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Page 1
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Clark DJ, et al. Among authors: ruggles k. Cell. 2019 Oct 31;179(4):964-983.e31. doi: 10.1016/j.cell.2019.10.007. Cell. 2019. PMID: 31675502 Free PMC article.
mRNA COVID-19 vaccine elicits potent adaptive immune response without the persistent inflammation seen in SARS-CoV-2 infection.
Ivanova EN, Shwetar J, Devlin JC, Buus TB, Gray-Gaillard S, Koide A, Cornelius A, Samanovic MI, Herrera A, Mimitou EP, Zhang C, Karmacharya T, Desvignes L, Ødum N, Smibert P, Ulrich RJ, Mulligan MJ, Koide S, Ruggles KV, Herati RS, Koralov SB. Ivanova EN, et al. medRxiv [Preprint]. 2023 Aug 23:2021.04.20.21255677. doi: 10.1101/2021.04.20.21255677. medRxiv. 2023. Update in: iScience. 2023 Nov 24;26(12):108572. doi: 10.1016/j.isci.2023.108572. PMID: 33907755 Free PMC article. Updated. Preprint.
Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.
Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA. Mertins P, et al. Mol Cell Proteomics. 2014 Jul;13(7):1690-704. doi: 10.1074/mcp.M113.036392. Epub 2014 Apr 9. Mol Cell Proteomics. 2014. PMID: 24719451 Free PMC article.
CPTAC Assay Portal: a repository of targeted proteomic assays.
Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC); Paulovich AG. Whiteaker JR, et al. Nat Methods. 2014 Jul;11(7):703-4. doi: 10.1038/nmeth.3002. Nat Methods. 2014. PMID: 24972168 Free PMC article. No abstract available.
Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts.
Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyö D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL. Ntai I, et al. Mol Cell Proteomics. 2016 Jan;15(1):45-56. doi: 10.1074/mcp.M114.047480. Epub 2015 Oct 26. Mol Cell Proteomics. 2016. PMID: 26503891 Free PMC article.
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D. Ruggles KV, et al. Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2. Mol Cell Proteomics. 2016. PMID: 26631509 Free PMC article.
PGx: Putting Peptides to BED.
Askenazi M, Ruggles KV, Fenyö D. Askenazi M, et al. J Proteome Res. 2016 Mar 4;15(3):795-9. doi: 10.1021/acs.jproteome.5b00870. Epub 2015 Dec 18. J Proteome Res. 2016. PMID: 26638927 Free PMC article.
Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.
Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG. Whiteaker JR, et al. Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13. Methods Mol Biol. 2016. PMID: 26867747 Free PMC article.
Proteogenomics connects somatic mutations to signalling in breast cancer.
Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC. Mertins P, et al. Among authors: ruggles kv. Nature. 2016 Jun 2;534(7605):55-62. doi: 10.1038/nature18003. Epub 2016 May 25. Nature. 2016. PMID: 27251275 Free PMC article.
128 results