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Zhongming Zhao

PhD, MS
Professor
713-500-3631
[email protected]

Chair Professor for Precision Health
Director, Center for Precision Health

Zhongming Zhao, Ph.D., M.S. is a professor at the School of Biomedical Informatics (SBMI) and appointed as the Chair Professor for Precision Health. He is the founding director of the new Center for Precision Health, which is a joint venture between SBMI and the UTHealth School of Public Health. Zhao holds a joint appointment between SBMI and the UTHealth School of Public Health. Before coming to UTHealth, Zhao was a professor in the Departments of Biomedical Informatics, Psychiatry and Cancer Biology at Vanderbilt University School of Medicine and held Ingram Professorship of Cancer Research. While at Vanderbilt University, Zhao also served as the chief bioinformatics officer of the Vanderbilt-Ingram Cancer Center (VICC), the director of the VICC Bioinformatics Resource Center, director of the Bioinformatics and Systems Medicine Laboratory and the associate director of the Vanderbilt Center for Quantitative Sciences. Zhao previously participated in a Keck Foundation Postdoctoral fellowship at the W.M. Keck Center for Computational and Structural Biology and the Consortium for Bioinformatics of the Gulf Coast Consortia in Houston. After completing the fellowship, Zhao started his role as a tenure-track assistant professor at the Virginia Commonwealth University School of Medicine. Zhao is a member of numerous organizations including the American Medical Informatics Association (AMIA), the Institute of Electrical and Electronics Engineers (IEEE) and the American Society of Human Genetics (ASHG). He has more than 20 years of bioinformatics and systems biology research experience, collaborated with more than 100 investigators, and has authored/co-authored more than 280 papers in these areas. His work has been supported by more than 50 funded grants totaling more than $100 million.

Education

  • PhD, 2000, Human and Molecular Genetics, University of Texas Health Science Center at Houston Graduate School of Biomedical Sciences and University of Texas MD Anderson Cancer Center
  • MS, 2002, Computer Science, University of Houston
  • MS, 1998, Biomathematics, University of Texas Health Science Center at Houston Graduate School of Biomedical Sciences and University of Texas MD Anderson Cancer Center
  • MS, 1996, Genetics, Peking University, Beijing, China
  • BS, 1991, Biology, Zhejiang University, Hangzhou, China

Links

Bioinformatics and Systems Medicine Laboratory (SBML)

Research

  • Bioinformatics: methodology and application
  • Next generation sequencing in precision medicine: WGS, WES, RNA-Seq, microRNA-Seq, ChIP-Seq, Methy-Seq, etc.
  • Integrative genomics and systems biology approaches to complex disease studies
  • Translational Bioinformatics
  • Cancer Precision Medicine
  • Genomic studies of mental disorders
  • Pharmacogenomics
  • Drug repositioning

