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Exploring autophagy with Gene Ontology.
Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Denny P, et al. Autophagy. 2018;14(3):419-436. doi: 10.1080/15548627.2017.1415189. Epub 2018 Feb 17. Autophagy. 2018. PMID: 29455577 Free PMC article. Review.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: denny p. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Gene Ontology Consortium: going forward.
Gene Ontology Consortium. Gene Ontology Consortium. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26. Nucleic Acids Res. 2015. PMID: 25428369 Free PMC article.
The Gene Ontology resource: enriching a GOld mine.
Gene Ontology Consortium. Gene Ontology Consortium. Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334. doi: 10.1093/nar/gkaa1113. Nucleic Acids Res. 2021. PMID: 33290552 Free PMC article.
Computational analysis of the LRRK2 interactome.
Manzoni C, Denny P, Lovering RC, Lewis PA. Manzoni C, et al. Among authors: denny p. PeerJ. 2015 Feb 19;3:e778. doi: 10.7717/peerj.778. eCollection 2015. PeerJ. 2015. PMID: 25737818 Free PMC article.
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K; UniProt Consortium. MacDougall A, et al. Bioinformatics. 2020 Nov 1;36(17):4643-4648. doi: 10.1093/bioinformatics/btaa485. Bioinformatics. 2020. PMID: 32399560 Free PMC article.
EuroPhenome: a repository for high-throughput mouse phenotyping data.
Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S, Lengger C, Maier H, Melvin D, Meziane H, Richardson D, Wells S, White J, Wood J; EUMODIC Consortium; de Angelis MH, Brown SD, Hancock JM, Mallon AM. Morgan H, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D577-85. doi: 10.1093/nar/gkp1007. Epub 2009 Nov 23. Nucleic Acids Res. 2010. PMID: 19933761 Free PMC article.
A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy.
Ashrafian H, Docherty L, Leo V, Towlson C, Neilan M, Steeples V, Lygate CA, Hough T, Townsend S, Williams D, Wells S, Norris D, Glyn-Jones S, Land J, Barbaric I, Lalanne Z, Denny P, Szumska D, Bhattacharya S, Griffin JL, Hargreaves I, Fernandez-Fuentes N, Cheeseman M, Watkins H, Dear TN. Ashrafian H, et al. Among authors: denny p. PLoS Genet. 2010 Jun 24;6(6):e1001000. doi: 10.1371/journal.pgen.1001000. PLoS Genet. 2010. PMID: 20585624 Free PMC article.
229 results