Yong Cheng, PhD
Yong Cheng, PhD


PhD – The Pennsylvania State University
MS – Nankai University, Tianjin, China
BS – Nankai University, Tianjin, China

Research Interests

My long-term research goal is to understand the organization, evolution and mechanisms underlying human regulatory networks. In particular, my research group combines experimental and computational approaches to understand the functions of cis-regulatory elements (CRMs) in hematopoiesis and its disorders.

  • Dynamic regulatory genomic landscape during hematopoiesis.
  • Functional annotation of causal non-coding variants in blood disorders.
  • Manipulating gene expression by modifying CRMs at genomic and epigenomics level.

Selected Publications

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 AC, Giardine B, The mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio AL, Weng Z, Hardison RC#, Snyder MP#. Principles of regulatory information conservation between mouse and human. Nature Nov 20;515:371-5, 2014. * Equal contribution

Yue F*, Cheng Y*, Breschi A*, Vierstra J*, Wu W*, Ryba T*, Sandstrom R*,Ma Z*, Davis C*,Pope BD*,Shen Y*, The mouse ENCODE Consortium. An integrated and comparative Encyclopedia of DNA elements in the mouse genome. Nature Nov 20;515:355-64, 2014. *Equal contribution

Sundaram V*, Cheng Y*, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res Dec;24(12):1963-76, 2014. * Equal contribution

Pope DB, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield T, Thurman RE, Cheng Y, Gülsoy F, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B , Gilbert DM. Topologically-associating domains are stable units of replication-timing regulation. Nature 20;515:402-5, 2014.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Comparative analysis of regulatory information and circuits across distant species. Nature Aug 28;512(7515):453-6, 2014.

Boyle P, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res Sep; 22(9):1790-7, 2012.

ENCODE Project Consortium.  An integrated encyclopedia of DNA elements in the human genome. Nature Sep 6;489(7414):57-74, 2012.

Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell Aug 17;150(4):725-37, 2012.

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. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res Oct; 21(10):1659-71, 2011.   

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. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res Dec; 19(12):2172-84, 2009.

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. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res Dec; 18(12): 1896-9054, 2008.

Last update: July 2016