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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2008 1
2010 2
2011 2
2012 6
2013 8
2014 6
2015 12
2016 10
2017 12
2018 8
2019 11
2020 8
2021 12
2022 6
2023 7
2024 9
2025 7
2026 10

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122 results

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Page 1
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. Nucleic Acids Res. 2025 Jan 6;53(D1):D543-D553. doi: 10.1093/nar/gkae1011. Nucleic Acids Res. 2025. PMID: 39494541 Free PMC article.
A standardized framework for circulating blood proteomics.
Cai X, Geyer PE, Perez-Riverol Y, Omenn GS, Dong L, Winkler R, Ahadi S, Lössl P, Yu X, Chang C, Ralser M, Jimenez CR, Zhao Y, Chen YJ, Poon TCW, Bache N, Shi L, Dai X, Wang Z, Zhu Y, Fang X, Schwenk JM, Van Eyk JE, Völker U, Guo T. Cai X, et al. Among authors: perez riverol y. Nat Genet. 2025 Oct;57(10):2371-2380. doi: 10.1038/s41588-025-02319-7. Epub 2025 Sep 23. Nat Genet. 2025. PMID: 40987950 Review.
AI proteomics: from protein identification to virtual cells.
Sun Y, A J, Liu Z, Sun R, Qian L, Payne SH, Bittremieux W, Ralser M, Li C, Chen Y, Dong Z, Perez-Riverol Y, Khan A, Sander C, Aebersold R, Vizcaíno JA, Krieger JR, Yao J, Han W, Zhang L, Zhu Y, Xuan Y, Sun BB, Qiao L, Hermjakob H, Tang H, Gao H, Deng Y, Zhong Q, Chang C, Bandeira N, Li M, E W, Sun S, Yang Y, Omenn GS, Zhang Y, Xu P, Fu Y, Liu X, Overall CM, Wang Y, Deutsch EW, Chen L, Cox J, Demichev V, He F, Huang J, Jin H, Liu C, Li N, Luan Z, Song J, Yu K, Wan W, Wang T, Zhang K, Zhang L, Bell PA, Mann M, Zhang B, Guo T. Sun Y, et al. Among authors: perez riverol y. Nat Methods. 2026 Sep;23(9):1697-1709. doi: 10.1038/s41592-026-03085-y. Epub 2026 Jul 28. Nat Methods. 2026. PMID: 42521824 Review.
Blood proteomics: insights from public data.
Larrea-Sebal A, Dai C, Brenes AJ, Korff K, Neely BA, Geyer PE, Dagley LF, Unwin RD, Naba A, MacCoss MJ, Guo T, Deutsch EW, Martin C, Schwenk JM, Perez-Riverol Y. Larrea-Sebal A, et al. Among authors: perez riverol y. Genome Biol. 2026 Mar 12;27(1):81. doi: 10.1186/s13059-026-04027-9. Genome Biol. 2026. PMID: 41821120 Free PMC article. Review.
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.
Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J. Thakur M, et al. Among authors: perez riverol y. Nucleic Acids Res. 2024 Jan 5;52(D1):D10-D17. doi: 10.1093/nar/gkad1088. Nucleic Acids Res. 2024. PMID: 38015445 Free PMC article. Review.
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.
Van Den Bossche T, Alexandrov T, Bilbao A, Bittremieux W, Brigante FI, Chambers MC, Charkow J, Deutsch E, Dowsey AW, El Abiead Y, Gabriels R, Hecht H, Heuckeroth S, Klein JA, Knierman M, Martens L, Moritz RL, McCall LI, Neumann S, Perez-Riverol Y, Röst HL, Price EJ, Shofstahl J, Tabb DL, Uszkoreit J, Vizcaíno JA, Wang M, Willems S, Winkelhardt D, Kohlbacher O, Wein SP. Van Den Bossche T, et al. Among authors: perez riverol y. J Proteome Res. 2025 Nov 7;24(11):5329-5335. doi: 10.1021/acs.jproteome.5c00435. Epub 2025 Oct 2. J Proteome Res. 2025. PMID: 41037468 Free PMC article. Review.
Universal Spectrum Identifier for mass spectra.
Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N. Deutsch EW, et al. Among authors: perez riverol y. Nat Methods. 2021 Jul;18(7):768-770. doi: 10.1038/s41592-021-01184-6. Epub 2021 Jun 28. Nat Methods. 2021. PMID: 34183830 Free PMC article.
Open-Source and FAIR Research Software for Proteomics.
Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE. Perez-Riverol Y, et al. J Proteome Res. 2025 May 2;24(5):2222-2234. doi: 10.1021/acs.jproteome.4c01079. Epub 2025 Apr 23. J Proteome Res. 2025. PMID: 40267229 Free PMC article. Review.
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.
Expanding the Use of Spectral Libraries in Proteomics.
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Deutsch EW, et al. Among authors: perez riverol y. J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11. J Proteome Res. 2018. PMID: 30270626 Free PMC article. Review.
122 results