Faculty

Paul Denis Thomas, PhD
Paul Denis Thomas, PhD
Associate Professor of Preventive Medicine;Director, Division of Bioinformatics
Preventive Medicine
2001 Soto St Health Sciences Campus Los Angeles
Dr. Thomas’s own research lab focuses on the development and application of computational methods for reconstructing gene evolution, and using these techniques to understand the function of human genes, and how genetic factors may impact disease risk. Dr. Thomas is a Principal Investigator for the Gene Ontology project, which is among the world’s largest bioinformatics projects. He is also a PI for the PortEco project, designed to help the research community get the most out of E. coli as a biological "model organism."

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nat Genet. 2019 Sep 23. . 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

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations Bioinformatics. 2019 Feb 01; 35(3):518-520. . View in PubMed

InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2019 Jan 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 Jan 08; 47(D1):D271-D279. . View in PubMed

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Nucleic Acids Res. 2019 Jan 08; 47(D1):D419-D426. . 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

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

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

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

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

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation Bioinformatics. 2016 07 15; 32(14):2230-2. . 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

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

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

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

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

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

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

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

PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 2003 Sep; 13(9):2129-41. . 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 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 Feb 16; 291(5507):1304-51. . View in PubMed

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