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| Registros recuperados: 1.312 | |
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| Zuoshuang Xiang; Yongqun He. |
| OntoFox ("http://ontofox.hegroup.org/":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 >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 |
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| 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–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 |
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| 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
collection of curated and peer-reviewed signaling pathways composed of human
biomolecular interactions and cellular processes. Created in a collaboration between the
U.S. National Cancer Institute and Nature Publishing Group, the database is a research
tool for cell biologists, biochemists, computational biologists and bioinformaticians.
The PID offers a range of tools to facilitate pathway exploration. Users can browse the
pre-defi ned set of pathways and also create interaction network maps centered on
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 |
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| 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 & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3150/version/1 |
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| 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 |
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| Evangelos Pafilis; Seán I. O'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 ("http://reflect.ws":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 & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3212/version/1 |
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| 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 field 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 |
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| 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.

 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 |
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| Wei-Yi Cheng; Jessica J. Kandel; Darrell J. Yamashiro; Peter Canoll; Dimitris Anastassiou. |
| Background
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. 

Findings
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 |
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| 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 |
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| 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'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'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 & Genomics; Microbiology; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4765/version/1 |
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| 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’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 |
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| Rajarshi Guha; Julien Gobeill; Patrick Ruch. |
| OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). 

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. 

RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays. 

CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays. 

AVAILABILITIES: the database is hosted by the... |
| Tipo: Poster |
Palavras-chave: Chemistry; Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3176/version/1 |
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| 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 |
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| Registros recuperados: 1.312 | |
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