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Author Details

Paul D Thomas
University of Southern California
1991
81
48
Gloria M Sheynkman (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36350672InterPro in 2022.Nucleic Acids Res2023
36350672InterPro in 2022.Nucleic Acids Res2023
37333156CAR T-cell design dependent remodeling of the brain tumor immune microenvironment identify macrophages as key players that inhibit or promote anti-tumor activity.Res Sq2023
36866529The Gene Ontology knowledgebase in 2023.Genetics2023
37333156CAR T-cell design dependent remodeling of the brain tumor immune microenvironment identify macrophages as key players that inhibit or promote anti-tumor activity.Res Sq2023
36866529The Gene Ontology knowledgebase in 2023.Genetics2023
34717010PANTHER: Making genome-scale phylogenetics accessible to all.Protein Sci2022
35961013A roadmap for the functional annotation of protein families: a community perspective.Database (Oxford)2022
35640593Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation.Nucleic Acids Res2022
35552456The Quest for Orthologs orthology benchmark service in 2022.Nucleic Acids Res2022
34717010PANTHER: Making genome-scale phylogenetics accessible to all.Protein Sci2022
35640593Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation.Nucleic Acids Res2022
35552456The Quest for Orthologs orthology benchmark service in 2022.Nucleic Acids Res2022
35961013A roadmap for the functional annotation of protein families: a community perspective.Database (Oxford)2022
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
33964129Reactome and the Gene Ontology: digital convergence of data resources.Bioinformatics2021
33600408Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.PLoS Comput Biol2021
33156333The InterPro protein families and domains database: 20 years on.Nucleic Acids Res2021
32637990The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics2021
33290554PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.Nucleic Acids Res2021
34461313Gene Ontology representation for transcription factor functions.Biochim Biophys Acta Gene Regul Mech2021
33600408Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.PLoS Comput Biol2021
34461313Gene Ontology representation for transcription factor functions.Biochim Biophys Acta Gene Regul Mech2021
33964129Reactome and the Gene Ontology: digital convergence of data resources.Bioinformatics2021
33156333The InterPro protein families and domains database: 20 years on.Nucleic Acids Res2021
33290554PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.Nucleic Acids Res2021
32637990The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics2021
32374845The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic Acids Res2020
32374845The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic Acids Res2020
33392435PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference.Plant Direct2020
33320871PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence.PLoS One2020
33392435PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference.Plant Direct2020
33320871PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence.PLoS One2020
30407594PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.Nucleic Acids Res2019
30407594PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.Nucleic Acids Res2019
30398656InterPro in 2019: improving coverage, classification and access to protein sequence annotations.Nucleic Acids Res2019
30371900Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.Nucleic Acids Res2019
30032202TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.Bioinformatics2019
30917779GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.BMC Bioinformatics2019
30804569Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).Nat Protoc2019
30793173CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.Bioinformatics2019
31548717Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.Nat Genet2019
31241141Advances and Applications in the Quest for Orthologs.Mol Biol Evol2019
30032202TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.Bioinformatics2019
31241141Advances and Applications in the Quest for Orthologs.Mol Biol Evol2019
31548717Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.Nat Genet2019
30804569Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).Nat Protoc2019
30917779GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.BMC Bioinformatics2019
30793173CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.Bioinformatics2019
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Collaborators

University of Southern California
Co-authored papers 39
Co-authored papers 10
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 10
University of Wurzburg
Co-authored papers 9
University College London, Institute of Structural and Molecular Biology
Co-authored papers 9
European Bioinformatics Institute
Co-authored papers 9
Lawrence Berkeley National Laboratory
Co-authored papers 9
Co-authored papers 8
Medical Research Council Laboratory of Molecular Biology
Co-authored papers 8
Georgetown University Medical Center
Co-authored papers 8
University of Geneva
Co-authored papers 8
University of Southern California
Co-authored papers 8
European Bioinformatics Institute
Co-authored papers 8
carnegie mellon university
Co-authored papers 8
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 8
Co-authored papers 8
carnegie mellon university
Co-authored papers 7
International Society for Biocuration, Lawrence Berkeley National Laboratory, University of Edinburgh, University of Edinburgh School of Biological Sciences
Co-authored papers 7
Georgetown University Medical Center
Co-authored papers 7
University of Lausanne
Co-authored papers 6
Co-authored papers 6
Westlake University
Co-authored papers 6
Guangzhou University
Co-authored papers 6
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 6
Co-authored papers 6
Oregon Research Institute
Co-authored papers 5
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 5
Co-authored papers 5
University College London
Co-authored papers 5
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 5