Paul D Thomas, PhD

Title(s)Professor of Population and Public Health Sciences
SchoolKeck School of Medicine of Usc
Address2001 Soto St
Health Sciences Campus
Los Angeles CA 90033
Phone+1 323 442 7975
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    Other Positions
    Title(s)Director, Division of Bioinformatics

    Title(s)Director of the Gene Sequence, Function, and Health Laboratory Initiative


    Collapse Biography 
    Collapse Awards and Honors
    Thomson-Reuters/Clarivate2014  - 2020Highly Cited Researcher (Biology and Biochemistry)

    Collapse Overview 
    Collapse 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.
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    Collapse Research 
    Collapse Research Activities and Funding
    Reactome and the Gene Ontology: Digital pathway convergence for core data resources
    NIH U24HG011851Sep 24, 2021 - Jun 30, 2026
    Role: Co-Principal Investigator
    EcoliHub2.0: A next-generation E. coli model organism resource (SRI Proposal ECU
    NIH U24GM088849Aug 1, 2009 - Jul 31, 2015
    Role: Principal Investigator
    Development and Maintenance of PANTHER Software
    NIH R01GM081084Apr 1, 2008 - Mar 31, 2012
    Role: Principal Investigator
    Gene Ontology Consortium
    NIH U41HG002273Jan 19, 2001 - Feb 28, 2022
    Role: Principal Investigator

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    Collapse Required Scholarly Project Mentor

