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Items: 1 to 50 of 143

1.

Advances and Applications in the Quest for Orthologs.

Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium .

Mol Biol Evol. 2019 Jun 26. pii: msz150. doi: 10.1093/molbev/msz150. [Epub ahead of print]

PMID:
31241141
2.

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

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.

Neuron. 2019 Jul 17;103(2):217-234.e4. doi: 10.1016/j.neuron.2019.05.002. Epub 2019 Jun 3.

PMID:
31171447
3.

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.

Liu M, Thomas PD.

BMC Bioinformatics. 2019 Mar 27;20(1):155. doi: 10.1186/s12859-019-2752-2.

4.

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).

Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD.

Nat Protoc. 2019 Mar;14(3):703-721. doi: 10.1038/s41596-019-0128-8. Epub 2019 Feb 25.

PMID:
30804569
5.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L.

Bioinformatics. 2019 Feb 21. pii: btz132. doi: 10.1093/bioinformatics/btz132. [Epub ahead of print]

PMID:
30793173
6.

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.

Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D419-D426. doi: 10.1093/nar/gky1038.

7.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

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.

Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360. doi: 10.1093/nar/gky1100.

8.

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.

Huang X, Albou LP, Mushayahama T, Muruganujan A, Tang H, Thomas PD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D271-D279. doi: 10.1093/nar/gky1009.

9.

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.

Tang H, Finn RD, Thomas PD.

Bioinformatics. 2019 Feb 1;35(3):518-520. doi: 10.1093/bioinformatics/bty625.

10.

Cytosolic carnitine acetyltransferase as a source of cytosolic acetyl-CoA: a possible mechanism for regulation of cardiac energy metabolism.

Altamimi TR, Thomas PD, Darwesh AM, Fillmore N, Mahmoud MU, Zhang L, Gupta A, Al Batran R, Seubert JM, Lopaschuk GD.

Biochem J. 2018 Mar 9;475(5):959-976. doi: 10.1042/BCJ20170823.

PMID:
29438065
11.

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.

Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D624-D632. doi: 10.1093/nar/gkx1134.

12.

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD.

Database (Oxford). 2016 Dec 26;2016. pii: baw155. doi: 10.1093/database/baw155. Print 2016.

13.

InterPro in 2017-beyond protein family and domain annotations.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.

14.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD.

Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189. doi: 10.1093/nar/gkw1138. Epub 2016 Nov 29.

15.

The Gene Ontology and the Meaning of Biological Function.

Thomas PD.

Methods Mol Biol. 2017;1446:15-24.

16.

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation.

Tang H, Thomas PD.

Genetics. 2016 Jun;203(2):635-47. doi: 10.1534/genetics.116.190033. Review.

17.

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.

Tang H, Thomas PD.

Bioinformatics. 2016 Jul 15;32(14):2230-2. doi: 10.1093/bioinformatics/btw222. Epub 2016 May 18.

PMID:
27193693
18.

Standardized benchmarking in the quest for orthologs.

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.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

19.

Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation.

Thomas PD, Kahn M.

Cell Biol Toxicol. 2016 Feb;32(1):61-81. doi: 10.1007/s10565-016-9318-0. Epub 2016 Mar 23. Review.

PMID:
27008332
20.

PANTHER version 10: expanded protein families and functions, and analysis tools.

Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD.

Nucleic Acids Res. 2016 Jan 4;44(D1):D336-42. doi: 10.1093/nar/gkv1194. Epub 2015 Nov 17.

21.

The InterPro protein families database: the classification resource after 15 years.

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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26.

22.

Big data and other challenges in the quest for orthologs.

Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C; Quest for Orthologs consortium.

Bioinformatics. 2014 Nov 1;30(21):2993-8. doi: 10.1093/bioinformatics/btu492. Epub 2014 Jul 26.

23.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26. Erratum in: Nucleic Acids Res. 2014 Oct 29;42(19):12330.

24.

CAFA and the open world of protein function predictions.

Dessimoz C, Škunca N, Thomas PD.

Trends Genet. 2013 Nov;29(11):609-10. doi: 10.1016/j.tig.2013.09.005. Epub 2013 Oct 15. No abstract available.

25.

Large-scale gene function analysis with the PANTHER classification system.

Mi H, Muruganujan A, Casagrande JT, Thomas PD.

Nat Protoc. 2013 Aug;8(8):1551-66. doi: 10.1038/nprot.2013.092. Epub 2013 Jul 18.

26.

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.

Mi H, Muruganujan A, Thomas PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D377-86. doi: 10.1093/nar/gks1118. Epub 2012 Nov 27.

27.

Gene Ontology annotations and resources.

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.

Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov 17.

28.

A protection system for the JET ITER-like wall based on imaging diagnostics.

