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EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.
Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, R Leach A, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, McEntyre J. Thakur M, et al. Among authors: vizcaino ja. Nucleic Acids Res. 2024 Nov 28:gkae1089. doi: 10.1093/nar/gkae1089. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39607697
REDIportal: toward an integrated view of the A-to-I editing.
D'Addabbo P, Cohen-Fultheim R, Twersky I, Fonzino A, Silvestris DA, Prakash A, Mazzacuva PL, Vizcaino JA, Green A, Sweeney B, Yates A, Lussi Y, Luo J, Martin MJ, Eisenberg E, Levanon EY, Pesole G, Picardi E. D'Addabbo P, et al. Among authors: vizcaino ja. Nucleic Acids Res. 2024 Nov 26:gkae1083. doi: 10.1093/nar/gkae1083. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39588754
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.
Klein J, Lam H, Mak TD, Bittremieux W, Perez-Riverol Y, Gabriels R, Shofstahl J, Hecht H, Binz PA, Kawano S, Van Den Bossche T, Carver J, Neely BA, Mendoza L, Suomi T, Claeys T, Payne T, Schulte D, Sun Z, Hoffmann N, Zhu Y, Neumann S, Jones AR, Bandeira N, Vizcaíno JA, Deutsch EW. Klein J, et al. Among authors: vizcaino ja. Anal Chem. 2024 Nov 19;96(46):18491-18501. doi: 10.1021/acs.analchem.4c04091. Epub 2024 Nov 8. Anal Chem. 2024. PMID: 39514576 Free PMC article.
The PRIDE database at 20 years: 2025 update.
Perez-Riverol Y, Bandla C, Kundu DJ, Kamatchinathan S, Bai J, Hewapathirana S, John NS, Prakash A, Walzer M, Wang S, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: vizcaino ja. Nucleic Acids Res. 2024 Nov 4:gkae1011. doi: 10.1093/nar/gkae1011. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39494541
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. Deutsch EW, et al. Among authors: vizcaino ja. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. bioRxiv. 2024. PMID: 39314370 Free PMC article. Preprint.
The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data.
Kopczynski D, Ejsing CS, McDonald JG, Bamba T, Baker ES, Bertrand-Michel J, Brügger B, Coman C, Ellis SR, Garrett TJ, Griffiths WJ, Guan XL, Han X, Höring M, Holčapek M, Hoffmann N, Huynh K, Lehmann R, Jones JW, Kaddurah-Daouk R, Köfeler HC, Meikle PJ, Metz TO, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Torta F, Vizcaíno JA, Welti R, Wenk MR, Wolrab D, Xia Y, Ekroos K, Ahrends R, Liebisch G. Kopczynski D, et al. Among authors: vizcaino ja. J Lipid Res. 2024 Sep;65(9):100621. doi: 10.1016/j.jlr.2024.100621. Epub 2024 Aug 14. J Lipid Res. 2024. PMID: 39151590 Free PMC article.
Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java.
Bielow C, Hoffmann N, Jimenez-Morales D, Van Den Bossche T, Vizcaíno JA, Tabb DL, Bittremieux W, Walzer M. Bielow C, et al. Among authors: vizcaino ja. J Am Soc Mass Spectrom. 2024 Aug 7;35(8):1875-1882. doi: 10.1021/jasms.4c00174. Epub 2024 Jun 25. J Am Soc Mass Spectrom. 2024. PMID: 38918936 Free PMC article.
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.
Ramsbottom KA, Prakash A, Perez-Riverol Y, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. Ramsbottom KA, et al. Among authors: vizcaino ja. J Proteome Res. 2024 Jul 5;23(7):2518-2531. doi: 10.1021/acs.jproteome.4c00187. Epub 2024 May 29. J Proteome Res. 2024. PMID: 38810119 Free PMC article.
168 results