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Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium; Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Cheng Y, et al. Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985. Nature. 2014. PMID: 25409826 Free PMC article.
Experimental validation of predicted mammalian erythroid cis-regulatory modules.
Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC. Wang H, et al. Among authors: cheng y. Genome Res. 2006 Dec;16(12):1480-92. doi: 10.1101/gr.5353806. Epub 2006 Oct 12. Genome Res. 2006. PMID: 17038566 Free PMC article.
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.
King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J; ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis; Chiaromonte F, Miller W, Hardison RC. King DC, et al. Among authors: cheng y. Genome Res. 2007 Jun;17(6):775-86. doi: 10.1101/gr.5592107. Genome Res. 2007. PMID: 17567996 Free PMC article.
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.
Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. Cheng Y, et al. Genome Res. 2009 Dec;19(12):2172-84. doi: 10.1101/gr.098921.109. Epub 2009 Nov 3. Genome Res. 2009. PMID: 19887574 Free PMC article.
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. Wu W, et al. Among authors: cheng y. Genome Res. 2011 Oct;21(10):1659-71. doi: 10.1101/gr.125088.111. Epub 2011 Jul 27. Genome Res. 2011. PMID: 21795386 Free PMC article.
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