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Page 1
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, Rehma… See abstract for full author list ➔ Jiang Y, et al. Among authors: huntley rp. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. Barrell D, et al. Among authors: huntley rp. Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403. doi: 10.1093/nar/gkn803. Epub 2008 Oct 27. Nucleic Acids Res. 2009. PMID: 18957448 Free PMC article.
QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. Binns D, et al. Bioinformatics. 2009 Nov 15;25(22):3045-6. doi: 10.1093/bioinformatics/btp536. Epub 2009 Sep 10. Bioinformatics. 2009. PMID: 19744993 Free PMC article.
The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium. UniProt Consortium. Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846. Epub 2009 Oct 20. Nucleic Acids Res. 2010. PMID: 19843607 Free PMC article.
QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R. Huntley RP, et al. Database (Oxford). 2009;2009:bap010. doi: 10.1093/database/bap010. Epub 2009 Sep 29. Database (Oxford). 2009. PMID: 20157483 Free PMC article.
The Renal Gene Ontology Annotation Initiative.
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. Alam-Faruque Y, et al. Among authors: huntley rp. Organogenesis. 2010 Apr-Jun;6(2):71-5. doi: 10.4161/org.6.2.11294. Organogenesis. 2010. PMID: 20885853 Free PMC article. Review.
UniProt Knowledgebase: a hub of integrated protein data.
Magrane M; UniProt Consortium. Magrane M, et al. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. Database (Oxford). 2011. PMID: 21447597 Free PMC article.
The UniProt-GO Annotation database in 2011.
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R. Dimmer EC, et al. Among authors: huntley rp. Nucleic Acids Res. 2012 Jan;40(Database issue):D565-70. doi: 10.1093/nar/gkr1048. Epub 2011 Nov 28. Nucleic Acids Res. 2012. PMID: 22123736 Free PMC article.
The impact of focused Gene Ontology curation of specific mammalian systems.
Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. Alam-Faruque Y, et al. Among authors: huntley rp. PLoS One. 2011;6(12):e27541. doi: 10.1371/journal.pone.0027541. Epub 2011 Dec 9. PLoS One. 2011. PMID: 22174742 Free PMC article.
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R. Mutowo-Meullenet P, et al. Among authors: huntley rp. Database (Oxford). 2013 Jan 17;2013:bas062. doi: 10.1093/database/bas062. Print 2013. Database (Oxford). 2013. PMID: 23327938 Free PMC article.
51 results