Publications

  1. Jia P, Zhao Z, Hulgan T, Bush W, Samuels DC, Bloss C, Heaton R, Ellis R, Schork N, Marra C, Collier AC, Clifford D, Gelman B, Sacktor N, Morgello S, Simpson D, McCutchan JA, Letendre S, Barnholtz-Sloan J, Franklin DR, and Grant I for the CHARTER Study Group, Kallianpur, AR (accepted) Genome-wide association study of HIV-Associated Neurocognitive Disorder (HAND): a CHARTER Group Study. American Journal of Medical Genetics
  2. Fang J, Cai C, Wang Q, Lin P, Zhao Z*, Cheng F* (2017) Systems pharmacology-based discovery of natural products for precision oncology through targeting cancer mutated genes. CPT: Pharmacometrics and Systems Pharmacology 6:177-187
  3. Cao Y, Zhu J, Han G, Jia P, Zhao Z* (2017) scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq. bioRxiv, 104810
  4. Zhao Z, Liu Z, Zheng W, Ruan J (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics 18(4):S1 (in press)
  5. Patton SM, Wang Q, Hulgan T, Connor JR, Jia P, Zhao Z, Letendre S, Ellis R, Bush WS, Samuels DC, Franklin DR, Kaur H, Iudicello J, Grant I, Kallianpur A (accepted) Cerebrospinal Fluid (CSF) Iron and Biomarkers of Iron Transport are Associated with Age, Sex, Ancestry, and CSF Viral Load in HIV-Infected Adults. Fluids and Barriers of the CNS
  6. Zhao J, Cheng F, Zhao Z* (2017) Tissue-specific signaling networks rewired by major somatic mutations in human cancer revealed by proteome-wide discovery. Cancer Research. Advanced online access March 31, 2017. DOI:10.1158/0008-5472.CAN-16-2460
  7. Han G, Zhao W, Ng KS, Karama JA, Jonasch E, Smith GB, Zhao Z*, Ding Z*, Jia P* (accepted) Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening. BMC Genomics
  8. Kim P, Zhao J, Lu P, Zhao Z* (2017) mutLBSgeneDB: mutated Ligand Binding Site gene DataBase. Nucleic Acids Research Online advanced access October 7, 2016, doi: 10.1093/nar/gkw905
  9. Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z* (2016) The potential roles of long non-coding RNAs (lncRNAs) in glioblastoma development. Molecular Cancer Therapeutics 15(12):2977-2986
  10. Shen Q, Cheng F, Song H, Lu W, Zhao Z* (co-corresponding author), Zhang J* (2016) Proteome-scale investigation of protein allosteric regulation perturbed by somatic mutations in 7,000 cancer genomes. American Journal of Human Genetics. 2016 Nov 24. pii: S0002-9297(16)30401-3. doi: 10.1016/j.ajhg.2016.09.020. [Epub ahead of print]
  11. Chen, J., Bacanu, S. A., Yu, H., Zhao, Z., Jia, P., Kendler, K. S., Kranzler, H. R., Gelernter, J., Farrer, L., Minica, C., Pool, R., Milaneschi, Y., Boomsma, D. I., Penninx, B. W., Tyndale, R. F., Ware, J. J., Vink, J. M., Kaprio, J., Munafo, M., and Chen, X. (2016). Genetic Relationship between Schizophrenia and Nicotine Dependence. Sci Rep, 6, 25671. doi: 10.1038/srep25671
  12. Cheng, F., Liu, C., Shen, B., and Zhao, Z. (2016). Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst Biol, 10 Suppl 3, 65. doi: 10.1186/s12918-016-0309-9
  13. Cheng, F., Murray, J. L., Zhao, J., Sheng, J., Zhao, Z., and Rubin, D. H. (2016). Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput Biol, 12(9), e1005074. doi: 10.1371/journal.pcbi.1005074
  14. Cheng, F., Zhao, J., Fooksa, M., and Zhao, Z. (2016). A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. J Am Med Inform Assoc, 23(4), 681-691. doi: 10.1093/jamia/ocw007
  15. Cheng, F., Zhao, J., and Zhao, Z. (2016). Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform, 17(4), 642-656. doi: 10.1093/bib/bbv068
  16. Edmonds, M. D., Boyd, K. L., Moyo, T., Mitra, R., Duszynski, R., Arrate, M. P., Chen, X., Zhao, Z., Blackwell, T. S., Andl, T., and Eischen, C. M. (2016). MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer. J Clin Invest, 126(1), 349-364. doi: 10.1172/jci82720
