Education

 

Graduate student in Bioinformatics and Computational Biology, ISU. 08/2004 ~ present

M.S., Computer Science, Iowa State University. 08/2002~07/2004

M.D., Clinical Medicine, Shandong Medical University, China. 09/1986~07/1992

 

Work Experience

 

2002.8 ~ present: L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Research assistant

1992.7 ~ 2000.6: Orthopedist , Orthopedic Dept, Shanghai Sixth Hospital

 

Research interests

 

  Structure modeling and protein structure prediction

 

 

Current interests

 

1. Protein secondary structure prediction.

1) We combine evolutionary information, solvent accessibility, and other parameters to predict protein secondary structure (Fragment Database Mining FDM). We have seen its performance combining with GOR-V (CDM-http://gor.bb.iastate.edu/sss/).

2)We use amino acid composition to predict folding class as well as secondary structure.

3)We are using reduced alphabet to do multiple sequence alignment, and predict protein secondary structure.

4)We are trying to construct database of segments of various sizes.

2. Conservation site prediction

We use entropy, surface area and packing style information for the prediction.

3. Based on templates, we use reduced structure model to do protein structure prediction, decoy generation, energy calculation, etc.

 

Skills

 

1. Experienced in programming using C++. Familiarity with various kinds of data structures and algorithms;

2. Familiarity with Database systems; familiarity with Java programming;

3. Familiarity with broad biological areas, including Biochemistry, Immunology, Pathology, Physiology, Microbiology, clinical medicine, etc.

 

Publications

 

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 Nov;15(11):2499-506. Epub 2006 Sep 25.

 

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 vitro (in Chinese), Journal of Biomedical Engineering, Vol.2, No.17, 2000:117