Chi Zhang
Chi Zhang
Assistant Professor

Ph.D. University of Kentucky, 2002
M.S. University of Kentucky, 2000
        (Computer Science)
B.S. Beijing University, 1995

Contact Information
N107 Beadle Center

Research Interests

The accomplishment of various genome sequencing projects, the avalanche of high throughput "omic'' data, and the increasing number of solved protein structures, have provided system-level measurements in model organisms. The conversion of the wealthy heterogeneous data to our understanding of the structure and dynamics of biological processes will only be possible by developing effective data-integration methods. My research aims at integrating and mining diverse high throughput data to extract biological insights and to address fundamental biological questions that would enhance our understanding of systems as a whole. This will be accomplished by designing statistically rigorous and physically sound models to integrate genome sequences, expression profiles, molecular interactions, and protein structures etc. My research interests also include Computational Systems Biology; Bioinformatics; interactions between pathogens and plant cells; and gene/protein interaction network in plant cells.


Liang S, Zhang C, Sarmiento J, Standley DM. Protein loop modeling with optimized backbone potential functions. Journal of Chemical Theory and Computation 2012; 8(5):1820-1827

Lu T, Yang Y, Yao B, Liu S, Zhou Y, Zhang C. Template-based structure prediction and classification of Transcription Factors in Arabidopsis Thaliana. Protein Science 2012; 21(6):828-838

Dou Y, Wang J, Yang J, Zhang C. L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier. PLoS ONE 2012; 7(4):e35666

Guo X, Ronhovde KJ, Yuan Y, Yao B, Soundararajan MP, Elthon T, Zhang C, Holding D. Increased glycolytic flux though pyrophosphate dependent fructose 6 phosphate 1-phosphotransferase accompanies endosperm modification in Quality Protein Maize. Plant Physicolgy 2012; 158(2):917-929

Liang S, Zheng D, Zhang C, Standley DM. Fast and accurate prediction of protein side-chain conformations. Bioinformatics 2011; 27(20):2913-4

Liu S, Zhang C, Liang SD, Zhou YQ. Fold Recognition by Concurrent Use of Solvent Accessibility and Residue Depth. Proteins: Structure, Function and Bioinformatics 2007; 68:636-645 (Cover Highlight)

Zhang C, Liu S, Zhou YQ. MC2: A fast and accurate method to identify high-quality protein-interaction modules by clique merging. Journal of Proteome research 2006; 5:801-807

Liang SD, Zhang C, Liu S, Zhou YQ. Protein binding site prediction with an empirical scoring function. Nucleic Acids Research 2006; 34:3698-3707

Liu S, Zhang C, Zhou YQ. Uneven Size distribution of mammalian genes in number of tissues expressed and in the number of co-expressed genes. Human Molecular Genetics 2006; 15:1313-1318 (Cover Article)

Zhou HY, Zhang C, Liu S, Zhou YQ. Web-based toolkits for topology prediction of trans-membrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis, and comparative analysis of domain combinations. Nucleic Acids Research 2005; 33:w193-w197

Zhang C, Liu S, Zhou YQ. Docking prediction using biological information, ZDOCK sampling technique and clustering guided by the DFIRE statistical energy function. Proteins: Structure, Function and Bioinformatics 2004; 60:314-318

Zhang C, Liu S, Zhu QQ, Zhou YQ. A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes. Journal of Medical Chemistry 2005; 48:2325-2335

Zhang C, Liu S, Zhou YQ. An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state. Proteins Science 2004; 13:400-411 (Selected as ?of special interest? by Current Opinion in Structural Biology)

Zhang C, Liu S, Zhou YQ. The dependence of all-atom statistical potentials on training structural database. Biophysical Journal 2004; 86:3349-3358

Zhou Y, Zhang C, Stell G, Wang J, Temperature dependence of the distribution of the first passage time: Results from all-atom discontinuous molecular dynamics simulations of the second beta-hairpin fragment of protein G, Journal of American Chemistry Society 2003; 125, 6300-6305