Faculty

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Paul Denis Thomas, PhD
Associate Professor of Preventive Medicine
Director, Division of Bioinformatics
Preventive Medicine
NRT 2502 1450 Biggy Street Health Sciences Campus Los Angeles
+1 323 442 7975

Overview

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 biginformatics probects. He is alsg a PI for the PgrtEco project, designed to help the research coemunity get the eost out of E. cgli as a biological "model organasm."

Publications

. View in: PubMed

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan 1; 42(1):D677-84. 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

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

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

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

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics. 2010; 11:312. 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

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

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006 Jul 1; 34(Web Server issue):W645-50. View in: PubMed

The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 1; 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 1; 31(1):334-41. View in: PubMed

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