Yong Cheng

Publications

• An encyclopedia of mouse DNA elements (Mouse ENCODE). Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. Genome Biol. 2012; 13 (8): 418
• Personal omics profiling reveals dynamic molecular and medical phenotypes. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Cell. 2012; 148 (6): 1293-307
• The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R, Bairoch A, Taylor AD, Kim KY, Lee EY, Hochstrasser D, Legrain P, Hancock WS. Nat Biotechnol. 2012; 30 (3): 221-3
• Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Cell. 2012; 150 (4): 725-37
• Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Lamonica JM, Deng W, Kadauke S, Campbell AE, Gamsjaeger R, Wang H, Cheng Y, Billin AN, Hardison RC, Mackay JP, Blobel GA. Proc Natl Acad Sci U S A. 2011; 108 (22): E159-68
• 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. Genome Res. 2009; 19 (12): 2172-84
• Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Mol Cell. 2009; 36 (4): 682-95
• Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Nucleic Acids Res. 2009; 37 (21): 7024-38
• SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. Blood. 2009; 113 (10): 2191-201
• Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Genome Res. 2008; 18 (12): 1896-905
• Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, Chiaromonte F, Miller W, Hardison RC. Genome Res. 2007; 17 (6): 775-86
• 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. Genome Res. 2006; 16 (12): 1480-92