Zhiyu Zhao

Assistant Professor

Research Focus

Much of the technology researchers use to make significant biological discoveries, such as next-generation sequencing and deep imaging, generate large amounts of data. These datasets are beyond the data-processing capability of human biologists and require the specialized help of bioinformatics – an interdisciplinary field of science that applies computational, mathematical and statistical methods to the analysis and interpretation of biological data.

At the CRI, I use my experience in computer science, mathematics and statistics to process big data, develop software tools and workflows and analyze various datasets generated by our biological experiments in cancer and stem cell research. My work includes studying data from next-generation sequencing experiments, such as RNA-seq; ChIP-seq; whole-genome sequencing; whole-exome sequencing; mitochondrial genome sequencing; and targeted DNA sequencing, as well as metabolomics; proteomics; and biomedical imaging data.

About Dr. Zhao

Zhiyu Zhao received her B.E. in 1997 and her M.E. in 2000 in computer engineering from the Huazhong University of Science and Technology, China. In 2004, she began her bioinformatics research at the Politecnico di Milano, Italy. In 2006, she earned her M.S. in computer science and in 2008 she received her Ph.D. in engineering and applied science from the University of New Orleans.

Dr. Zhao joined the faculty at the Children’s Medical Research Institute at UT Southwestern as a research assistant professor in May 2012.

Publications

Agathocleous, M., Meecham, C.E., Burgess, R.J., Piskounova, E., Zhao, Z., Crane, G.M., Cowin, B.L., Bruner, E., Murphy, M.M., Chen, W., Spangrude, G.J., Hu, Z., DeBerardinis, R.J., and Morrison, S.J. (2017). Ascorbate regulates haematopoietic stem cell function and leukaemogenesis. Nature 549, 476-481. (PubMed)

Zhou, B.O., Yu, H., Yue, R., Zhao, Z., Rios, J.J., Naveiras, O., Morrison, S.J. (2017).Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF.  Nature Cell 8, 891-903. (PubMed)

Shimada, I.S., Acar, M., Burgess, R.J., Zhao, Z., Morrison, S.J. (2017). Prdm16 is required for the maintenance of neural stem cells in the postnatal forebrain and their differentiation into ependymal cells. Genes Dev. 11, 1134-1146. (PubMed)

Eskiocak, U., Ramesh, V., Gill, J.G., Zhao, Z., Yuan, S.W., Wang, M., Vandergriff, T., Shackleton, M., Quintana, E., Frankel, A.E., Johnson, T.M., DeBerardinis, R.J., Morrison, S.J. (2016). Synergistic effects of ion transporter and MAP kinase pathway inhibitors in melanoma. Nat Comm. 7, 12336. (PubMed)

Acar, M., Kocherlakota, K.S., Murphy, M.M., Peyer, J.G., Oguro, H., Inra, C.N., Jaiyeola, C.J., Zhao, Z., Luby-Phelps, K., and Morrison, S.J. (2015). Deep imaging of bone marrow shows non-dividing stem cells are mainly perisinusoidal. Nature 526, 126-130. (PubMed)

Piskounova, E., Agathocleous, M., Murphy, M.M., Hu, Z., Mann, S., Zhao, Z., Leitch, A.M., Johnson, T.M., DeBerardinis, R.J., and Morrison, S.J. (2015). Oxidative stress inhibits distant metastasis by human melanoma cells. Nature 527, 186-191. (PubMed)

Inra, C., Zhou, B.O., Acar, M., Murphy, M.M., Zhao, Z., and Morrison, S.J. (2015). A perisinusoidal niche for extramedullary hematopoiesis in the spleen. Nature 527, 466-471. (PubMed)

Zhao, Z., Worthylake, D., LeCour, L., Maresh, G.A., Pincus, S.H. (2012). Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody. PLoS One 7, e52613. (PubMed)

Deng, N., Puetter, A., Zhang, K., Johnson, K., Zhao, Z., Taylor, C., Flemington, E.K., Zhu, D. (2011). Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res. 39, e61. (PubMed)

Lu, Z., Zhao, Z., Fu, B. (2010). Efficient protein alignment algorithm for protein search. BMC Bioinformatics. 11, S34. (PubMed)

Lu, Z., Zhao, Z., Garcia, S., Krishnaswamy, K., Fu, B. (2009). Search similar protein structures with classification, sequence and 3d alignments. J Bioinform Comput Biol. 7,755-71. (PubMed)

Zhao, Z., Fu, B., Alanis, F.J., Summa, C.M. (2008). Feedback algorithm and web-server for protein structure alignment.  J Bioinform Comput Biol. 15,505-24. (PubMed)