Skip to main content
Yong Cheng, PhD
Yong Cheng, PhD


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

Research Interests

Our lab is interested in understanding the functions of the human genome, especially non-coding regulatory elements. We use high-throughput functional genomic approaches to investigate regulatory elements in normal blood development and disorders. We also interested in the application of regulatory elements in treating genetic disorders using genome editing and gene therapy.

Selected Publications

* First or co-first authors; # Corresponding or co-corresponding

Li Y, Che J, Tsai SQ, Cheng Y#. Easy-Prime: a machine learning based prime editor design tool. Genome Biology Aug 19, 2021. PMID: 34412673

Cheng L, Li Y, Qi Q, Xu P, Feng R, Palmer L, Chen J, Wu R, Yee T, Zhang J, Yao Y, Sharma A, Hardison RC, Weiss MJ#, Cheng Y#, Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression. Nature Genetics May, 2021. PMID: 33958780

Qi Q, Cheng L, Tang X, He Y, Li Y, Yee T, Shrestha D, Feng R, Xu P, Zhou X, Pruett-Miller S, Hardison RC, Weiss MJ, Cheng Y#. Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood Mar 11;137(10):1327-1339, 2021. PubMed PMID

Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.  Nat Biotechnol. Jun 15, 2020.

Cheng Y#, Tsai SQ#. Illuminating the genome-wide activity of genome editors for safe and effective therapeutics. Genome Biol Dec 22;19(1):226, 2018. doi: 10.1186/s13059-018-1610-2.

Ganuza M, Chabot A, Tang X, Bi W, Natarajan S, Carter R, Gawad C, Kang G, Cheng Y, McKinney-Freeman S. Muri6. Murine hematopoietic stem cell activity is derived from pre-circulation embryos but not yolk sacs Nat Commun Dec 20;9(1):5405, 2018.

Karmaus PWF, Chen X, Lim SA, Herrada AA, Nguyen TM, Xu B, Dhungana Y, Rankin S, Chen W, Rosencrance C, Yang K, Fan Y, Cheng Y, Easton J, Neale G, Vogel P, Chi H. Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity.  Nature Dec 19, 2018. doi: 10.1038/s41586-018-0806-7.6.

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. Principles of regulatory information conservation between mouse and human. The mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio AL, Weng Z, Hardison RC, Snyder MP 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

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.

See full list of publications

Last update: October 2021