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Paul D Thomas, PhD

Professor of Population and Public Health Sciences

Director, Division of Bioinformatics

Director of the Gene Sequence, Function, and Health Laboratory Initiative

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Phone +1 323 442 7975
Email pdthomas@usc.edu
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Overview

Trained in computational biology (specifically computational protein folding using statistical-mechanics based techniques with Dr. Ken Dill), Dr. Thomas turned to genomics as soon as the Human Genome Project began pilot work in 1995. The culmination of this early work was the publication of the paper describing the sequencing of the first human genome in 2001; Dr. Thomas led the work described in the 10-page section of the paper entitled An overview of the predicted protein coding genes in the human genome. Since that time, Dr. Thomas’s group has continued to innovate in the area of computational analysis of genomic data, with an emphasis on gene function and evolution. In addition to founding and continuing development on the PANTHER phylogenomics project, Dr. Thomas is a director of the Gene Ontology Consortium, one of the largest and best-known bioinformatics projects in the world.

Awards

  • Thomson-Reuters/Clarivate: Highly Cited Researcher (Biology and Biochemistry), 2014-2020

Publications

  • New developments for the Quest for Orthologs benchmark service NAR Genom Bioinform. 2024 Dec; 6(4):lqae167. . View in PubMed
  • InterPro: the protein sequence classification resource in 2025 Nucleic Acids Res. 2024 Nov 20. . View in PubMed
  • Quest for Orthologs in the Era of Biodiversity Genomics Genome Biol Evol. 2024 Oct 15. . View in PubMed
  • Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy Database (Oxford). 2024 Aug 13; 2024. . View in PubMed
  • AI and the democratization of knowledge Sci Data. 2024 Mar 05; 11(1):268. . View in PubMed
  • Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium bioRxiv. 2023 Nov 22. . View in PubMed
  • The Gene Ontology knowledgebase in 2023 Genetics. 2023 05 04; 224(1). . View in PubMed
  • SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay Sci Rep. 2023 05 10; 13(1):7612. . View in PubMed
  • InterPro in 2022 Nucleic Acids Res. 2023 01 06; 51(D1):D418-D427. . View in PubMed
  • PANTHER: Making genome-scale phylogenetics accessible to all Protein Sci. 2022 01; 31(1):8-22. . View in PubMed
  • The Quest for Orthologs orthology benchmark service in 2022 Nucleic Acids Res. 2022 07 05; 50(W1):W623-W632. . View in PubMed
  • A roadmap for the functional annotation of protein families: a community perspective Database (Oxford). 2022 08 12; 2022. . View in PubMed
  • Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation Nucleic Acids Res. 2022 07 05; 50(W1):W57-W65. . View in PubMed
  • Gene Ontology representation for transcription factor functions Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec; 1864(11-12):194752. . View in PubMed
  • Reactome and the Gene Ontology: digital convergence of data resources Bioinformatics. 2021 Oct 11; 37(19):3343-3348. . View in PubMed
  • Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees PLoS Comput Biol. 2021 02; 17(2):e1007948. . View in PubMed
  • Ten Years of Collaborative Progress in the Quest for Orthologs Mol Biol Evol. 2021 07 29; 38(8):3033-3045. . View in PubMed
  • PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API Nucleic Acids Res. 2021 01 08; 49(D1):D394-D403. . View in PubMed
  • The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) Bioinformatics. 2021 04 05; 36(24):5712-5718. . View in PubMed
  • The InterPro protein families and domains database: 20 years on Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354. . View in PubMed
  • PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference Plant Direct. 2020 Dec; 4(12):e00293. . View in PubMed
  • The Quest for Orthologs benchmark service and consensus calls in 2020 Nucleic Acids Res. 2020 07 02; 48(W1):W538-W545. . View in PubMed
  • PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence PLoS One. 2020; 15(12):e0243791. . View in PubMed
  • GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness BMC Bioinformatics. 2019 Mar 27; 20(1):155. . View in PubMed
  • Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nat Genet. 2019 10; 51(10):1429-1433. . View in PubMed
  • Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v14. 0). Nat Protoc. 2019 03; 14(3):703-721. . View in PubMed
  • Advances and Applications in the Quest for Orthologs Mol Biol Evol. 2019 10 01; 36(10):2157-2164. . View in PubMed
  • PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Nucleic Acids Res. 2019 01 08; 47(D1):D419-D426. . View in PubMed
  • InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2019 01 08; 47(D1):D351-D360. . View in PubMed
  • Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life Nucleic Acids Res. 2019 01 08; 47(D1):D271-D279. . View in PubMed
  • TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations Bioinformatics. 2019 02 01; 35(3):518-520. . View in PubMed
  • SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the SynapseNeuron. 2019 07 17; 103(2):217-234. e4. . View in PubMed
