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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: warwick vesztrocy a. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, de Farias TM, Zile K, Stevenson C, Long J, Redestig H, Gonnet GH, Dessimoz C. Altenhoff AM, et al. Among authors: warwick vesztrocy a. Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019. Nucleic Acids Res. 2018. PMID: 29106550 Free PMC article.
GOATOOLS: A Python library for Gene Ontology analyses.
Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. Klopfenstein DV, et al. Among authors: warwick vesztrocy a. Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z. Sci Rep. 2018. PMID: 30022098 Free PMC article.
OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. Altenhoff AM, et al. Among authors: warwick vesztrocy a. Genome Res. 2019 Jul;29(7):1152-1163. doi: 10.1101/gr.243212.118. Epub 2019 Jun 24. Genome Res. 2019. PMID: 31235654 Free PMC article.
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff AM, Train CM, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova HS, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. Altenhoff AM, et al. Among authors: warwick vesztrocy a. Nucleic Acids Res. 2021 Jan 8;49(D1):D373-D379. doi: 10.1093/nar/gkaa1007. Nucleic Acids Res. 2021. PMID: 33174605 Free PMC article.
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Altenhoff AM, Warwick Vesztrocy A, Bernard C, Train CM, Nicheperovich A, Prieto Baños S, Julca I, Moi D, Nevers Y, Majidian S, Dessimoz C, Glover NM. Altenhoff AM, et al. Among authors: warwick vesztrocy a. Nucleic Acids Res. 2024 Jan 5;52(D1):D513-D521. doi: 10.1093/nar/gkad1020. Nucleic Acids Res. 2024. PMID: 37962356 Free PMC article.
New genome assembly of the barn owl (Tyto alba alba).
Ducrest AL, Neuenschwander S, Schmid-Siegert E, Pagni M, Train C, Dylus D, Nevers Y, Warwick Vesztrocy A, San-Jose LM, Dupasquier M, Dessimoz C, Xenarios I, Roulin A, Goudet J. Ducrest AL, et al. Among authors: warwick vesztrocy a. Ecol Evol. 2020 Feb 19;10(5):2284-2298. doi: 10.1002/ece3.5991. eCollection 2020 Mar. Ecol Evol. 2020. PMID: 32184981 Free PMC article.
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