid herpesvirus 1 (SuHV-1) is the causative agent of pseudorabies (PR), a disease of great importance due to the huge losses it causes in the swine industry. The aim of this study was to determine a method for genotyping SuHV-1 based on partial sequences of the gene coding for glycoprotein C (gC) and to elucidate the possible reasons for the variability of this region. A total of 109 gCsequences collected from GenBank were divided into five major groups after reconstruction of a phylogenetic tree by Bayesian inference. The analysis showed that a portion of gC (approximately 671 bp) is under selective pressure at various points that coincide with regions of protein disorder. It was also possible to divide SuHV-1 into five genotypes that evolved under...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Pseudorabies; Glycoprotein; Bioinformatics.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822012000400048

Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66
Provedor de dados: 58
Autores: Naveed,Muhammad; Ahmed,Iftikhar; Khalid,Nauman; Mumtaz,Abdul Samad.
Glucose dehydrogenase (GDH; EC 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p &lt; 0.05) promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Glucose dehydrogenase; Pyrroloquinoline quinone; Leclercia sp; PGPR; Bioinformatics.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000200031

Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples
Provedor de dados: 58
Autores: Hassan,Mariam; Essam,Tamer; Megahed,Salwa.
Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree)...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Method; Microbiome; Next-generation sequencing; QIIME.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500001

Application of Oligonucleotide Microarray for the Detection and Genotyping of cry Genes in Bacillu thuringiensis
Provedor de dados: 117
Autores: Xu-Guang,Liu; Fu-Ping,Song; Si-Yuan,Wen; Sheng-Qi,Wang; Da-Fang,Huang; Jie,Zhang.
We have developed a parallel, rapid, high-throughput oligonucleotide microarray-based assay for the reliable detection and genotyping of three cry genes (cry1, cry2 and cry9) in Bacillus thuringiensis (Bt). After the non-polymerase chain reaction (PCR), amplified Bt genomic DNA were fluorescent-labeled using a random primer.   The corresponding oligonucleotide probes were designed for the different cry genes that can hybridize Bt genomic DNA after cluster analysis and were printed on glass slides. This microarray has unambiguously detected and identified the cry genes in 10 isolates and reference Bt. Our data demonstrates that the microarray assay is simple and rapid for the detection and genotyping of genes. This type of assay is also a potentially...
Tipo: Journal article
Palavras-chave: Oligonucleotide microarray; Cry genes; Genotyping; Random primer labeling; Bioinformatics.
Ano: 2010
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392010000200004

Generalized composite interval mapping offers improved efficiency in the analysis of loci influencing non-normal continuous traits
Provedor de dados: 118
Autores: Mora,Freddy; Scapim,Carlos Alberto; Baharum,Adam; Teixeira do Amaral Júnior,Antonio.
In genetic studies, most Quantitative Trait Loci (QTL) mapping methods presuppose that the continuous trait of interest follows a normal (Gaussian) distribution. However, many economically important traits of agricultural crops have a non-normal distribution. Composite interval mapping (CIM) has been successfully applied to the detection of QTL in animal and plant breeding. In this study we report a generalized CIM (GCIM) method that permits QTL analysis of non-normally distributed variables. GCIM was based on the classic Generalized Linear Model method. We applied the GCIM method to a F2 population with co-dominant molecular markers and the existence of a QTL controlling a trait with Gamma distribution. Computer simulations indicated that the GCIM method...
Tipo: Journal article
Palavras-chave: Bioinformatics; Generalized Linear Model; Molecular markers; Quantitative Trait Loci (QTL).
Ano: 2010
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-16202010000300007