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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: dessimoz c. Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z. Sci Rep. 2018. PMID: 30022098 Free PMC article.
New developments for the Quest for Orthologs benchmark service.
Altenhoff A, Nevers Y, Tran V, Jyothi D, Martin M, Cosentino S, Majidian S, Marcet-Houben M, Fuentes-Palacios D, Persson E, Walsh T, Lecompte O, Gabaldón T, Kelly S, Hu Y, Iwasaki W, Capella-Gutierrez S, Dessimoz C, Thomas PD, Ebersberger I, Sonnhammer E. Altenhoff A, et al. Among authors: dessimoz c. NAR Genom Bioinform. 2024 Dec 11;6(4):lqae167. doi: 10.1093/nargab/lqae167. eCollection 2024 Dec. NAR Genom Bioinform. 2024. PMID: 39664814 Free PMC article.
Primer on the Gene Ontology.
Gaudet P, Škunca N, Hu JC, Dessimoz C. Gaudet P, et al. Among authors: dessimoz c. Methods Mol Biol. 2017;1446:25-37. doi: 10.1007/978-1-4939-3743-1_3. Methods Mol Biol. 2017. PMID: 27812933 Free PMC article.
A Gene Ontology Tutorial in Python.
Vesztrocy AW, Dessimoz C. Vesztrocy AW, et al. Among authors: dessimoz c. Methods Mol Biol. 2017;1446:221-229. doi: 10.1007/978-1-4939-3743-1_16. Methods Mol Biol. 2017. PMID: 27812946
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: dessimoz c. Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019. Nucleic Acids Res. 2018. PMID: 29106550 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: dessimoz c. 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.
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: dessimoz c. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Identifying orthologs with OMA: A primer.
Zahn-Zabal M, Dessimoz C, Glover NM. Zahn-Zabal M, et al. Among authors: dessimoz c. F1000Res. 2020 Jan 17;9:27. doi: 10.12688/f1000research.21508.1. eCollection 2020. F1000Res. 2020. PMID: 32089838 Free PMC article.
123 results