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Pan-cancer proteogenomics connects oncogenic drivers to functional states.
Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L; Clinical Proteomic Tumor Analysis Consortium. Li Y, et al. Among authors: ruiz serra v. Cell. 2023 Aug 31;186(18):3921-3944.e25. doi: 10.1016/j.cell.2023.07.014. Epub 2023 Aug 14. Cell. 2023. PMID: 37582357 Free article.
The structural coverage of the human proteome before and after AlphaFold.
Porta-Pardo E, Ruiz-Serra V, Valentini S, Valencia A. Porta-Pardo E, et al. Among authors: ruiz serra v. PLoS Comput Biol. 2022 Jan 24;18(1):e1009818. doi: 10.1371/journal.pcbi.1009818. eCollection 2022 Jan. PLoS Comput Biol. 2022. PMID: 35073311 Free PMC article.
Local energetic frustration conservation in protein families and superfamilies.
Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Freiberger MI, et al. Among authors: ruiz serra v. Nat Commun. 2023 Dec 16;14(1):8379. doi: 10.1038/s41467-023-43801-2. Nat Commun. 2023. PMID: 38104123 Free PMC article.