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    Paul Denis Thomas, PhD

    TitleAssociate Professor of Preventive Medicine
    SchoolKeck School of Medicine of USC
    DepartmentPreventive Medicine
    AddressNRT 2502 1450 Biggy Street
    Health Sciences Campus
    Los Angeles California 90033
    Phone+1 323 442 7975
    Emailpdthomas@usc.edu
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      Other Positions
      TitleDirector, Division of Bioinformatics


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      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."


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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Thomas P. The Gene Ontology and the Meaning of Biological Function. Methods Mol Biol. 2017; 1446:15-24. PMID: 27812932.
        View in: PubMed
      2. Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas P. 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. PMID: 28025345.
        View in: PubMed
      3. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas P. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2017 Jan 04; 45(D1):D183-D189. PMID: 27899595.
        View in: PubMed
      4. Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas P, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 04; 45(D1):D190-D199. PMID: 27899635.
        View in: PubMed
      5. Tang H, Thomas P. Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. Genetics. 2016 Jun; 203(2):635-47. PMID: 27270698; PMCID: PMC4896183 [Available on 06/01/17].
      6. Tang H, Thomas P. PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics. 2016 Jul 15; 32(14):2230-2. PMID: 27193693.
        View in: PubMed
      7. Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Gabaldón T, Lewis SE, Thomas P, Sonnhammer E, Dessimoz C. Standardized benchmarking in the quest for orthologs. Nat Methods. 2016 May; 13(5):425-30. PMID: 27043882; PMCID: PMC4827703 [Available on 10/04/16].
      8. Thomas P, Kahn M. 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. PMID: 27008332.
        View in: PubMed
      9. Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas P. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42. PMID: 26578592; PMCID: PMC4702852.
      10. Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas P, Finn RD. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. PMID: 25428371; PMCID: PMC4383996.
      11. Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas P, Dessimoz C. Big data and other challenges in the quest for orthologs. Bioinformatics. 2014 Nov 01; 30(21):2993-8. PMID: 25064571; PMCID: PMC4201156.
      12. Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas P, Altman T. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. PMID: 24285306; PMCID: PMC3965092.
      13. Dessimoz C, Škunca N, Thomas P. CAFA and the open world of protein function predictions. Trends Genet. 2013 Nov; 29(11):609-10. PMID: 24138813.
        View in: PubMed
      14. Mi H, Muruganujan A, Casagrande JT, Thomas P. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013 Aug; 8(8):1551-66. PMID: 23868073.
        View in: PubMed
      15. Mi H, Muruganujan A, Thomas P. 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. PMID: 23193289; PMCID: PMC3531194.
      16. Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas P, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. PMID: 23161678; PMCID: PMC3531070.
      17. Thomas P, Wood V, Mungall CJ, Lewis SE, Blake JA. 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. PMID: 22359495; PMCID: PMC3280971.
      18. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas P, Wu CH, Yeats C, Yong SY. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. PMID: 22096229; PMCID: PMC3245097.
      19. Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas P. BioPAX support in CellDesigner. Bioinformatics. 2011 Dec 15; 27(24):3437-8. PMID: 22021903; PMCID: PMC3232372.
      20. Gaudet P, Livstone MS, Lewis SE, Thomas P. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform. 2011 Sep; 12(5):449-62. PMID: 21873635; PMCID: PMC3178059.
      21. Mi H, Thomas P, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB. PharmGKB summary: dopamine receptor D2. Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. PMID: 20736885; PMCID: PMC3091980.
      22. Mi H, Thomas P. Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5. PMID: 21519400; PMCID: PMC3081276.
      23. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas P, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 2010; 11(7):R73. PMID: 20626842; PMCID: PMC2926784.
      24. Thomas P. GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics. 2010 Jun 09; 11:312. PMID: 20534164; PMCID: PMC2905364.
      25. Marini NJ, Thomas P, Rine J. The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet. 2010 May 27; 6(5):e1000968. PMID: 20523748; PMCID: PMC2877731.
      26. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas P. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. PMID: 20015972; PMCID: PMC2808919.
      27. Thomas P, Mi H, Swan GE, Lerman C, Benowitz N, Tyndale RF, Bergen AW, Conti DV. A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. PMID: 19525886.
        View in: PubMed
      28. Bergen AW, Conti DV, Van Den Berg D, Lee W, Liu J, Li D, Guo N, Mi H, Thomas P, Lessov-Schlaggar CN, Krasnow R, He Y, Nishita D, Jiang R, McClure JB, Tildesley E, Hops H, Tyndale RF, Benowitz NL, Lerman C, Swan GE. Dopamine genes and nicotine dependence in treatment-seeking and community smokers. Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. PMID: 19494806; PMCID: PMC3558036.
      29. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas P, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009 Jan; 37(Database issue):D211-5. PMID: 18940856; PMCID: PMC2686546.
      30. Conti DV, Lee W, Li D, Liu J, Van Den Berg D, Thomas P, Bergen AW, Swan GE, Tyndale RF, Benowitz NL, Lerman C. 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. PMID: 18593715; PMCID: PMC2525499.
      31. Thomas P, Mi H, Lewis S. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. PMID: 17208035.
        View in: PubMed
      32. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas P, Valentin F, Wilson D, Wu CH, Yeats C. New developments in the InterPro database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D224-8. PMID: 17202162; PMCID: PMC1899100.
      33. Mi H, Guo N, Kejariwal A, Thomas P. 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. PMID: 17130144; PMCID: PMC1716723.
      34. Thomas P, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. 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. PMID: 16912992; PMCID: PMC1538848.
      35. Brunham LR, Singaraja RR, Pape TD, Kejariwal A, Thomas P, Hayden MR. Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene. PLoS Genet. 2005 Dec; 1(6):e83. PMID: 16429166; PMCID: PMC1342637.
      36. Lazareva-Ulitsky B, Diemer K, Thomas P. On the quality of tree-based protein classification. Bioinformatics. 2005 May 01; 21(9):1876-90. PMID: 15647305.
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      37. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas P. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8. PMID: 15608197; PMCID: PMC540032.
      38. Clark AG, Glanowski S, Nielsen R, Thomas P, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science. 2003 Dec 12; 302(5652):1960-3. PMID: 14671302.
        View in: PubMed
      39. Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas P, Ashburner M. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep; 13(9):2118-28. PMID: 12952880; PMCID: PMC403707.
      40. Thomas P, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003 Sep; 13(9):2129-41. PMID: 12952881; PMCID: PMC403709.
      41. Thomas P, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O. 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. PMID: 12520017; PMCID: PMC165562.
      42. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas P, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science. 2001 Feb 16; 291(5507):1304-51. PMID: 11181995.
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