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The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C. Altenhoff AM, et al. Among authors: fernandez jm. Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308. Nucleic Acids Res. 2020. PMID: 32374845 Free PMC article.
The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives.
Pognan F, Steger-Hartmann T, Díaz C, Blomberg N, Bringezu F, Briggs K, Callegaro G, Capella-Gutierrez S, Centeno E, Corvi J, Drew P, Drewe WC, Fernández JM, Furlong LI, Guney E, Kors JA, Mayer MA, Pastor M, Piñero J, Ramírez-Anguita JM, Ronzano F, Rowell P, Saüch-Pitarch J, Valencia A, van de Water B, van der Lei J, van Mulligen E, Sanz F. Pognan F, et al. Among authors: fernandez jm. Pharmaceuticals (Basel). 2021 Mar 8;14(3):237. doi: 10.3390/ph14030237. Pharmaceuticals (Basel). 2021. PMID: 33800393 Free PMC article.
Recommendations for the FAIRification of genomic track metadata.
Gundersen S, Boddu S, Capella-Gutierrez S, Drabløs F, Fernández JM, Kompova R, Taylor K, Titov D, Zerbino D, Hovig E. Gundersen S, et al. Among authors: fernandez jm. F1000Res. 2021 Apr 1;10:ELIXIR-268. doi: 10.12688/f1000research.28449.1. eCollection 2021. F1000Res. 2021. PMID: 34249331 Free PMC article.
DOME: recommendations for supervised machine learning validation in biology.
Walsh I, Fishman D, Garcia-Gasulla D, Titma T, Pollastri G; ELIXIR Machine Learning Focus Group; Harrow J, Psomopoulos FE, Tosatto SCE. Walsh I, et al. Nat Methods. 2021 Oct;18(10):1122-1127. doi: 10.1038/s41592-021-01205-4. Nat Methods. 2021. PMID: 34316068 Free article. No abstract available.
WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.
Bouyssié D, Altıner P, Capella-Gutierrez S, Fernández JM, Hagemeijer YP, Horvatovich P, Hubálek M, Levander F, Mauri P, Palmblad M, Raffelsberger W, Rodríguez-Navas L, Di Silvestre D, Kunkli BT, Uszkoreit J, Vandenbrouck Y, Vizcaíno JA, Winkelhardt D, Schwämmle V. Bouyssié D, et al. Among authors: fernandez jm. J Proteome Res. 2024 Jan 5;23(1):418-429. doi: 10.1021/acs.jproteome.3c00636. Epub 2023 Dec 1. J Proteome Res. 2024. PMID: 38038272
Interoperability with Moby 1.0--it's better than sharing your toothbrush!
BioMoby Consortium; Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A. BioMoby Consortium, et al. Among authors: fernandez jm, fernandez santa cruz r. Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Brief Bioinform. 2008. PMID: 18238804 Review.
974 results