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| 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. 

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 |
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| 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 & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5894/version/1 |
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| 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's presence. However, we demonstrate by data mining thousands of CEL files from NCBI'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 |
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| 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.

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).

Location: ISMB/ECCB,... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6148/version/1 |
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| 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:

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;

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 |
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| William Hogan. |
| Effective translational research requires automated analysis of large datasets collected by multiple researchers working at multiple locations. Reliable, machine interpretation of-—and reasoning with—-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 |
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| Wan-Jiung(Wan-Chung) Hu. |
| Alzheimer'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'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's disease. After knowing the exact disease pathogenesis, we can develop new... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5934/version/1 |
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| Wan-Jiung(Wan-Chung) Hu. |
| Alzheimer'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'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's disease. After knowing the exact disease pathogenesis, we can develop new... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5934/version/2 |
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| Wan-Jiung(Wan-Chung) Hu. |
| Alzheimer'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'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's disease. After knowing the exact disease pathogenesis, we can develop new... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5934/version/3 |
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| 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.
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 |
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| 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 |
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| 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 "anatomical structure of organs" and "abnormal states in the human body". 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 |
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| 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 "anatomical structure of organs" and "abnormal states in the human body". 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 |
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| 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 |
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| 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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4891/version/1 |
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| Registros recuperados: 1.312 | |
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