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| 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 |
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| Donald C. Cooper. |
| “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.” -Wikipedia
On April 3rd, 2012 Nature Precedings, Nature Publishing Group’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 “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 |
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| 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 |
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| 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’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. 
Some of the important... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2101/version/1 |
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| 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'-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 & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6832/version/1 |
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| 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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7054/version/1 |
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| 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 (<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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6552/version/1 |
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| 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 & Genomics; Neuroscience; Pharmacology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3447/version/1 |
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| 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 |
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| Martin Krallinger. |
| This is the second part of the talk ‘A Framework for BioCuration Workflows’, given by Martin Krallinger from the Spanish National Cancer Research Centre at the 'Text Mining for the BioCuration Workflow' 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 |
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| 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 "Virtual X" 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 'comp', 'spatial', 'array' and 'dyn' 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 |
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| 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 |
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| 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 |
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| 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 |
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| Bob O'Hara; Päivi Komulainen; Outi Savolainen; Mikko J. Sillanpää. |
| 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 & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4137/version/1 |
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| Pinar Wennerberg; Manuel Möller; 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 |
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| Pinar Wennerberg; Manuel Möller; 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 |
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| Registros recuperados: 1.312 | |
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