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| 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 & Genomics; Microbiology; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4898/version/1 |
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| 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 “if-then” 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 |
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| 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.
They do not translation into proteins, rather they inhibit protein expression by binding to the 3’untranslated regions (3’ 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 |
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| Rolf Huehne; Juergen Suehnel. |
| The JenaLib database ("www.fli-leibniz.de/IMAGE.html":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:
(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 |
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| 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 & Genomics; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6967/version/2 |
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| 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. 

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 |
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| Susanna-Assunta Sansone; Philippe Rocca-Serra. |
| *See also "related poster":http://precedings.nature.com/documents/3144/version/1*

Today’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 ‘omics’). 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.

Standards initiatives normally cater to particular domains. However, several synergistic... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3145/version/1 |
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| Michael T. Cooling. |
| CellML 1.1 [1] is an XML-based model exchange protocol with inherent support for modularity.
To assist in answering complex biomedical research questions, we are developing libraries of modular model components that facilitate mathematical model construction. 
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].
 

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 |
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| 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.

As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:
"http://www.biopython.org/DIST/LICENSE":http://www.biopython.org/DIST/LICENSE

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 |
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| 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. 

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 |
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| 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.

Tasar culture is a forest based... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6161/version/1 |
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| I. C. Baianu. |
| This novel Soybean Composition Database from the AFC-NMR & 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.
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. 

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 & Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6201/version/1 |
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| T. Michael Keesey. |
| _Names on Nodes_^1^ is an open‑source^2^ Flex application which utilizes a mathematical approach to automate the application of phylogenetically‑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‑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 |
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| 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 Schrödinger 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 |
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| 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 & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6035/version/1 |
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| 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 |
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| 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 |
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| Registros recuperados: 1.312 | |
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