    Collapse Bibliographic 
    Collapse Publications
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. AI and the democratization of knowledge. Sci Data. 2024 Mar 05; 11(1):268. Dessimoz C, Thomas PD. PMID: 38443367; PMCID: PMC10915151.
      View in: PubMed   Mentions:    Fields:    
    2. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. bioRxiv. 2023 Nov 22. Alliance of Genome Resources Consortium . PMID: 38045425; PMCID: PMC10690154.
      View in: PubMed   Mentions:
    3. 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. Pernet O, Weisenhaus M, Stafylis C, Williams C, Campan M, Pettersson J, Green N, Lee DM, Thomas PD, Ward P, Hu H, Klausner JD, Kovacs AAZ, U. S. C. Variant Study Group. PMID: 37165019; PMCID: PMC10170421.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    4. The Gene Ontology knowledgebase in 2023. Genetics. 2023 05 04; 224(1). Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. PMID: 36866529; PMCID: PMC10158837.
      View in: PubMed   Mentions: 235     Fields:    
    5. InterPro in 2022. Nucleic Acids Res. 2023 01 06; 51(D1):D418-D427. Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A. PMID: 36350672; PMCID: PMC9825450.
      View in: PubMed   Mentions: 414     Fields:    Translation:HumansCells
    6. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford). 2022 08 12; 2022. de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. PMID: 35961013; PMCID: PMC9374478.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    7. Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. Nucleic Acids Res. 2022 07 05; 50(W1):W57-W65. Liu Z, Mushayahama T, Queme B, Ebert D, Muruganujan A, Mills C, Thomas PD, Mi H. PMID: 35640593; PMCID: PMC9252745.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 2022 07 05; 50(W1):W623-W632. Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C, OpenEBench team the Quest for Orthologs Consortium, Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. PMID: 35552456; PMCID: PMC9252809.
      View in: PubMed   Mentions: 21     Fields:    
    9. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 2022 01; 31(1):8-22. Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou LP, Mi H. PMID: 34717010; PMCID: PMC8740835.
      View in: PubMed   Mentions: 303     Fields:    
    10. Reactome and the Gene Ontology: digital convergence of data resources. Bioinformatics. 2021 Oct 11; 37(19):3343-3348. Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou LP, Thomas PD, Mungall CJ, Blake JA, D'Eustachio P. PMID: 33964129; PMCID: PMC8504636.
      View in: PubMed   Mentions: 11     Fields:    
    11. Gene Ontology representation for transcription factor functions. Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec; 1864(11-12):194752. Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. PMID: 34461313.
      View in: PubMed   Mentions: 11     Fields:    
    12. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol. 2021 07 29; 38(8):3033-3045. Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I, QFO Consortium. PMID: 33822172; PMCID: PMC8321534.
      View in: PubMed   Mentions: 12     Fields:    
    13. The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinformatics. 2021 04 05; 36(24):5712-5718. Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M. PMID: 32637990; PMCID: PMC8023674.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    14. Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees. PLoS Comput Biol. 2021 02; 17(2):e1007948. Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, Marjoram P. PMID: 33600408; PMCID: PMC7924801.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    15. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354. Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. PMID: 33156333; PMCID: PMC7778928.
      View in: PubMed   Mentions: 787     Fields:    Translation:Cells
    16. 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. Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, Thomas PD. PMID: 33290554; PMCID: PMC7778891.
      View in: PubMed   Mentions: 578     Fields:    Translation:Cells
    17. PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. Plant Direct. 2020 Dec; 4(12):e00293. Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E. PMID: 33392435; PMCID: PMC7773024.
      View in: PubMed   Mentions: 17  
    18. PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PLoS One. 2020; 15(12):e0243791. Mills C, Muruganujan A, Ebert D, Marconett CN, Lewinger JP, Thomas PD, Mi H. PMID: 33320871; PMCID: PMC7737992.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    19. The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 2020 07 02; 48(W1):W538-W545. Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C. PMID: 32374845; PMCID: PMC7319555.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimals
    20. 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. Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. PMID: 31548717; PMCID: PMC7012280.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    21. Advances and Applications in the Quest for Orthologs. Mol Biol Evol. 2019 10 01; 36(10):2157-2164. Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. PMID: 31241141; PMCID: PMC6759064.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimals
    22. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 07 17; 103(2):217-234.e4. Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M. PMID: 31171447; PMCID: PMC6764089.
      View in: PubMed   Mentions: 299     Fields:    Translation:HumansAnimalsCells
    23. GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. BMC Bioinformatics. 2019 Mar 27; 20(1):155. Liu M, Thomas PD. PMID: 30917779; PMCID: PMC6437941.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    24. Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019 03; 14(3):703-721. Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD. PMID: 30804569; PMCID: PMC6519457.
      View in: PubMed   Mentions: 620     Fields:    Translation:HumansAnimals
    25. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Bioinformatics. 2019 02 01; 35(3):518-520. Tang H, Finn RD, Thomas PD. PMID: 30032202; PMCID: PMC6361231.
      View in: PubMed   Mentions: 14     Fields:    
    26. 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. Huang X, Albou LP, Mushayahama T, Muruganujan A, Tang H, Thomas PD. PMID: 30371900; PMCID: PMC6323951.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    27. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019 01 08; 47(D1):D351-D360. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. PMID: 30398656; PMCID: PMC6323941.
      View in: PubMed   Mentions: 719     Fields:    Translation:HumansAnimalsCells
    28. 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. Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. PMID: 30407594; PMCID: PMC6323939.
      View in: PubMed   Mentions: 1340     Fields:    Translation:Animals
    29. 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. Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. PMID: 29145643; PMCID: PMC5753285.
      View in: PubMed   Mentions: 601     Fields:    Translation:HumansAnimalsCells
    30. The Gene Ontology and the Meaning of Biological Function. Methods Mol Biol. 2017; 1446:15-24. Thomas PD. PMID: 27812932; PMCID: PMC6438694.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansAnimals
    31. 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. Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD. PMID: 28025345; PMCID: PMC5199145.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    32. 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. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. PMID: 27899595; PMCID: PMC5210595.
      View in: PubMed   Mentions: 1103     Fields:    
    33. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. 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 PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. PMID: 27899635; PMCID: PMC5210578.
      View in: PubMed   Mentions: 712     Fields:    Translation:HumansCells
    34. Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. Genetics. 2016 06; 203(2):635-47. Tang H, Thomas PD. PMID: 27270698; PMCID: PMC4896183.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    35. PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics. 2016 07 15; 32(14):2230-2. Tang H, Thomas PD. PMID: 27193693.
      View in: PubMed   Mentions: 118     Fields:    Translation:Humans
    36. Standardized benchmarking in the quest for orthologs. Nat Methods. 2016 05; 13(5):425-30. 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, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. PMID: 27043882; PMCID: PMC4827703.
