W. Jim Zheng, PhD

Associate Professor


Phone: 713.500.3641
Fax: 713.500.3929

Staff Support

Yukiko Bryson
Phone: 713.500.3992


  • 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