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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.
Using MACS to identify peaks from ChIP-Seq data.
Feng J, Liu T, Zhang Y. Feng J, et al. Among authors: liu t. Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:2.14.1-2.14.14. doi: 10.1002/0471250953.bi0214s34. Curr Protoc Bioinformatics. 2011. PMID: 21633945 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.
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.
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.
Identifying ChIP-seq enrichment using MACS.
Feng J, Liu T, Qin B, Zhang Y, Liu XS. Feng J, et al. Among authors: liu xs, liu t. Nat Protoc. 2012 Sep;7(9):1728-40. doi: 10.1038/nprot.2012.101. Epub 2012 Aug 30. Nat Protoc. 2012. PMID: 22936215 Free PMC article.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. Landt SG, et al. Among authors: liu xs, liu t. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111. Genome Res. 2012. PMID: 22955991 Free PMC article.
Comparative analysis of metazoan chromatin organization.
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Ho JW, et al. Among authors: liu xs, liu t. Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415. Nature. 2014. PMID: 25164756 Free PMC article.
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