Arnoux G, Devaux S, Alves D, Balboa I, Balorin C, Balshaw N, Beldishevski M, Carvalho P, Clever M, Cramp S, de Pablos JL, de la Cal E, Falie D, Garcia-Sanchez P, Felton R, Gervaise V, Goodyear A, Horton A, Jachmich S, Huber A, Jouve M, Kinna D, Kruezi U, Manzanares A, Martin V, McCullen P, Moncada V, Obrejan K, Patel K, Lomas PJ, Neto A, Rimini F, Ruset C, Schweer B, Sergienko G, Sieglin B, Soleto A, Stamp M, Stephen A, Thomas PD, Valcárcel DF, Williams J, Wilson J, Zastrow KD; JET-EFDA Contributors.

Rev Sci Instrum. 2012 Oct;83(10):10D727. doi: 10.1063/1.4738742.

PMID:
23130796
29.

Upgrade of the infrared camera diagnostics for the JET ITER-like wall divertor.

Balboa I, Arnoux G, Eich T, Sieglin B, Devaux S, Zeidner W, Morlock C, Kruezi U, Sergienko G, Kinna D, Thomas PD, Rack M; JET EFDA Contributors.

Rev Sci Instrum. 2012 Oct;83(10):10D530. doi: 10.1063/1.4740523.

PMID:
23130793
30.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium.

PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16.

31.

InterPro in 2011: new developments in the family and domain prediction database.

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.

Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948. Epub 2011 Nov 16.

32.

BioPAX support in CellDesigner.

Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD.

Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21.

33.

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

Gaudet P, Livstone MS, Lewis SE, Thomas PD.

Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.

34.

Ontologies and standards in bioscience research: for machine or for human.

Mi H, Thomas PD.

Front Physiol. 2011 Feb 21;2:5. doi: 10.3389/fphys.2011.00005. eCollection 2011.

35.

Self-generated Domains of Quality of Life in Children with and Without Cerebral Palsy.

Vinson J, Shank L, Thomas PD, Warschausky S.

J Dev Phys Disabil. 2010 Oct 1;22(5):497-508.

36.

PharmGKB summary: dopamine receptor D2.

Mi H, Thomas PD, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB.

Pharmacogenet Genomics. 2011 Jun;21(6):350-6. doi: 10.1097/FPC.0b013e32833ee605. No abstract available.

37.

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.

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.

Genome Biol. 2010;11(7):R73. doi: 10.1186/gb-2010-11-7-r73. Epub 2010 Jul 13.

38.

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

Thomas PD.

BMC Bioinformatics. 2010 Jun 9;11:312. doi: 10.1186/1471-2105-11-312.

39.

The use of orthologous sequences to predict the impact of amino acid substitutions on protein function.

Marini NJ, Thomas PD, Rine J.

PLoS Genet. 2010 May 27;6(5):e1000968. doi: 10.1371/journal.pgen.1000968.

40.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16.

41.

Fatal cerebral arterial gas embolism after endoscopic retrograde cholangiopancreatography.

Rangappa P, Uhde B, Byard RW, Wurm A, Thomas PD.

Indian J Crit Care Med. 2009 Apr-Jun;13(2):108-12. doi: 10.4103/0972-5229.56061.

42.

Parenting and social functioning of children with and without cerebral palsy.

Cunningham SD, Warschausky S, Thomas PD.

Rehabil Psychol. 2009 Feb;54(1):109-15.

PMID:
19618710
43.

A systems biology network model for genetic association studies of nicotine addiction and treatment.

Thomas PD, Mi H, Swan GE, Lerman C, Benowitz N, Tyndale RF, Bergen AW, Conti DV; Pharmacogenetics of Nicotine Addiction and Treatment Consortium.

Pharmacogenet Genomics. 2009 Jul;19(7):538-51. doi: 10.1097/FPC.0b013e32832e2ced.

44.

Dopamine genes and nicotine dependence in treatment-seeking and community smokers.

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.

Neuropsychopharmacology. 2009 Sep;34(10):2252-64. doi: 10.1038/npp.2009.52. Epub 2009 Jun 3.

45.

InterPro: the integrative protein signature database.

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.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

46.

Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation.

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.

Hum Mol Genet. 2008 Sep 15;17(18):2834-48. doi: 10.1093/hmg/ddn181. Epub 2008 Jul 1.

47.

Ontology annotation: mapping genomic regions to biological function.

Thomas PD, Mi H, Lewis S.

Curr Opin Chem Biol. 2007 Feb;11(1):4-11. Epub 2007 Jan 5. Review.

PMID:
17208035
48.

New developments in the InterPro database.

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.

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

49.
50.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.

Mi H, Guo N, Kejariwal A, Thomas PD.

Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. Epub 2006 Nov 27.

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