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Proteogenomic data and resources for pan-cancer analysis.
Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH; Clinical Proteomic Tumor Analysis Consortium. Li Y, et al. Among authors: wang y, wang p, wang jm, wang lb. Cancer Cell. 2023 Aug 14;41(8):1397-1406. doi: 10.1016/j.ccell.2023.06.009. Cancer Cell. 2023. PMID: 37582339 Free PMC article. Review.
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: wang lb. 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.
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation.
Geffen Y, Anand S, Akiyama Y, Yaron TM, Song Y, Johnson JL, Govindan A, Babur Ö, Li Y, Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F, Cantley LC, Ding L, Getz G; Clinical Proteomic Tumor Analysis Consortium. Geffen Y, et al. Among authors: wang lb. Cell. 2023 Aug 31;186(18):3945-3967.e26. doi: 10.1016/j.cell.2023.07.013. Epub 2023 Aug 14. Cell. 2023. PMID: 37582358 Free PMC article.
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin.
Liang WW, Lu RJ, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L; Clinical Proteomic Tumor Analysis Consortium. Liang WW, et al. Cancer Cell. 2023 Sep 11;41(9):1567-1585.e7. doi: 10.1016/j.ccell.2023.07.013. Epub 2023 Aug 14. Cancer Cell. 2023. PMID: 37582362 Free PMC article.
Deep learning integrates histopathology and proteogenomics at a pan-cancer level.
Wang JM, Hong R, Demicco EG, Tan J, Lazcano R, Moreira AL, Li Y, Calinawan A, Razavian N, Schraink T, Gillette MA, Omenn GS, An E, Rodriguez H, Tsirigos A, Ruggles KV, Ding L, Robles AI, Mani DR, Rodland KD, Lazar AJ, Liu W, Fenyö D; Clinical Proteomic Tumor Analysis Consortium. Wang JM, et al. Cell Rep Med. 2023 Sep 19;4(9):101173. doi: 10.1016/j.xcrm.2023.101173. Epub 2023 Aug 14. Cell Rep Med. 2023. PMID: 37582371 Free PMC article.
Pan-cancer proteogenomics characterization of tumor immunity.
Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P; Clinical Proteomic Tumor Analysis Consortium. Petralia F, et al. Among authors: wang y, wang p, wang jm. Cell. 2024 Feb 29;187(5):1255-1277.e27. doi: 10.1016/j.cell.2024.01.027. Epub 2024 Feb 14. Cell. 2024. PMID: 38359819 Free PMC article.
dbCRID: a database of chromosomal rearrangements in human diseases.
Kong F, Zhu J, Wu J, Peng J, Wang Y, Wang Q, Fu S, Yuan LL, Li T. Kong F, et al. Among authors: wang y, wang q. Nucleic Acids Res. 2011 Jan;39(Database issue):D895-900. doi: 10.1093/nar/gkq1038. Epub 2010 Nov 4. Nucleic Acids Res. 2011. PMID: 21051346 Free PMC article.
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