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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.
PMID: 38364782 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, Gonzalez-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, Gumuş ZH, Hostetter G, Fenyo D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P, Clinical Proteomic Tumor Analysis Consortium
Cell. 2024 Feb 29;187(5):1255-1277.e27. doi: 10.1016/j.cell.2024.01.027. Epub 2024 Feb 14.
PMID: 38359819 Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma.
Savage SR, Wang Y, Chen L, Jewell S, Newton C, Dou Y, Li QK, Bathe OF, Robles AI, Omenn GS, Thiagarajan M, Zhang H, Hostetter G, Zhang B
Clin Proteomics. 2024 Jan 30;21(1):7. doi: 10.1186/s12014-024-09450-3. Epub 2024 Jan 30.
PMID: 38291365 IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining.
Savage SR, Zhang Y, Jaehnig EJ, Liao Y, Shi Z, Pham HA, Xu H, Zhang B
Mol Cell Proteomics. 2024 Jan;23(1):100682. doi: 10.1016/j.mcpro.2023.100682. Epub 2023 Nov 21.
PMID: 37993103 Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors.
Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O'Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X
Science. 2023 Sep 8;381(6662):eabn4180. doi: 10.1126/science.abn4180. Epub 2023 Sep 8.
PMID: 37676964 A proteogenomics data-driven knowledge base of human cancer.
Liao Y, Savage SR, Dou Y, Shi Z, Yi X, Jiang W, Lei JT, Zhang B
Cell Syst. 2023 Sep 20;14(9):777-787.e5. doi: 10.1016/j.cels.2023.07.007. Epub 2023 Aug 23.
PMID: 37619559 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, Fenyo D, Clinical Proteomic Tumor Analysis Consortium
Cell Rep Med. 2023 Sep 19;4(9):101173. doi: 10.1016/j.xcrm.2023.101173. Epub 2023 Aug 14.
PMID: 37582371 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
Cell. 2023 Aug 31;186(18):3945-3967.e26. doi: 10.1016/j.cell.2023.07.013. Epub 2023 Aug 14.
PMID: 37582358 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, Fenyo 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
Cell. 2023 Aug 31;186(18):3921-3944.e25. doi: 10.1016/j.cell.2023.07.014. Epub 2023 Aug 14.
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