Education

• Ph.D. (expected), Bioinformatics and Computational Biology, Iowa State University, 2009
• M.S. Computer Science, Iowa State University, 2004
• M.S. Surgery, Shanghai Second Medical University , China, 1999
• B.S. Clinical Medicine, Shandong Medical University , China, 1992

 

Working Experience

• 08/2002 ~ present: L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Research assistant
• 07/1992~ 05/2000: Orthopedic Dept, Shanghai Sixth Hospital , Orthopedist

Skills

C++, Matlab, Perl, NAMD.

Research Experience at ISU

1. Characterization of conformational changes due to phosphorylation
    Using coarse grained models such as GNM and ANM, and molecular dynamics approaches to study the mechanisms of transformation changes.

2. Phosphorylation site prediction
     Using support vector machine (SVM), and training on known database of post-translational sites, we developed parameters to improve prediction accuracy of phosphorylation sites.

3. Comparative modeling
     Starting from sequence-structure alignment, we did energy minimization to find the optimal fold of a query sequence.

4. Protein secondary structure prediction
     We combined evolutionary information, solvent accessibility, and other parameters to predict protein secondary structures (Fragment Database Mining). We had seen its performance combining with GOR V, which used information theory and Bayesian Statistics.

 

Publications

• Haitao Cheng , Taner Z. Sen, Robert L. Jernigan and Andrzej Kloczkowski. Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM) . Bioinformatics. 2007, 23: 2628-2630.
• Taner Z. Sen, Haitao Cheng , Andrzej Kloczkowski, Robert L. Jernigan. A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining . Protein Sci. 2006 15(11):2499-506
• Haitao Cheng , Taner Z. Sen, Andrzej Kloczkowski, Dimitris Margaritis, Robert L. Jernigan. Prediction of protein secondary structure by mining structural fragment database . Polymer 2005 46: 4314–4321
• Changchun Chen, Haitao Cheng , Kang Sun etc. Degradation of the bioabsorbable chitin-reinforced polylactic acid composite in vivo and in vitro (in Chinese), Journal of Biomedical Engineering 2000 2(17): 117
• Basic Surgical Techniques (R615/11) (in Chinese) Chief Editor. Beijing : Press of Science and Technology Literature, 09/2000
• English-Chinese Clinical Surgery Dictionary (R6-61: H31/1) Editor. Beijing : Press of People's Health, 04/2000