Yuannyu Zhang received her Ph.D. in Bioinformatics from Harbin Medical University, where she studied the molecular features of cancer-associated genes. In 2012, she started her postdoctoral training at Shanghai Jiao Tong University School of Medicine, and developed new computational pipelines to identify candidate cancer driver genes by integrating genomics data in liver cancer. From 2014 to 2017, she was an assistant professor at CAS-MPG Partner Institute for Computational Biology at the Chinese Academy of Sciences. She collaborated with Dr. Jian Xu at Children’s Medical Center Research Institute at UT Southwestern (CRI) as a visiting scholar and developed computational methods for analyzing chromatin interactions identified by biotinylated dCas9-mediated CAPTURE. In 2017, she joined CRI and UT Southwestern as a postdoctoral researcher where she studied pathogenic non-coding variants, structural variants, and epigenetic alterations in hematopoietic malignancies. In 2020, she was promoted to an assistant professor at CRI.

Dr. Zhang uses her skills as a bioinformatician to discover the gene regulatory mechanisms responsible for normal blood development and blood disorders such as leukemia.

Research Summary



Harbin Medical University (2008), Medicine
Graduate School
Harbin Medical University (2012), Bioinformatics

Research Interest

  • Blood disorders
  • Computational genomics and gene regulation


Featured Publications LegendFeatured Publications

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9.
Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J, Genome Biol. 2020 Mar 21 1 59
Non-Coding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies.
Li K, Zhang Y, Liu X, Liu Y, Gu Z, Cao H, Dickerson KE, Chen M, Chen W, Shao Z, Ni M, Xu J, Cancer Discov 2020 Mar
Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing.
Li K, Liu Y, Cao H, Zhang Y, Gu Z, Liu X, Yu A, Kaphle P, Dickerson KE, Ni M, Xu J, Nat Commun 2020 Jan 11 1 485
MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes.
Li M, Tu S, Li Z, Tan F, Liu J, Wang Q, Zhang Y, Xu J, Zhang Y, Zhou F, Shao Z, Cell Discov 2019 5 40
Regulation of embryonic haematopoietic multipotency by EZH1.
Vo LT, Kinney MA, Liu X, Zhang Y, Barragan J, Sousa PM, Jha DK, Han A, Cesana M, Shao Z, North TE, Orkin SH, Doulatov S, Xu J, Daley GQ Nature 2018 Jan 553 7689 506-510
In Situ Capture of Chromatin Interactions by Biotinylated dCas9.
Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, Shao Z, Xu J Cell 2017 Aug 170 5 1028-1043.e19
Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation.
Liu X, Zhang Y, Ni M, Cao H, Signer RAJ, Li D, Li M, Gu Z, Hu Z, Dickerson KE, Weinberg SE, Chandel NS, DeBerardinis RJ, Zhou F, Shao Z, Xu J Nat. Cell Biol. 2017 Jun 19 6 626-638
Integrated analysis of mutation data from various sources identifies key genes and signaling pathways in hepatocellular carcinoma.
Zhang Y, Qiu Z, Wei L, Tang R, Lian B, Zhao Y, He X, Xie L, PLoS ONE 2014 9 7 e100854
Pitfalls in experimental designs for characterizing the transcriptional, methylational and copy number changes of oncogenes and tumor suppressor genes.
Zhang Y, Xia J, Zhang Y, Qin Y, Yang D, Qi L, Zhao W, Wang C, Guo Z, PLoS ONE 2013 8 3 e58163