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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: renaux a. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 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. Among authors: renaux a. Bioinformatics. 2020 Nov 1;36(17):4643-4648. doi: 10.1093/bioinformatics/btaa485. Bioinformatics. 2020. PMID: 32399560 Free PMC article.
Prioritization of oligogenic variant combinations in whole exomes.
Gravel B, Renaux A, Papadimitriou S, Smits G, Nowé A, Lenaerts T. Gravel B, et al. Among authors: renaux a. Bioinformatics. 2024 Mar 29;40(4):btae184. doi: 10.1093/bioinformatics/btae184. Bioinformatics. 2024. PMID: 38603604 Free PMC article.
Faster and more accurate pathogenic combination predictions with VarCoPP2.0.
Versbraegen N, Gravel B, Nachtegael C, Renaux A, Verkinderen E, Nowé A, Lenaerts T, Papadimitriou S. Versbraegen N, et al. Among authors: renaux a. BMC Bioinformatics. 2023 May 1;24(1):179. doi: 10.1186/s12859-023-05291-3. BMC Bioinformatics. 2023. PMID: 37127601 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; The UniProt Consortium. MacDougall A, et al. Among authors: renaux a. Bioinformatics. 2021 Apr 1;36(22-23):5562. doi: 10.1093/bioinformatics/btaa663. Bioinformatics. 2021. PMID: 33821964 Free PMC article. No abstract available.
17 results