W. Jim Zheng, PhD

Associate Professor

W. Jim Zheng, PhD, MS, joined UTHealth School of Biomedical Informatics (SBMI) on February 1st, 2013 as an associate professor and associate director of the Center for Computational Biomedicine. He spent most of his career in bioinformatics research in both industrial and academic settings. His research interests are eukaryotic genome information integration, modeling and visualization in three-dimension, large-scale biological data integration and mining for translational medicine. In his early career after being formally trained in both biology and computer science, Dr. Zheng worked on R&D projects in industry, conducting bioinformatics research in the area of functional genomics and data management, genome annotation, comparative genomics, gene discovery in disease-relevant genomic regions, and developing commercial genomic databases and bioinformatics software. Dr. Zheng and his colleagues developed Genome3D, the first model-view framework to integrate and visualize 3D eukaryotic genome. His current work also includes the development of novel data mining methods to extract useful information from biomedical literature for novel therapeutic strategy development against cancer and other human diseases. Dr. Zheng serves on the editorial board of several bioinformatics journals and is currently receiving funding from both NIH and NSF.

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

Contact

Wenjin.J.Zheng@uth.tmc.edu
Phone: 713.500.3641
Fax: 713.500.3929

Staff Support

Yukiko Bryson
Phone: 713.500.3992

Education

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

Research Interests

  • Bioinformatics
  • Systems Biology
  • Genomics
  • Biological Data Mining
  • Biological Networks
  • Biomedical Ontology and Knowledge Representation
  1. Wenjin Zheng, Liangyi Kang, Guanying Qiu: Attenuation of the host symptom by CMV (Cucumber Mosaic Virus) satellite RNA (1-CARNA) is not related to the expression of viral coat protein, Acta Agriculturae Nucleatae Sinica 1992 6(2) p 111-115
  2. Wenjin Zheng, H. Eric Xu and Stephen Albert Johnston: The cysteine peptidase, bleomycin hydrolase, is a new component of the galactose regulon in yeast. J Biological Chemistry, 272: 30350-30355, 1997
  3. 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
  4. Wenjin Zheng and Stephen A Johnston: The nucleic acid binding activity of yeast bleomycin hydrolase is involved in bleomycin detoxification. Molecular & Cellular Biology, 18(6): 3580-3585, 1998
  5. Paul A O'Farrell, Fernando Gonzalez, Wenjin Zheng, Stephen Albert Johnston and Leemor Joshua-Tor: Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease. Structure Fold Des. 7(6):619-627, 1999
  6. Lisa Yan, Mikhail Velikanov, Paul Flook, Wenjin Zheng, Sandor Szalma,and Scott Kahn: Assessment of Putative Protein Targets Derived from the SARS Genome. FEES Letters. 554(3):257-63, 2003
  7. W. Jim Zheng, Velin Z. Spassov, Lisa Yan, Paul K. Flook and Sandor Szalma: A hidden Markov model with molecular mechanics energy scoring function for transmembrane helix prediction. Computational Biology and Chemistry. 28(4):265-74 2004.
  8. Daniel A Shegogue, W. Jim Zheng: Capturing Biological Information with Class-Responsibility-Collaboration Cards. Bioinformatics. 21(3):415-7. 2005
  9. Daniel A Shegogue, W. Jim Zheng: Object-oriented biological system integration: a SARS coronavirus example. Bioinformatics. 21(10):2502-9. 2005
  10. Daniel A Shegogue, W. Jim Zheng: Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinformatics. 6(1): 113. 2005
  11. W. Jim Zheng: Engineering Approaches toward Biological Information Integration at the Systems Level. Current Bioinformatics. 1(1):85-93, 2006
  12. Linyong Mao, W. Jim Zheng: Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs. BMC Bioinformatics. 7 (Suppl4):S21, 2006 2
  13. Lam C. Tsoi, W. Jim Zheng: A Method of Microarray Data Storage Using Array Data Type. Computational Biology and Chemistry. 3l(2):143. 2007
  14. Sarah Bradshaw, W. Jim Zheng, Lam C. Tsoi, Gary S. Gilkeson, Xian K. Zhang: A role for Fli-1 in B cell proliferation: implications for SLE pathogenesis. Clinical Immunology, 129(1):19-30, 2008
  15. Jingshan Huang, Jiangbo Dang, Michael N. Huhns, W. Jim Zheng: Using Artificial Neural Network to Align Biological Ontology. BMC Genomics, 9 Suppl2:Sl6, 2008
  16. Hiroshi Kitagaki, Lauren A Cowart, Nabil Matmati, David Montefusco, Jason Gandy, Silvia Vaena de Avalos, Sergei A Novgorodov, Jim Zheng, Lina M Obeid, and Yusuf A Hannun: !SCI-Dependent Metabolic Adaptation Reveals an Indispensable Role for Mitochondria in Induction of Nuclear Genes During the Diauxic Shift in S. cerevisiae. Biol. Chern., 284(16):10818-30, 2009.
  17. Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng: Text Mining Approach to Evaluate Terms for Ontology Development. J Biomedical J~(Informatics, 42(5):824-30, 2009.
  18. 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.
  19. 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).
  20. Kaushlendra Tripathi, Nabil Matmati, W. Jim Zheng, Yusuf A. Hannun, Bidyut K. Mohanty: Cellular Morphogenesis Under Stress Is Influenced by the Sphingolipid Pathway gene ISCl and DNA Integrity Checkpoint Genes in Saccharomyces cerevisiae. Genetics, Oct, 189(2):533-47, 2011
  21. Muhammad Nazmus Sakib, Jijun Tang, W. Jim Zheng, Chin-Tser Huang: Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files. PLoS One, Dec. 2, 6(12):e28251, 2011
  22. Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng: Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. BMC Bioinformatics, Nov. 11, 12:438, 2011.
  23. Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu: Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation. Pacific Symposium on Biocomputing, 2012:422-33
  24. Tingting Qin, Lam C. Tsoi, Kellie J. Sims, Xinghua Lu, W. Jim Zheng: Signal network prediction by the Ontology Fingerprint enhanced
  25. Diane Gesty-Palmer, Ling Yuan, Bronwen Martin, William H. Wood III, Mi-Hye Lee, Michael G. Janech, Lam C. Tsoi, W. Jim Zheng, and Louis M. Luttrel, β-Arrestin Selective G Protein-Coupled Receptor Agonists Engender Unique Biological Efficacy In Vivo, Molecular Endocrinology, 27(2):296-314, 2013
  26. Saleh M. Rachidi, Tingting Qin, Shaoli Sun, W. Jim Zheng, Zihai Li, Molecular Profiling of Multiple Human Cancers Defines an Inflammatory Cancer-Associated Molecular Pattern and Uncovers KPNA2 as a Uniform Poor Prognostic Cancer Marker, PLoS One, 8(3):e57911, 2013
  27. Jeremiah J. Shepherd, Lingxi Zhou, William Arndt, Yan Zhang, W. Jim Zheng, Jijun Tang: Exploring genomes with a game engine.  Faraday Discuss, accepted, 2014
  28. 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, accepted, 2014
  29. Links

