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DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations.
Wen B, Wang C, Li K, Han P, Holt MV, Savage SR, Lei JT, Dou Y, Shi Z, Li Y, Zhang B
Nat Methods. 2025 Sep;22(9):1857-1867. doi: 10.1038/s41592-025-02797-x. Epub 2025 Aug 26.
PMID: 40859022 Publisher Correction: Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
Muller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J
Nat Commun. 2025 Jul 17;16(1):6591. doi: 10.1038/s41467-025-62094-1. Epub 2025 Jul 17.
PMID: 40675995 Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
Muller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J
Nat Commun. 2025 May 22;16(1):4771. doi: 10.1038/s41467-025-59779-y. Epub 2025 May 22.
PMID: 40404650 Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets.
Kołodziejczak-Guglas I, Simões RLS, de Souza Santos E, Demicco EG, Lazcano Segura RN, Ma W, Wang P, Geffen Y, Storrs E, Petralia F, Colaprico A, da Veiga Leprevost F, Pugliese P, Ceccarelli M, Noushmehr H, Nesvizhskii AI, Kamińska B, Priebe W, Lubiński J, Zhang B, Lazar AJ, Kurzawa P, Mesri M, Robles AI, Clinical Proteomic Tumor Analysis Consortium, Ding L, Malta TM, Wiznerowicz M
Cell Genom. 2025 Jun 11;5(6):100851. doi: 10.1016/j.xgen.2025.100851. Epub 2025 Apr 17.
PMID: 40250426 Precision proteogenomics reveals pan-cancer impact of germline variants.
Martins Rodrigues F, Terekhanova NV, Imbach KJ, Clauser KR, Esai Selvan M, Mendizabal I, Geffen Y, Akiyama Y, Maynard M, Yaron TM, Li Y, Cao S, Storrs EP, Gonda OS, Gaite-Reguero A, Govindan A, Kawaler EA, Wyczalkowski MA, Klein RJ, Turhan B, Krug K, Mani DR, Leprevost FDV, Nesvizhskii AI, Carr SA, Fenyo D, Gillette MA, Colaprico A, Iavarone A, Robles AI, Huang KL, Kumar-Sinha C, Aguet F, Lazar AJ, Cantley LC, Marigorta UM, Gumuş ZH, Bailey MH, Getz G, Porta-Pardo E, Ding L, Clinical Proteomic Tumor Analysis Consortium
Cell. 2025 May 1;188(9):2312-2335.e26. doi: 10.1016/j.cell.2025.03.026. Epub 2025 Apr 14.
PMID: 40233739 Multi-scale signaling and tumor evolution in high-grade gliomas.
Liu J, Cao S, Imbach KJ, Gritsenko MA, Lih TM, Kyle JE, Yaron-Barir TM, Binder ZA, Li Y, Strunilin I, Wang YT, Tsai CF, Ma W, Chen L, Clark NM, Shinkle A, Naser Al Deen N, Caravan W, Houston A, Simin FA, Wyczalkowski MA, Wang LB, Storrs E, Chen S, Illindala R, Li YD, Jayasinghe RG, Rykunov D, Cottingham SL, Chu RK, Weitz KK, Moore RJ, Sagendorf T, Petyuk VA, Nestor M, Bramer LM, Stratton KG, Schepmoes AA, Couvillion SP, Eder J, Kim YM, Gao Y, Fillmore TL, Zhao R, Monroe ME, Southard-Smith AN, Li YE, Jui-Hsien Lu R, Johnson JL, Wiznerowicz M, Hostetter G, Newton CJ, Ketchum KA, Thangudu RR, Barnholtz-Sloan JS, Wang P, Fenyo D, An E, Thiagarajan M, Robles AI, Mani DR, Smith RD, Porta-Pardo E, Cantley LC, Iavarone A, Chen F, Mesri M, Nasrallah MP, Zhang H, Resnick AC, Chheda MG, Rodland KD, Liu T, Ding L, Philadelphia Coalition for a Cure, Clinical Proteomic Tumor Analysis Consortium
Cancer Cell. 2024 Jul 8;42(7):1217-1238.e19. doi: 10.1016/j.ccell.2024.06.004.
PMID: 38981438 Pan-cancer proteogenomics expands the landscape of therapeutic targets.
Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B
Cell. 2024 Aug 8;187(16):4389-4407.e15. doi: 10.1016/j.cell.2024.05.039. Epub 2024 Jun 24.
PMID: 38917788 Advancing action on the political determinants of health in the United States.
Savage SR, Kraft SA, Tanner C, Houde M
J Public Health Policy. 2024 Sep;45(3):484-494. doi: 10.1057/s41271-024-00497-y. Epub 2024 Jun 20.
PMID: 38902356 Correction to: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.
Savage SR, Zhang B
Clin Proteomics. 2024 Mar 7;21(1):20. doi: 10.1186/s12014-024-09473-w. Epub 2024 Mar 7.
PMID: 38454337 Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.
Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schurer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG
Cell. 2024 Feb 15;187(4):1016. doi: 10.1016/j.cell.2024.01.016.
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