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W. Jim Zheng, PhD


W. Jim Zheng, PhD, MS, joined UTHealth School of Biomedical Informatics in 2013 as an associate professor and associate director of the Center for Computational Biomedicine. After receiving his M.S. in computer science from UT Dallas and his Ph.D. from UT Southwestern, when he discovered a novel enzyme mechanism [1], Dr. Zheng has spent most of his career in bioinformatics research in both industrial and academic settings. In his early career, Dr. Zheng worked on bioinformatics research and development projects in industry that involved functional genomics and data management, genome annotation, comparative genomics, and gene discovery in disease-relevant genomic regions. He also developed commercial genomic databases and bioinformatics software.

Dr. Zheng’s research interests focus on how to integrate, model, visualize and mine eukaryotic genome information for translational medicine. He is also pursuing novel approaches for knowledge representation. Dr. Zheng and his colleagues developed Genome3D, the first model-view framework to integrate and visualize the eukaryotic genome in three dimensions [2]. His group also developed the concept of Ontology Fingerprints—the first Gene Ontology term embedding for genes computationally developed from mining the biomedical literature [3, 4]. Dr. Zheng and colleagues are developing various deep learning models for biomedical research and disease risk prediction. He shared his perspectives on data science, informatics, and artificial intelligence in an article in JAMA [5]. Taking a data driven approach, Dr. Zheng’s group and his colleagues recently discovered extensive presence of murine viral genome sequences in patient derived xenografts (PDX). The finding raised some serious concerns about the quality control of this important platform for cancer drug development, and offered some suggestions to improve drug development process [6].

Dr. Zheng also established and directs the Data Science and Informatics Core for Cancer Research (DSICCR)—a cutting-edge data science resource with faculty expertise includes high-throughput genomic data analysis, systems biology, electronic health record mining, and clinical data warehouses development. He also directs the Bioinformatics and High-Performance Computing Service Center - part of the Center for Clinical and Translational Sciences supported by the NIH CTSA award.

Dr. Zheng’s current translational research involves development of novel data mining methods to extract information from the biomedical literature for novel therapeutic strategies against cancer, Alzheimer’s disease, and other chronic diseases. Dr. Zheng serves on the editorial board of two bioinformatics journals and his research is currently supported by the NIH and the Cancer Prevention and Research Institute of Texas.

“The paradigm shift from data generation to data analysis in biomedical research has created an enormous amount of opportunities for informaticians”, said Zheng. “Translating biomedical discoveries to bedside practices becomes possible through informatics research.”


  1. Wenjin Zheng, Stephen A. Johnston, Leemor Joshua-Tor: The unique active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase and peptide ligase. Cell, 93:103-109, 1998, PMID: 9546396
  2. Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng: Genome3D: A view-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinformatics, Sep 2; 11:444, 2010 (Highly Accessed), PMCID: PMC2941692
  3. Lam C. Tsoi, Michael Boehnke, Richard Klein, W. Jim Zheng: Evaluation of Genome-wide Association Study Results through Development of Ontology Fingerprint. Bioinformatics, 25(10):1314-20, 2009. PMID: 19349285
  4. Tingting Qin, Nabil Matmati, Lam C. Tsoi, Bidyut K. Mohanty, Nan Gao, Jijun Tang, Andrew B. Lawson, Yusuf A. Hannun, W. Jim Zheng: Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. Nucleic Acid Research, 42(18):e138, 2014, PMCID: PMC4191379
  5. Lisha Zhu, W. Jim Zheng: Informatics, Data Science and Artificial Intelligence, JAMA, 320(11):1103-1104, 2018, PMID: 30326503
  6. Zihao Yuan, Xuejun Fan, Jay-Jiguang Zhu, Tong-Ming Fu, Jiaqian Wu, Hua Xu, Ningyan Zhang, Zhiqiang An, W. Jim Zheng: Presence of complete murine viral genome sequences in patient-derived xenografts. Nature Communications, 12, 2031, doi:10.1038/s41467-021-22200-5, 2021, PMID: 33795676

Dr. Zheng’s full publication records can be accessed at:

Phone: 713-500-3641
Fax: 713-500-3929

Staff Support

 Felicia Davis
Phone: 713-500-3667


  • MS, Computer Science, 2000, University of Texas at Dallas
  • PhD,Biochemistry & Molecular Biology, 1997 University of Texas Southwestern Medical Center at Dallas
  • MS, Biophysics, 1989, Wuhan University, Wuhan, China
  • BS, Virology & Molecular Biology, 1986 Wuhan University, Wuhan, China

Areas of Expertise

  • Bioinformatics
  • Systems Biology
  • Genomics
  • Biological Data Mining
  • Biological Networks
  • Biomedical Ontology and Knowledge Representation