A5016748504- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Research Data Management Practices
- Plant-Microbe Interactions and Immunity
- Cell Image Analysis Techniques
- Scientific Computing and Data Management
- Legume Nitrogen Fixing Symbiosis
- Genetics, Bioinformatics, and Biomedical Research
- Environmental Monitoring and Data Management
University of Georgia
2025
Lawrence Berkeley National Laboratory
2008-2012
European Bioinformatics Institute
2005-2010
Wellcome Trust
2007-2010
Joint Genome Institute
2008
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular cellular biology are freely available for community use in the annotation genes, gene products sequences. Many model organism databases genome groups GO contribute their sets to resource. database integrates contributed annotations full access this information formats. Members Consortium continually work collectively,...
AmiGO is a web application that allows users to query, browse and visualize ontologies related gene product annotation (association) data. can be used online at the Gene Ontology (GO) website access data provided by GO Consortium; it also downloaded installed local annotations. free open source software developed maintained Consortium.
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
Abstract Leveraging the use of multiplex multi-omic networks, key insights into genetic and epigenetic mechanisms supporting biofuel production have been uncovered. Here, we introduce RWRtoolkit, a generation, exploration, statistical package built for R command line users. RWRtoolkit enables efficient exploration large highly complex biological networks generated from custom experimental data and/or publicly available datasets, is species agnostic. A range functions can be used to find...
Abstract We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R command-line users. RWRtoolkit enables the efficient exploration of large highly complex biological networks generated from custom experimental data and/or publicly available datasets, is species agnostic. A range functions can be used to find topological distances between entities, determine relationships within sets interest, search context around statistically evaluate strength sets....
Abstract 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. results can be used reason over the ontology, make cross-ontology queries.
Abstract One of the premises OBO Foundry is that development an orthogonal set ontologies will increase domain expert contributions and logical interoperability, decrease maintenance workload. For these reasons, Cell Ontology (CL) being re-engineered. This process requires extraction sub-modules from existing ontologies, which presents a number practical engineering challenges. These extracted modules may be intended to cover narrow or broad species. In addition, applications resources make...