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2021 1
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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: storrs ep. 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 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. 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.
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. 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 article.
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. Schapiro D, et al. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 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.
High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival.
Storrs EP, Chati P, Usmani A, Sloan I, Krasnick BA, Babbra R, Harris PK, Sachs CM, Qaium F, Chatterjee D, Wetzel C, Goedegebuure SP, Hollander T, Anthony H, Ponce J, Khaliq AM, Badiyan S, Kim H, Denardo DG, Lang GD, Cosgrove ND, Kushnir VM, Early DS, Masood A, Lim KH, Hawkins WG, Ding L, Fields RC, Das KK, Chaudhuri AA. Storrs EP, et al. NPJ Precis Oncol. 2023 Oct 19;7(1):105. doi: 10.1038/s41698-023-00455-z. NPJ Precis Oncol. 2023. PMID: 37857854 Free PMC article.
Pollock: fishing for cell states.
Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA, Karpova A, Wang LB, Li Y, Southard-Smith A, Jayasinghe RG, Yao L, Liu R, Wu Y, Terekhanova NV, Zhu H, Herndon JM, Puram S, Chen F, Gillanders WE, Fields RC, Ding L. Storrs EP, et al. Bioinform Adv. 2022 May 13;2(1):vbac028. doi: 10.1093/bioadv/vbac028. eCollection 2022. Bioinform Adv. 2022. PMID: 35603231 Free PMC article.
Co-evolution of tumor and immune cells during progression of multiple myeloma.
Liu R, Gao Q, Foltz SM, Fowles JS, Yao L, Wang JT, Cao S, Sun H, Wendl MC, Sethuraman S, Weerasinghe A, Rettig MP, Storrs EP, Yoon CJ, Wyczalkowski MA, McMichael JF, Kohnen DR, King J, Goldsmith SR, O'Neal J, Fulton RS, Fronick CC, Ley TJ, Jayasinghe RG, Fiala MA, Oh ST, DiPersio JF, Vij R, Ding L. Liu R, et al. Among authors: storrs ep. Nat Commun. 2021 May 7;12(1):2559. doi: 10.1038/s41467-021-22804-x. Nat Commun. 2021. PMID: 33963182 Free PMC article.