Zhiyu Zhao, Assistant Professor, Research

Research Focus

Much of the technology researchers use to make significant biological discoveries, such as next-generation sequencing and deep imaging, generates large amounts of data. These datasets are beyond the data-processing capability of 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.

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….
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Solmonson, A., Faubert, B., Gu, W., Rao, A., Cowdin, M.A., Mendez-Monte, I., Kelekar, S., Rogers, T.J., Pan, C., Guevara, G., Tarangelo, A., Zacharias, L.G., Martin-Sandoval, M.S., Do, D., Pachnis, P., Dumesnil, D., Mathews, T., Tasdogan, A., Pham, A., Cai, L., Zhao, Z., Ni, M., Cleaver, O., Sadek, H.A., Morrison, S.J., and R.J. DeBerardinis. (2022). Compartmentalized metabolism supports midgestation mammalian development. Nature 604, 349-353. (PubMed)

Shen, B., Tasdogan, A., Ubellacker, J.M., Zhang, J., Nosyreva, E.D., Du, L., Murphy, M.M., Hu, S., Yi, Y., Kara, N., Liu, X., Guela, S., Jia, Y., Ramesh, V., Embree, C., Mitchell, E.C., Zhao, Y.C., Ju, L.A., Hu, Z., Crane, G.M., Zhao, Z., Syeda, R., and S.J. Morrison. (2021). A mechanosensitive peri-arteriolar niche for osteogenesis and lymphopoiesis. Nature 591, 438-44. (PubMed)

Tasdogan, A., Faubert, B., Ramesh, V., Ubellacker, J.M., Shen, B., Solmonson, A., Murphy, M.M., Gu, Z., Gu, W., Martin, M., Mathews, T., Kasitinon, S.Y., Vandergriff, T., Zhao, Z., Schadendorf, D., DeBerardinis, R.J., and S.J. Morrison. (2019). Metabolic heterogeneity confers differences in melanoma metastatic potential. Nature 577, 115-120. (PubMed)

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 S.J. Morrison. (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., and S.J. Morrison. (2017).Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF.  Nature Cell Biology 8, 891-903. (PubMed)

Shimada, I.S., Acar, M., Burgess, R.J., Zhao, Z., and S.J. Morrison. (2017). Prdm16 is required for the maintenance of neural stem cells in the postnatal forebrain and their differentiation into ependymal cells. Genes & Development 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., and S.J. Morrison. (2016). Synergistic effects of ion transporter and MAP kinase pathway inhibitors in melanoma. Nature Communications 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 S.J. Morrison. (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 S.J. Morrison. (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 S.J. Morrison. (2015). A perisinusoidal niche for extramedullary hematopoiesis in the spleen. Nature 527, 466-471. (PubMed)

Zhao, Z., Worthylake, D., LeCour, L., Maresh, G.A., and S.H. Pincus. (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., and D. Zhu. (2011). Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Research 39:e61.(PubMed)

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

Lu, Z., Zhao, Z., Garcia, S., Krishnaswamy, K., and B. Fu. (2009). Search similar protein structures with classification, sequence and 3d alignments. Journal of Bioinformatics and Computational Biology 7, 755-71. (PubMed)

Zhao, Z., Fu, B., Alanis, F.J., and C.M. Summa. (2008). Feedback algorithm and web-server for protein structure alignment. Journal of Bioinformatics and Computational Biology 15, 505-24. (PubMed)

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