Yuannyu Zhang

Assistant Professor

Research Focus

High-throughput sequencing technology allows scientists to quickly and accurately sequence multiple DNA molecules in parallel and is an indispensable tool for studying human diseases including cancer. However, a major challenge is how to integrate and interpret this large amount of data using advanced computational methods.

As a bioinformatician, my research focus is on using an integrative approach to analyze data from whole genome sequencing, whole exome sequencing, ChIP-seq, ATAC-seq and RNA-seq as well as other data generated from 3D genome structure, metabolomics, and proteomics. By developing and implementing bioinformatics methods and algorithms, I am working to discover the gene regulatory mechanisms responsible for normal blood development and blood disorders such as leukemia.

About Dr. Zhang

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 (CRI) at UT Southwestern 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.

Publications

Li, K. *, Zhang, Y. *, Liu, X. *, Liu, Y. *, Gu, Z., Cao, H., Dickerson, K.E., Chen, M., Chen, W., Shao, Z., Ni, M., and Xu, J. (2020). Non-coding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. Cancer Discov. 10, 724 (PubMed) *equal contribution

Liu, X. *, Chen, Y. *, Zhang, Y. *, Liu, Y., Liu, N., Botten, G.A., Cao, H., Orkin, S.H., Zhang, M.Q., and Xu, J. (2020). Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol. 21, 59 (PubMed) *equal contribution

Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K.E., Ni, M., and Xu, J. (2020) Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing. Nat Commun. 11, 485. (PubMed)

Li, M., Tu, S., Li, Z., Tan, F., Liu, J., Wang, Q., Zhang, Y., Xu, J., Zhang, Y., Zhou, F., et al. (2019). MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. Cell Discov. 5, 40. (PubMed)

Gu, Z., Liu, Y., Cai, F., Patrick, M., Zmajkovic, J., Cao, H., Zhang, Y., Tasdogan, A., Chen, M., Qi, L., Liu, X., Li, K., Lyu, J., Dickerson, K.E., Chen, W., Ni, M., Merritt, M.E., Morrison. S.J., Skoda, R.C., DeBerardinis, R.J., and Xu, J. (2019) Loss of EZH2 reprograms BCAA metabolism to drive leukemic transformation. Cancer Discov. 9, 1228-1247. (PubMed)

V,o L.T., Kinney, M.A., Liu, X., Zhang, Y., Barragan, J., Sousa, P.M., Jha, D.K., Han, A., Cesana, M., Shao, Z., North, T.E., Orkin, S.H., Doulatov, S., Xu, J., Daley, G.Q. (2018). Regulation of haematopoietic multipotency by EZH1. Nature 553, 506-510. (PubMed)

Liu, X. *, Zhang, Y. *, Chen, Y. *, Li, M. *, Zhou, F. *, Li ,K., Cao, H., Ni, M., Liu, Y., Gu, Z., Dickerson, K.E., Xie, S., Hon, G.C., Xuan, Z., Zhang, M.Q., Shao, Z., and Xu, J#. (2017) In situ capture of chromatin interactions by biotinylated dCas9. Cell 170, 1028–1043. (PudMed) *equal contribution

Liu, X. *, Zhang, Y. *, Ni, M. *, Cao, H., Signer, R.A.J., Li, D., Li, M., Gu, Z., Hu, Z., Dickerson, K.E., Weinberg, S.E., Chandel, N.S., DeBerardinis, R.J., Zhou, F., Shao, Z.., and Xu, J. (2017). Mitochondrial biogenesis in erythropoiesis is regulated by mTORC1-mediated protein translation. Nat. Cell Biol. 19, 626-638. (PubMed) *equal contribution

Zhang, Y., Qiu, Z., Wei, L., Tang, R., Lian, B., Zhao, Y., He, X., and Xie, L. (2014). Integrated analysis of mutation data from various sources identifies key genes and signaling pathways in hepatocellular carcinoma. PLoS One 9, e100854. (PubMed)

Zhang, Y., Xia, J., Zhang, Y., Qin, Y., Yang, D., Qi, L., Zhao, W., Wang, C., and Guo, Z. (2013). Pitfalls in experimental designs for characterizing the transcriptional, methylational and copy number changes of oncogenes and tumor suppressor genes. PLoS One 8, e58163. (PubMed)