Selected Patents

U.S. Patent No. 7291767
Issue Date: October 10th, 2003
Inventors: Oriedo, J. V. B.; McCrery, D.; Savickas, P.; Miller, B. A.; Pell, R.·; Larrinua, I. M.; Weglarz, T.; Gachotte, D.; Reddy, A. S.; Ruegger, M.; Blakeslee, B.; Pogue, G. P.; Crosley, R.; Zheng, W.; Della-Cioppa, G. R.; Wolfe, G.
Title: Nucleic acids compositions conferring dwarfing phenotype

International Patent No: AU2002359567
Issue Date: June 10th, 2003
Inventors: Tang, Y. T.; Chawla, N. K.; Lu, D. A.M.; Khan, F. A.; Gandhi, A. R.; Swarnakar, A.; Azimzai, Y.; Marquis, J. P.; Sprague, W. W.; Emerling, B. M.; Yue, H.; Borowsky, M. L.; Becha, S. D.; Ison, C. H.; Elliott, V. S.; Hafalia, A. J. A.; Ring, H. Z.; Warren, B. A.; Gietzen, K. J.; Tran, U. K.; Lee, S. Y.; Lee, E. A.; Richardson, T. W.; Kable, A. E.; Burford, N.; Lehr Mason, P.M.; Gorvad, A. E.; Lee, S.; Blake, J. J.; Honchell, C. D.; Thangavelu, K.; Ramkumar, J.; Chien, D.; Jin, P.; Chang, H.; Baughn, M. R.; Nguyen, D. B.; Khare, R.; Bhatia, U.; Burrill, J.D.; Ho, A.; Zheng, W.
Title: Molecules for disease detection and treatment

International Patent No: AU2003279799
Issue Date: April 23rd, 2004
Inventors: Richardson, T. W.; Marquis, J.P.; LAL, P. G.; Nguyen, D. B.; Lee, S. Y.; Tran, U. K.; Bhatia, U. G.; Lee, S.; Blake, J. J.; Ho, A.; Zheng, W.; Gao, J.; Tran, B.; Yang, Y. G.; Gietzen, K. J.; Hafalia, A. J. A.; Elliott, V. S.; Swarnakar, A.; Tang, Y. T.; Yue, H.; Lu, D. A.M.; Khare, R.; Chawla, N.K.
Title: Proteins associated with cell growth, differentiation, and death

International Patent No: AU2002357850
Issue Date: June 30th, 2003
Inventors: Baughn, M. R.; Bhatia, U.; Blake, J. J.; Burrill, J.D.; Elliott, V. S.; Emerling, B. M.; Forsythe, I. J.; Gietzen, K. J.; Gorvad, A. E.; Griffin, J. A.; Hafalia, A. J. A.; Ho, A.; Jackson, A. A.; Jiang, X.; Kable, A. E.; Kearney, L.; Khare, R.; Lee, E. A.; Lee, S.; Lu, D. A. M.; Marquis, J.P.; Lehr-Mason, P.M.; Ramkumar, J.; Richardson, T. W.; Sprague, W. W.; Tran, U. K.; Chawla, N. K.; Warren, B. A.; Yue, H.; Zheng, W.
Title: Neurotransmission-associated proteins