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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton … See abstract for full author list ➔ Zhou N, et al. Among authors: rodriguez jm. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
APPRIS WebServer and WebServices.
Rodriguez JM, Carro A, Valencia A, Tress ML. Rodriguez JM, et al. Nucleic Acids Res. 2015 Jul 1;43(W1):W455-9. doi: 10.1093/nar/gkv512. Epub 2015 May 18. Nucleic Acids Res. 2015. PMID: 25990727 Free PMC article.
APPRIS 2017: principal isoforms for multiple gene sets.
Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML. Rodriguez JM, et al. Among authors: rodriguez rivas j. Nucleic Acids Res. 2018 Jan 4;46(D1):D213-D217. doi: 10.1093/nar/gkx997. Nucleic Acids Res. 2018. PMID: 29069475 Free PMC article.
Most highly expressed protein-coding genes have a single dominant isoform.
Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML. Ezkurdia I, et al. Among authors: rodriguez jm. J Proteome Res. 2015 Apr 3;14(4):1880-7. doi: 10.1021/pr501286b. Epub 2015 Mar 11. J Proteome Res. 2015. PMID: 25732134 Free PMC article.
APPRIS: selecting functionally important isoforms.
Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML. Rodriguez JM, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D54-D59. doi: 10.1093/nar/gkab1058. Nucleic Acids Res. 2022. PMID: 34755885 Free PMC article.
1,006 results