      View in: PubMed   Mentions: 95     Fields:    Translation:AnimalsCells
    37. 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. Thomas PD, Kahn M. PMID: 27008332; PMCID: PMC7458431.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    38. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42. Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PMID: 26578592; PMCID: PMC4702852.
      View in: PubMed   Mentions: 466     Fields:    Translation:Humans
    39. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. 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 PD, Finn RD. PMID: 25428371; PMCID: PMC4383996.
      View in: PubMed   Mentions: 676     Fields:    Translation:Cells
    40. Big data and other challenges in the quest for orthologs. Bioinformatics. 2014 Nov 01; 30(21):2993-8. Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs consortium. PMID: 25064571; PMCID: PMC4201156.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    41. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. 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 PD, Altman T. PMID: 24285306; PMCID: PMC3965092.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    42. CAFA and the open world of protein function predictions. Trends Genet. 2013 Nov; 29(11):609-10. Dessimoz C, Škunca N, Thomas PD. PMID: 24138813.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    43. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013 Aug; 8(8):1551-66. Mi H, Muruganujan A, Casagrande JT, Thomas PD. PMID: 23868073; PMCID: PMC6519453.
      View in: PubMed   Mentions: 1320     Fields:    
    44. 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. Mi H, Muruganujan A, Thomas PD. PMID: 23193289; PMCID: PMC3531194.
      View in: PubMed   Mentions: 940     Fields:    
    45. Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. Gene Ontology Consortium, 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 PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. PMID: 23161678; PMCID: PMC3531070.
      View in: PubMed   Mentions: 295     Fields:    
    46. 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. Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA, Gene Ontology Consortium. PMID: 22359495; PMCID: PMC3280971.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    47. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. 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 PD, Wu CH, Yeats C, Yong SY. PMID: 22096229; PMCID: PMC3245097.
      View in: PubMed   Mentions: 583     Fields:    Translation:Cells
    48. BioPAX support in CellDesigner. Bioinformatics. 2011 Dec 15; 27(24):3437-8. Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD. PMID: 22021903; PMCID: PMC3232372.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    49. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform. 2011 Sep; 12(5):449-62. Gaudet P, Livstone MS, Lewis SE, Thomas PD. PMID: 21873635; PMCID: PMC3178059.
      View in: PubMed   Mentions: 408     Fields:    
    50. PharmGKB summary: dopamine receptor D2. Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. Mi H, Thomas PD, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB. PMID: 20736885; PMCID: PMC3091980.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    51. Ontologies and standards in bioscience research: for machine or for human. Front Physiol. 2011; 2:5. Mi H, Thomas PD. PMID: 21519400; PMCID: PMC3081276.
      View in: PubMed   Mentions: 5  
    52. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 2010; 11(7):R73. 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 PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. PMID: 20626842; PMCID: PMC2926784.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansAnimalsCells
    53. GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics. 2010 Jun 09; 11:312. Thomas PD. PMID: 20534164; PMCID: PMC2905364.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    54. The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet. 2010 May 27; 6(5):e1000968. Marini NJ, Thomas PD, Rine J. PMID: 20523748; PMCID: PMC2877731.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    55. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. PMID: 20015972; PMCID: PMC2808919.
      View in: PubMed   Mentions: 320     Fields:    Translation:HumansAnimalsCells
    56. A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. Thomas PD, Mi H, Swan GE, Lerman C, Benowitz N, Tyndale RF, Bergen AW, Conti DV, Pharmacogenetics of Nicotine Addiction and Treatment Consortium. PMID: 19525886; PMCID: PMC6485245.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    57. Dopamine genes and nicotine dependence in treatment-seeking and community smokers. Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. Bergen AW, Conti DV, Van Den Berg D, Lee W, Liu J, Li D, Guo N, Mi H, Thomas PD, 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. PMID: 19494806; PMCID: PMC3558036.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    58. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009 Jan; 37(Database issue):D211-5. 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 PD, Valentin F, Wilson D, Wu CH, Yeats C. PMID: 18940856; PMCID: PMC2686546.
      View in: PubMed   Mentions: 1044     Fields:    
    59. 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. Conti DV, Lee W, Li D, Liu J, Van Den Berg D, Thomas PD, Bergen AW, Swan GE, Tyndale RF, Benowitz NL, Lerman C, Pharmacogenetics of Nicotine Addiction and Treatment Consortium. PMID: 18593715; PMCID: PMC2525499.
      View in: PubMed   Mentions: 87     Fields:    Translation:Humans
    60. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. Thomas PD, Mi H, Lewis S. PMID: 17208035.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimals
    61. New developments in the InterPro database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D224-8. 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 PD, Valentin F, Wilson D, Wu CH, Yeats C. PMID: 17202162; PMCID: PMC1899100.
      View in: PubMed   Mentions: 227     Fields:    Translation:Cells
    62. 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. Mi H, Guo N, Kejariwal A, Thomas PD. PMID: 17130144; PMCID: PMC1716723.
      View in: PubMed   Mentions: 179     Fields:    Translation:HumansAnimals
    63. 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. Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. PMID: 16912992; PMCID: PMC1538848.
      View in: PubMed   Mentions: 273     Fields:    Translation:HumansAnimals
    64. Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene. PLoS Genet. 2005 Dec; 1(6):e83. Brunham LR, Singaraja RR, Pape TD, Kejariwal A, Thomas PD, Hayden MR. PMID: 16429166; PMCID: PMC1342637.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    65. On the quality of tree-based protein classification. Bioinformatics. 2005 May 01; 21(9):1876-90. Lazareva-Ulitsky B, Diemer K, Thomas PD. PMID: 15647305.
      View in: PubMed   Mentions: 9     Fields:    
    66. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. PMID: 15608197; PMCID: PMC540032.
      View in: PubMed   Mentions: 385     Fields:    Translation:HumansAnimalsCells
    67. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science. 2003 Dec 12; 302(5652):1960-3. Clark AG, Glanowski S, Nielsen R, Thomas PD, 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. PMID: 14671302.
      View in: PubMed   Mentions: 278     Fields:    Translation:HumansAnimalsCells
    68. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003 Sep; 13(9):2129-41. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PMID: 12952881; PMCID: PMC403709.
      View in: PubMed   Mentions: 1501     Fields:    Translation:HumansAnimalsCells
    69. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep; 13(9):2118-28. Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. PMID: 12952880; PMCID: PMC403707.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    70. 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. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O. PMID: 12520017; PMCID: PMC165562.
      View in: PubMed   Mentions: 314     Fields:    Translation:HumansAnimalsCells
    71. The sequence of the human genome. Science. 2001 02 16; 291(5507):1304-51. 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 PD, 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, Deslattes 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. PMID: 11181995.
      View in: PubMed   Mentions: 3082     Fields:    Translation:HumansAnimalsCells
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