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DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.
Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA. Mercer TR, et al. Among authors: li g. Nat Genet. 2013 Aug;45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23. Nat Genet. 2013. PMID: 23793028 Free PMC article.
CTCF-mediated functional chromatin interactome in pluripotent cells.
Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. Handoko L, et al. Among authors: li g. Nat Genet. 2011 Jun 19;43(7):630-8. doi: 10.1038/ng.857. Nat Genet. 2011. PMID: 21685913 Free PMC article.
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y. Li G, et al. Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014. Cell. 2012. PMID: 22265404 Free PMC article.
ChIA-PET analysis of transcriptional chromatin interactions.
Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y. Zhang J, et al. Among authors: li g. Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25. Methods. 2012. PMID: 22926262
Large-scale functional organization of long-range chromatin interaction networks.
Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y. Sandhu KS, et al. Among authors: li g. Cell Rep. 2012 Nov 29;2(5):1207-19. doi: 10.1016/j.celrep.2012.09.022. Epub 2012 Oct 25. Cell Rep. 2012. PMID: 23103170 Free PMC article.
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.
Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Zhang Y, et al. Among authors: li g. Nature. 2013 Dec 12;504(7479):306-310. doi: 10.1038/nature12716. Epub 2013 Nov 10. Nature. 2013. PMID: 24213634 Free PMC article.
Dissecting the chromatin interactome of microRNA genes.
Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y, Chen LL, Chen M. Chen D, et al. Among authors: li g. Nucleic Acids Res. 2014 Mar;42(5):3028-43. doi: 10.1093/nar/gkt1294. Epub 2013 Dec 18. Nucleic Acids Res. 2014. PMID: 24357409 Free PMC article.
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