  17. Hart, T., Dider, S., Han, W., Xu, H., Zhao, Z., and Xie, L. (2016). Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Sci Rep, 6, 20441. doi: 10.1038/srep20441
  18. Heist, R. S., Shim, H. S., Gingipally, S., Mino-Kenudson, M., Le, L., Gainor, J. F., Zheng, Z., Aryee, M., Xia, J., Jia, P., Jin, H., Zhao, Z., Pao, W., Engelman, J. A., and Iafrate, A. J. (2016). MET Exon 14 Skipping in Non-Small Cell Lung Cancer. Oncologist, 21(4), 481-486. doi: 10.1634/theoncologist.2015-0510
  19. Hemnes, A. R., Zhao, M., West, J., Newman, J. H., Rich, S., Archer, S. L., Robbins, I. M., Blackwell, T. S., Cogan, J., Loyd, J. E., Zhao, Z., Gaskill, C., Jetter, C., Kropski, J. A., Majka, S. M., and Austin, E. D. (2016). Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension. Am J Respir Crit Care Med, 194(4), 464-475. doi: 10.1164/rccm.201508-1678OC
  20. Huang, K., Liu, Y., Huang, Y., Li, L., Cooper, L., Ruan, J., and Zhao, Z. (2016). Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics, 17 Suppl 7, 524. doi: 10.1186/s12864-016-2893-x
  21. Jia, P., and Zhao, Z. (2016). Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform. doi: 10.1093/bib/bbw037
  22. Kallianpur, A. R., Wang, Q., Jia, P., Hulgan, T., Zhao, Z., Letendre, S. L., Ellis, R. J., Heaton, R. K., Franklin, D. R., Barnholtz-Sloan, J., Collier, A. C., Marra, C. M., Clifford, D. B., Gelman, B. B., McArthur, J. C., Morgello, S., Simpson, D. M., McCutchan, J. A., and Grant, I. (2016). Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era. J Infect Dis, 213(7), 1065-1073. doi: 10.1093/infdis/jiv754
  23. Kim, P., Cheng, F., Zhao, J., and Zhao, Z. (2016). ccmGDB: a database for cancer cell metabolism genes. Nucleic Acids Res, 44(D1), D959-968. doi: 10.1093/nar/gkv1128
  24. Liu, S., Yin, F., Zhao, M., Zhou, C., Ren, J., Huang, Q., Zhao, Z., Mitra, R., Fan, W., and Fan, M. (2016). The homing and inhibiting effects of hNSCs-BMP4 on human glioma stem cells. Oncotarget, 7(14), 17920-17931. doi: 10.18632/oncotarget.7472
  25. Pardo, L., Schluter, A., Valor, L. M., Barco, A., Giralt, M., Golbano, A., Hidalgo, J., Jia, P., Zhao, Z., Jove, M., Portero-Otin, M., Ruiz, M., Gimenez-Llort, L., Masgrau, R., Pujol, A., and Galea, E. (2016). Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. Glia, 64(5), 853-874. doi: 10.1002/glia.22969
  26. Tenenbaum, J. D., Avillach, P., Benham-Hutchins, M., Breitenstein, M. K., Crowgey, E. L., Hoffman, M. A., Jiang, X., Madhavan, S., Mattison, J. E., Nagarajan, R., Ray, B., Shin, D., Visweswaran, S., Zhao, Z., and Freimuth, R. R. (2016). An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc, 23(4), 791-795. doi: 10.1093/jamia/ocv213
  27. Wang, Y., Guo, X., Bray, M. J., Ding, Z., and Zhao, Z. (2016). An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC). BMC Genomics, 17 Suppl 7, 515. doi: 10.1186/s12864-016-2906-9
  28. Zhao, J., Cheng, F., Wang, Y., Arteaga, C. L., and Zhao, Z. (2016). Systematic Prioritization of Druggable Mutations in approximately 5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. Mol Cell Proteomics, 15(2), 642-656. doi: 10.1074/mcp.M115.053199
  29. Zhao, M., Kim, P., Mitra, R., Zhao, J., and Zhao, Z. (2016). TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res, 44(D1), D1023-1031. doi: 10.1093/nar/gkv1268
  30. Zhao, M., and Zhao, Z. (2016). Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study. BMC Genomics, 17 Suppl 7, 532. doi: 10.1186/s12864-016-2904-y
  31. Zhao, Z., Liu, Y., Huang, Y., Huang, K., and Ruan, J. (2016). Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. BMC Syst Biol, 10 Suppl 3, 61. doi: 10.1186/s12918-016-0305-0