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Ten Simple Rules for Taking Advantage of Git and GitHub.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA. Perez-Riverol Y, et al. PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. PLoS Comput Biol. 2016. PMID: 27415786 Free PMC article. No abstract available.
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. Vizcaíno JA, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29. Nucleic Acids Res. 2013. PMID: 23203882 Free PMC article.
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V. Perez-Riverol Y, et al. Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20. Anal Chem. 2013. PMID: 23448308
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. Griss J, et al. Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30. Mol Cell Proteomics. 2014. PMID: 24980485 Free PMC article.
On best practices in the development of bioinformatics software.
Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC. Leprevost Fda V, et al. Front Genet. 2014 Jul 2;5:199. doi: 10.3389/fgene.2014.00199. eCollection 2014. Front Genet. 2014. PMID: 25071829 Free PMC article. No abstract available.
101 results