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Transfer learning enables predictions in network biology.
Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Theodoris CV, et al. Among authors: zeng z. Nature. 2023 Jun;618(7965):616-624. doi: 10.1038/s41586-023-06139-9. Epub 2023 May 31. Nature. 2023. PMID: 37258680 Free PMC article.
TIMER2.0 for analysis of tumor-infiltrating immune cells.
Li T, Fu J, Zeng Z, Cohen D, Li J, Chen Q, Li B, Liu XS. Li T, et al. Among authors: zeng z. Nucleic Acids Res. 2020 Jul 2;48(W1):W509-W514. doi: 10.1093/nar/gkaa407. Nucleic Acids Res. 2020. PMID: 32442275 Free PMC article.
CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor Cells and T Cells.
Kumar S, Zeng Z, Bagati A, Tay RE, Sanz LA, Hartono SR, Ito Y, Abderazzaq F, Hatchi E, Jiang P, Cartwright ANR, Olawoyin O, Mathewson ND, Pyrdol JW, Li MZ, Doench JG, Booker MA, Tolstorukov MY, Elledge SJ, Chédin F, Liu XS, Wucherpfennig KW. Kumar S, et al. Among authors: zeng z. Cancer Discov. 2021 Aug;11(8):2050-2071. doi: 10.1158/2159-8290.CD-20-1144. Epub 2021 Mar 11. Cancer Discov. 2021. PMID: 33707234 Free PMC article.
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.
Zeng Z, Wong CJ, Yang L, Ouardaoui N, Li D, Zhang W, Gu S, Zhang Y, Liu Y, Wang X, Fu J, Zhou L, Zhang B, Kim S, Yates KB, Brown M, Freeman GJ, Uppaluri R, Manguso R, Liu XS. Zeng Z, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1391-D1397. doi: 10.1093/nar/gkab804. Nucleic Acids Res. 2022. PMID: 34534350 Free PMC article.
Hippo Signaling Pathway Regulates Cancer Cell-Intrinsic MHC-II Expression.
Zeng Z, Gu SS, Ouardaoui N, Tymm C, Yang L, Wong CJ, Li D, Zhang W, Wang X, Weirather JL, Rodig SJ, Hodi FS, Brown M, Liu XS. Zeng Z, et al. Cancer Immunol Res. 2022 Dec 2;10(12):1559-1569. doi: 10.1158/2326-6066.CIR-22-0227. Cancer Immunol Res. 2022. PMID: 36219700
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: zeng z. 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.
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade.
Gu SS, Wang X, Hu X, Jiang P, Li Z, Traugh N, Bu X, Tang Q, Wang C, Zeng Z, Fu J, Meyer C, Zhang Y, Cejas P, Lim K, Wang J, Zhang W, Tokheim C, Sahu AD, Xing X, Kroger B, Ouyang Z, Long H, Freeman GJ, Brown M, Liu XS. Gu SS, et al. Among authors: zeng z. Genome Biol. 2020 Oct 15;21(1):263. doi: 10.1186/s13059-020-02166-1. Genome Biol. 2020. PMID: 33059736 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. 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.
8,418 results