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TRPS1 Is a Lineage-Specific Transcriptional Dependency in Breast Cancer.
Witwicki RM, Ekram MB, Qiu X, Janiszewska M, Shu S, Kwon M, Trinh A, Frias E, Ramadan N, Hoffman G, Yu K, Xie Y, McAllister G, McDonald R, Golji J, Schlabach M, deWeck A, Keen N, Chan HM, Ruddy D, Rejtar T, Sovath S, Silver S, Sellers WR, Jagani Z, Hogarty MD, Roberts C, Brown M, Stegmaier K, Long H, Shivdasani RA, Pellman D, Polyak K. Witwicki RM, et al. Among authors: xie y. Cell Rep. 2018 Oct 30;25(5):1255-1267.e5. doi: 10.1016/j.celrep.2018.10.023. Cell Rep. 2018. PMID: 30380416 Free PMC article.
Androgen Receptor Is a Non-canonical Inhibitor of Wild-Type and Mutant Estrogen Receptors in Hormone Receptor-Positive Breast Cancers.
Ponnusamy S, Asemota S, Schwartzberg LS, Guestini F, McNamara KM, Pierobon M, Font-Tello A, Qiu X, Xie Y, Rao PK, Thiyagarajan T, Grimes B, Johnson DL, Fleming MD, Pritchard FE, Berry MP, Oswaks R, Fine RE, Brown M, Sasano H, Petricoin EF, Long HW, Narayanan R. Ponnusamy S, et al. Among authors: xie y. iScience. 2019 Nov 22;21:341-358. doi: 10.1016/j.isci.2019.10.038. Epub 2019 Oct 23. iScience. 2019. PMID: 31698248 Free PMC article.
Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway.
Kurppa KJ, Liu Y, To C, Zhang T, Fan M, Vajdi A, Knelson EH, Xie Y, Lim K, Cejas P, Portell A, Lizotte PH, Ficarro SB, Li S, Chen T, Haikala HM, Wang H, Bahcall M, Gao Y, Shalhout S, Boettcher S, Shin BH, Thai T, Wilkens MK, Tillgren ML, Mushajiang M, Xu M, Choi J, Bertram AA, Ebert BL, Beroukhim R, Bandopadhayay P, Awad MM, Gokhale PC, Kirschmeier PT, Marto JA, Camargo FD, Haq R, Paweletz CP, Wong KK, Barbie DA, Long HW, Gray NS, Jänne PA. Kurppa KJ, et al. Among authors: xie y. Cancer Cell. 2020 Jan 13;37(1):104-122.e12. doi: 10.1016/j.ccell.2019.12.006. Cancer Cell. 2020. PMID: 31935369 Free PMC article.
Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.
Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y, Weng QY, Fisher DE, Long HW, Brown M, Kim HJ, Wucherpfennig KW. Tay RE, et al. Among authors: xie y. J Exp Med. 2020 Jul 6;217(7):e20191453. doi: 10.1084/jem.20191453. J Exp Med. 2020. PMID: 32374402 Free PMC article.
Integrative analyses of single-cell transcriptome and regulome using MAESTRO.
Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, Liu XS. Wang C, et al. Among authors: xie y. Genome Biol. 2020 Aug 7;21(1):198. doi: 10.1186/s13059-020-02116-x. Genome Biol. 2020. PMID: 32767996 Free PMC article.
Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence.
Wu Z, Zhou J, Zhang X, Zhang Z, Xie Y, Liu JB, Ho ZV, Panda A, Qiu X, Cejas P, Cañadas I, Akarca FG, McFarland JM, Nagaraja AK, Goss LB, Kesten N, Si L, Lim K, Liu Y, Zhang Y, Baek JY, Liu Y, Patil DT, Katz JP, Hai J, Bao C, Stachler M, Qi J, Ishizuka JJ, Nakagawa H, Rustgi AK, Wong KK, Meyerson M, Barbie DA, Brown M, Long H, Bass AJ. Wu Z, et al. Among authors: xie y. Nat Genet. 2021 Jun;53(6):881-894. doi: 10.1038/s41588-021-00859-2. Epub 2021 May 10. Nat Genet. 2021. PMID: 33972779 Free PMC article.
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis.
Qiu X, Feit AS, Feiglin A, Xie Y, Kesten N, Taing L, Perkins J, Gu S, Li Y, Cejas P, Zhou N, Jeselsohn R, Brown M, Shirley Liu X, Long HW. Qiu X, et al. Among authors: xie y. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):652-661. doi: 10.1016/j.gpb.2020.11.007. Epub 2021 Jul 18. Genomics Proteomics Bioinformatics. 2021. PMID: 34284136 Free PMC article.
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