Paul D. Thomas, Ph.D. recently joined USC as an Associate Professor in the Preventive Medicine Department, and is the Director of the Bioinformatics Division. He also co-directs the USC Center for Biomedical Information Sciences (CBIS).
Current research
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 was recently named a Principal Investigator for the next cycle of the Gene Ontology Project. He is also a co-PI for the EcoliHub project, designed to help the research community get the most out of E. coli as a biological "model organism."
Best-known contributions
While at Celera Genomics, Dr. Thomas contributed to the first analysis of the human genome published in Science magazine, co-writing (with Mani Subramanian) the 10-page overview of the function and evolution of human genes. Dr. Thomas is also known for the development of the PANTHER (Protein Analysis Through Evolutionary Relationships) web server, which is used by a broad community of researchers seeking information about gene function and evolution, and which receives about 2 million hits every month.
Selected publications
1. Marini, Thomas & Rine, The use of orthologous sequences to predict the impact of amino acid substitutions on protein function, PLoS Genet., in press.
2. Thomas et al. A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet. and Genomics 2009.
3. PD Thomas, Single nucleotide polymorphisms in human disease and evolution: phylogenies and genealogies, in Encyclopedia of Life Sciences, Wiley, 2008.
4. Thomas, Mi & Lewis, Ontology annotation: mapping genomic regions to biological function, Curr Opin Chem Biol., 2007.
5. Thomas & Kejariwal, Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects, Proc Nat Acad Sci USA, 2004.
6. Clark et al., Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios, Science, 2003.
7. Thomas et al., PANTHER: a library of protein families and subfamilies indexed by function, Genome Res., 2003.
8. Venter et al., The sequence of the human genome, Science, 2001.
Publication list (PubMed)
Contact information
University of Southern California
1450 Biggy Street, NRT 2502
Mail Code: LG591 MC9601
Los Angeles, CA 90033-9011
Phone: 323-442-7799
Fax: 323-442-7995
Email: pdthomas@usc.edu
