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Items: 1 to 20 of 69

1.

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.

2.

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.

3.

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.

4.

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.

5.

Childhood predictors of lung function trajectories and future COPD risk: a prospective cohort study from the first to the sixth decade of life.

Bui DS, Lodge CJ, Burgess JA, Lowe AJ, Perret J, Bui MQ, Bowatte G, Gurrin L, Johns DP, Thompson BR, Hamilton GS, Frith PA, James AL, Thomas PS, Jarvis D, Svanes C, Russell M, Morrison SC, Feather I, Allen KJ, Wood-Baker R, Hopper J, Giles GG, Abramson MJ, Walters EH, Matheson MC, Dharmage SC.

Lancet Respir Med. 2018 Jul;6(7):535-544. doi: 10.1016/S2213-2600(18)30100-0. Epub 2018 Apr 5.

6.

Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains.

Davis RG, Park HM, Kim K, Greer JB, Fellers RT, LeDuc RD, Romanova EV, Rubakhin SS, Zombeck JA, Wu C, Yau PM, Gao P, van Nispen AJ, Patrie SM, Thomas PM, Sweedler JV, Rhodes JS, Kelleher NL.

Anal Chem. 2018 Mar 20;90(6):3802-3810. doi: 10.1021/acs.analchem.7b04108. Epub 2018 Feb 26.

PMID:
29481055
7.

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.

8.

Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients.

Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J.

Am J Transplant. 2017 Sep;17(9):2458-2467. doi: 10.1111/ajt.14359. Epub 2017 Jun 27.

9.

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.

Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A; NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2301-2306. doi: 10.1073/pnas.1621192114. Epub 2017 Feb 13.

10.

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.

11.

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.

12.

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.

13.

The Gene Ontology and the Meaning of Biological Function.

Thomas PD.

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

PMID:
27812932
14.

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.

15.

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
16.

Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection.

Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, Thomas PM, Friedewald JJ, Salomon DR, Abecassis MM, Kelleher NL.

Proteomics. 2016 Jul;16(14):2048-58. doi: 10.1002/pmic.201600008.

17.

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.

18.

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.

19.

Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach.

Lehmann R, Childs L, Thomas P, Abreu M, Fuhr L, Herzel H, Leser U, Relógio A.

PLoS One. 2015 May 6;10(5):e0126283. doi: 10.1371/journal.pone.0126283. eCollection 2015.

20.

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.

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