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EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.
Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, Thornton JE, Gregory RI, Morrissey C, Vessella RL, Montironi R, Magi-Galluzzi C, Kantoff PW, Balk SP, Liu XS, Brown M. Xu K, et al. Among authors: liu xs, liu t. Science. 2012 Dec 14;338(6113):1465-9. doi: 10.1126/science.1227604. Science. 2012. PMID: 23239736 Free PMC article.
Cistrome: an integrative platform for transcriptional regulation studies.
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS. Liu T, et al. Among authors: liu xs. Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83. Genome Biol. 2011. PMID: 21859476 Free PMC article.
Systematic evaluation of factors influencing ChIP-seq fidelity.
Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. Chen Y, et al. Among authors: liu xs, liu t. Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22. Nat Methods. 2012. PMID: 22522655 Free PMC article.
Computational methodology for ChIP-seq analysis.
Shin H, Liu T, Duan X, Zhang Y, Liu XS. Shin H, et al. Among authors: liu xs, liu t. Quant Biol. 2013 Mar 1;1(1):54-70. doi: 10.1007/s40484-013-0006-2. Quant Biol. 2013. PMID: 25741452 Free PMC article.
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS. Qin Q, et al. Among authors: liu xs, liu t. BMC Bioinformatics. 2016 Oct 3;17(1):404. doi: 10.1186/s12859-016-1274-4. BMC Bioinformatics. 2016. PMID: 27716038 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: liu xs, liu t. Genome Biol. 2020 Aug 7;21(1):198. doi: 10.1186/s13059-020-02116-x. Genome Biol. 2020. PMID: 32767996 Free PMC article.
Fast alignment and preprocessing of chromatin profiles with Chromap.
Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H. Zhang H, et al. Among authors: liu xs, liu t. Nat Commun. 2021 Nov 12;12(1):6566. doi: 10.1038/s41467-021-26865-w. Nat Commun. 2021. PMID: 34772935 Free PMC article.
A comprehensive view of nuclear receptor cancer cistromes.
Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. Tang Q, et al. Among authors: liu xs, liu t. Cancer Res. 2011 Nov 15;71(22):6940-7. doi: 10.1158/0008-5472.CAN-11-2091. Epub 2011 Sep 22. Cancer Res. 2011. PMID: 21940749 Free PMC article.
CistromeFinder for ChIP-seq and DNase-seq data reuse.
Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. Sun H, et al. Among authors: liu j, liu xs, liu t. Bioinformatics. 2013 May 15;29(10):1352-4. doi: 10.1093/bioinformatics/btt135. Epub 2013 Mar 18. Bioinformatics. 2013. PMID: 23508969 Free PMC article.
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