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Page 1
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: tokheim c. 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.
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation.
Zhang W, Roy Burman SS, Chen J, Donovan KA, Cao Y, Shu C, Zhang B, Zeng Z, Gu S, Zhang Y, Li D, Fischer ES, Tokheim C, Shirley Liu X. Zhang W, et al. Among authors: tokheim c. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):882-898. doi: 10.1016/j.gpb.2022.11.008. Epub 2022 Dec 6. Genomics Proteomics Bioinformatics. 2022. PMID: 36494034 Free PMC article.
Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA.
Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Yang L, et al. Among authors: tokheim c. Nat Protoc. 2023 Aug;18(8):2404-2414. doi: 10.1038/s41596-023-00841-8. Epub 2023 Jun 30. Nat Protoc. 2023. PMID: 37391666 Review.
Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.
Sahu A, Wang X, Munson P, Klomp JPG, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JAP, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KT. Sahu A, et al. Among authors: tokheim c. Cancer Discov. 2023 Mar 1;13(3):672-701. doi: 10.1158/2159-8290.CD-22-0244. Cancer Discov. 2023. PMID: 36745048 Free PMC article.
In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target.
Wang X, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z, Zhang Y, Li Z, Zhang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang P, Cejas P, Lim K, Long H, Brown M, Liu XS. Wang X, et al. Among authors: tokheim c. Cell. 2021 Oct 14;184(21):5357-5374.e22. doi: 10.1016/j.cell.2021.09.006. Epub 2021 Sep 27. Cell. 2021. PMID: 34582788 Free PMC article.
Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade.
Gu SS, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos MP, Font-Tello A, Gjini E, Lako A, Lim K, Conway J, Tewari AK, Zeng Z, Sahu AD, Tokheim C, Weirather JL, Fu J, Zhang Y, Kroger B, Liang JH, Cejas P, Freeman GJ, Rodig S, Long HW, Gewurz BE, Hodi FS, Brown M, Liu XS. Gu SS, et al. Among authors: tokheim c. Cancer Discov. 2021 Jun;11(6):1524-1541. doi: 10.1158/2159-8290.CD-20-0812. Epub 2021 Feb 15. Cancer Discov. 2021. PMID: 33589424 Free PMC article.
Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.
Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ. Zeng Z, et al. Among authors: tokheim c. Clin Cancer Res. 2021 Sep 15;27(18):5049-5061. doi: 10.1158/1078-0432.CCR-20-3251. Epub 2020 Dec 15. Clin Cancer Res. 2021. PMID: 33323402 Free PMC article.
33 results