  • The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database Nucleic Acids Res. 2018 01 04; 46(D1):D624-D632. . View in PubMed
  • PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Nucleic Acids Res. 2017 01 04; 45(D1):D183-D189. . View in PubMed
  • The Gene Ontology and the Meaning of Biological Function Methods Mol Biol. 2017; 1446:15-24. . View in PubMed
  • InterPro in 2017-beyond protein family and domain annotations Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. . View in PubMed
  • Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation Cell Biol Toxicol. 2016 Feb; 32(1):61-81. . View in PubMed
  • PANTHER version 10: expanded protein families and functions, and analysis tools Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42. . View in PubMed
  • Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation Genetics. 2016 06; 203(2):635-47. . View in PubMed
  • Standardized benchmarking in the quest for orthologs Nat Methods. 2016 05; 13(5):425-30. . View in PubMed
  • Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes Database (Oxford). 2016; 2016. . View in PubMed
  • PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation Bioinformatics. 2016 07 15; 32(14):2230-2. . View in PubMed
  • The InterPro protein families database: the classification resource after 15 years Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. . View in PubMed
  • Big data and other challenges in the quest for orthologs Bioinformatics. 2014 Nov 01; 30(21):2993-8. . View in PubMed
  • PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. . View in PubMed
  • CAFA and the open world of protein function predictions Trends Genet. 2013 Nov; 29(11):609-10. . View in PubMed
  • Large-scale gene function analysis with the PANTHER classification system Nat Protoc. 2013 Aug; 8(8):1551-66. . View in PubMed
  • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees Nucleic Acids Res. 2013 Jan; 41(Database issue):D377-86. . View in PubMed
  • Gene Ontology annotations and resources Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. . View in PubMed
  • InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. . View in PubMed
  • On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report PLoS Comput Biol. 2012; 8(2):e1002386. . View in PubMed
  • BioPAX support in CellDesigner Bioinformatics. 2011 Dec 15; 27(24):3437-8. . View in PubMed
  • Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium Brief Bioinform. 2011 Sep; 12(5):449-62. . View in PubMed
  • PharmGKB summary: dopamine receptor D2 Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. . View in PubMed
  • Ontologies and standards in bioscience research: for machine or for human Front Physiol. 2011; 2:5. . View in PubMed
  • GIGA: a simple, efficient algorithm for gene tree inference in the genomic age BMC Bioinformatics. 2010 Jun 09; 11:312. . View in PubMed
  • The use of orthologous sequences to predict the impact of amino acid substitutions on protein function PLoS Genet. 2010 May 27; 6(5):e1000968. . View in PubMed
  • Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire Genome Biol. 2010; 11(7):R73. . View in PubMed
  • PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. . View in PubMed
  • Dopamine genes and nicotine dependence in treatment-seeking and community smokers Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. . View in PubMed
  • A systems biology network model for genetic association studies of nicotine addiction and treatment Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. . View in PubMed
  • InterPro: the integrative protein signature database Nucleic Acids Res. 2009 Jan; 37(Database issue):D211-5. . View in PubMed
  • Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation Hum Mol Genet. 2008 Sep 15; 17(18):2834-48. . View in PubMed
  • Ontology annotation: mapping genomic regions to biological function Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. . View in PubMed
  • PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res. 2007 Jan; 35(Database issue):D247-52. . View in PubMed
  • New developments in the InterPro database Nucleic Acids Res. 2007 Jan; 35(Database issue):D224-8. . View in PubMed
  • Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W645-50. . View in PubMed
  • Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene PLoS Genet. 2005 Dec; 1(6):e83. . View in PubMed
  • On the quality of tree-based protein classification Bioinformatics. 2005 May 01; 21(9):1876-90. . View in PubMed
  • The PANTHER database of protein families, subfamilies, functions and pathways Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8. . View in PubMed
  • Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios Science. 2003 Dec 12; 302(5652):1960-3. . View in PubMed
  • Assessment of genome-wide protein function classification for Drosophila melanogaster Genome Res. 2003 Sep; 13(9):2118-28. . View in PubMed
  • PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 2003 Sep; 13(9):2129-41. . View in PubMed
  • PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification Nucleic Acids Res. 2003 Jan 01; 31(1):334-41. . View in PubMed
  • The sequence of the human genome Science. 2001 02 16; 291(5507):1304-51. . View in PubMed

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