Department of Systems Biology and Translational Medicine

SBTM Microarray/Omics Core Laboratory

Cardiovascular Research Institute

Cardiovascular Forum

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Hung-Chung (Joe) Huang

Assistant Research Scientist
Dr. VanBuren’s Lab
Department of Systems Biology and Translational Medicine

B.S., Technology for Medical Sciences, 1986, Kaohsiung Medical College
M.S., Biochemistry and Molecular Biology, 1995, Oklahoma State University
Ph.D., Computational Biochemistry, 2001, University of Houston

Computational Systems Biology: The Science for Human Health and Wellness in Silica

A multitude of biological facts have been uncovered since the explosion of biological data resulting from genomic and proteomic approaches. Isolated facts alone, however, are not sufficient for interpreting complex biological systems, where interactions among components occur at various systems levels, including the levels of cells, tissues, organs, organisms, and the ecological environment. A combination of experimental and computational approaches is expected to resolve this problem. In this respect, computational systems biology addresses questions fundamental to our understanding of life, yet progress here will lead to practical innovations in medicine, drug discovery, and engineering. [according to Nature, 2002; 420:206-10]

Prior to entering graduate school, I was a medical technologist. My Master's thesis described the cloning of a dopamine receptor gene in cattle parasite (tick). I worked on protein purification and crystallization during the early stages of my PhD studies. In my PhD dissertation work I used Brownian dynamics and molecular dynamics simulations to study the behavior and structure-function relationship of important structural proteins or enzymes. As a postdoctoral researcher with Prof. George Fox’s group (UH) I developed algorithms to compare and objectively classify important RNA motifs using available 3-D coordinates. My recent work at UT-Dallas reinforced my ability to solve scientific problems with knowledge in Statistics, Mathematics, and Computer Science. All these studies and experiences have provided me with the skills to solve biomedical problems in the exciting field of Computational Systems Biology.

Research interests:

  1. Evaluation of the theoretical relevance networks derived from biological data by comparing them with previously established pathway and gene regulatory networks.
  2. Biomarker discovery via microarray data annotaion and analysis.
  3. Comparison and prediction of non-coding RNA structures.
  4. Genomic studies related to the cure and treatment of infectious diseases like SARS, AIDS, TB…etc.
  5. Drug design in silica on biomolecules, e.g., hydration site studies around the active sites of enzymes via molecular dynamics simulations.


Selected Publications:

1. Zheng, X.; Huang, H.-C.; Li, W.; Liu, P; Li, Q.-Z.; Liu, Y. Modeling Nonlinearity in Dilution Design Microarray Data. Accepted and to appear in Bioinformatics 2007.
2. Li, W.-Y.; Peng, Y.-X.; Huang, H.-C.; Liu, Y. Biomarker Discovery and Visualization in Gene Expression Data with Efficient Generalized Matrix Approximations. Journal of Bioinformatics and Computational Biology (JBCB). Accepted and to appear.
3. Li, W.-Y.; Liu, Y.; Huang, H.-C.; Peng, Y.-X.; Lin, Y.-J.; Ng, W.-K.; Ong, K.-L. Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks. Accepted and to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006.
4. Zhao, Q.; Nagaswamy, U.; Lee, H.; Xia, Y.; Huang, H.-C.; Gao, X.; Fox, G. E.  NMR Structure and Mg2+ Binding of an RNA Segment that Underlies the L7/L12 Stalk in the E. coli 50S Ribosomal Subunit.  Nucleic Acids Research 2005 June 6, 33(10):3145-53.
5. Nagaswamy, U.; Huang, H.-C.; Larios-Sanz, M.; Wang, J.; Zhao, Q.; Fox, G. E. NCIR-Non-Canonical Interactions in RNA.  Nucleic Acids Research: Volume 33, Database issue January 1, 2005; Molecular Biology Database Collection entry number 380.
6. Huang, H.-C.; Nagaswamy, U.; Fox, G. E.  The Application of Cluster Analysis in the Inter-comparison of Loop Structures in RNA.  RNA 2005 Apr, 11(4), 412-23.
7. Huang, H.-C.; Briggs, J. M.  The Association between a Negatively Charged Ligand and the Electronegative Binding Pocket of its Receptor.  Biopolymers 2002, 63, 247-60.
8. Briggs, J. M.; Mustata, G. I.; Huang, H.-C.; Soares, T. A.  Molecular Dynamics Studies and Structural Analyses of Alanine Racemase - as a Drug Design Target.  Cell Mol. Biol. Lett. 2001, 6(2B), 547. 
9. Strych, U.; Huang, H.-C.; Krause, K. L.; Benedik, M. J.  Characterization of the Alanine Racemases from Pseudomonas aeruginosa PAO1.  Curr. Microbiol. 2000, 41, 290-4.






Joe photo

Hung-Chung (Joe) Huang, MT, MS , PhD
702 SW HK Dodgen Loop
Medical Research Building
Temple, TX 76504

Full CV: PDF | Word

Email: hc.jhuang *at* tamu *dot* edu

Office: 254-742-7176