Chi Zhang

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.

Recent Publications

• W. Lu, F. Ma, A. Churbanov, Y. Wan, Y. Li, G. Kang, Z. Yuan, D. Wang, Chi Zhang, J. Xu, M. Lewis, Q. Li. Virus-Host Mucosal Interactions During Early SIV Rectal Transmission. Virology (2014); 464-465C:406-414.
• A. Block, T. Toruno, C. Elowsky, Chi Zhang, J. Steinbrenner, J. Beynon, J. Alfano. The Pseudomonas syringae type III effector HopD1 suppresses effector-triggered immunity, localizes to the endoplasmic reticulum, and targets the Arabidopsis transcription factor NTL9. New Phytologist (2014); 201(4):1358-1370.
• M. Gelli, Y. Duo, A.R. Konda, J. Rajewski, Chi Zhang, D. Holding, I. Dweikat. Identification of differentially expressed genes associated with nitrogen stress by transcriptional profiling between sorghum genotypes. BMC Genomics (2014); 15:179.
• Y. Dou, B. Yao, Chi Zhang. PhosphoSVM: Prediction of phosphorylation sites by integrating various protein sequence attributes with Support Vector Machine, Amino Acid (2014), DOI: 10.1007/s00726-014-1711-5.
• X. Liu, T. Lu, B. Yu, Chi Zhang. Identification of RNA Silencing Components in Soybean and Sorghum. BMC Bioinformatics (2014); 15:4.
• G. Li, J. Froehlich, C. Elowsky, J. Msanne, A. Ostosh, Chi Zhang, T. Awada, J. Alfano. Distinct Pseudomonas type III effectors utilize a cleavable transit peptide to target chloroplasts. The Plant Journal (2014); 77(2):310-321.
• T. Lu, Z. Zhang, Chi Zhang. Glycosyl rotation and distortion by key residues in Endocellulase Cel6A from Theromobifida fusca. Glycobiology (2014); 24(3):247-251.
• L. Yuan, Y. Dou, S. Kianian, Chi Zhang, D Holding. Deletion mutagenesis identifies a haploinsufficient role for gamma-zein in opaque-2 endosperm modification. Plant Physiology (2014); 164(1):119-130.
• S. Liang, Chi Zhang, Y. Zhou. LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains. Journal of Computational Chemistry (2013); 35(4): 335-341.
• T. Lu, Y. Dou, Chi Zhang. Fuzzy clustering of CPP family in plants with evolution and interaction analyses. BMC Bioinformatics (2013); 14(Suppl 13):S10.
• S. Liang, D. Zheng, D.M. Standley, Chi Zhang. A novel protein function prediction approach using gene overlap networks. BMC Systems Biology (2013); 7:16.
• B. Yao, D. Zheng, S. Liang, Chi Zhang. Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS (2013); 8(4):e62249.
• T. Lu, B. Yao, Chi Zhang. DFVF: database of fungal virulence factors, DATABASE (2012); 2012:bas032.
• B. Yao, L. Zhang, S. Liang, Chi Zhang. SVMTriP: A method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity, PLoS One (2012); 7(9):e45152.
• M. Xie, G. Ren, Chi Zhang, B. Yu. The DNA and RNA binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation. The Plant J (2012); 72:491-500.
• G. Ren, M. Xie, Y. Dou, S. Zhang, Chi Zhang, B. Yu. Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci USA (2012); 109(31):12817-12821.
• S. Liang, Chi Zhang, J. Sarmiento, D.M. Standley. Protein loop modeling with optimized backbone potential functions, J. Chem Theory & Comput (2012); 8(5):1820-1827.
• Y. Dou, J. Wang, J. Yang, Chi Zhang. L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier. PLoS One (2012); 7(4):e35666. 
• T. Lu, Y. Yang, B. Yao, S. Liu, Y. Zhou, Chi Zhang. Template-based structure prediction and classification of Transcription Factors in Arabidopsis Thaliana. Protein Science (2012); 21(6):828-838.
• X. Guo, K.J. Ronhovde, L. Yuan, B. Yao, M.P. Soundararajan, T. Elthon, Chi Zhang, D. Holding. Pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase incuction and attenuation of Hsp gene expression during endosperm modification in Quality Protein Maize. Plant Physiology (2012); 158(2):917-929. 
• S. Liang, D. Zheng, Chi Zhang, D.M. Standley. Fast and accurate prediction of protein side-chain conformations. Bioinformatics (2011); 27(20):2913-2914. 
• S. Liang, Chi Zhang, D.M. Standley. Protein loop selection using orientation dependent force fields derived by parameter optimization. Proteins (2011); 79(7):2260-2267.
• S. Liang, D. Zheng, D.M. Standley, B. Yao, M. Zacharias, Chi Zhang. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics (2010); 11:381.
• S. Liang, D. Zheng, Chi Zhang, M Zacharias. Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics (2009); 10:302.
• S. Liu, Chi Zhang, S. Liang, Y. Zhou. Fold Reorganization by Concurrent Use of Solvent Accessibility and Residue Depth. Proteins (2007); 68, 636-645. 
• S. Liang, S. Liu, Chi Zhang, Y. Zhou. A Simple Reference State Makes a Significant Improvement in Near-native Selections from Structurally Refined Docking Decoys. Proteins (2007); 69:244-253. 
• Chi Zhang, S. Liu, Y. Zhou. MC²: Identifying high-quality protein-interaction modules by cliquemerging. J. Proteome Res. (2006); 5:801-807. 
• S. Liu, Chi Zhang, Y. Zhou. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes. Human Molec. Genetics (2006); 15:1313-1318, [Cover Article]. 
• Yaoqi Zhou, H. Zhou, Chi Zhang, S. Liu. What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem. Biophys. (2006);  46(2):165-174 [Review].
• S. Liang, Chi Zhang, S. Liu, Y. Zhou. Protein binding site prediction with an empirical scoring function. Nucl. Acids Res. (2006); 34:3698-3707. 
• Z. Xu, Chi Zhang, S. Liu, Y. Zhou. QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins (2006); 63:961-966. 
• S. Liu, Chi Zhang, Y. Zhou. Domain graph of Arabidopsis thaliana proteome by comparative analysis. J. Proteome Res. (2005); 4:435-444. 
• Chi Zhang, S. Liu, Y. Zhou. Docking prediction using biological information, ZDOCK sampling technique and clustering guided by the DFIRE statistical energy function. Proteins (2005); (CAPRI issue) 60:314-318.
• Chi Zhang, S. Liu, Q. Zhu, Y. Zhou. A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes. J. Med. Chem. (2005); 48:2325-2335. 
• B. P. Pandey, Chi Zhang, X. Yuan, J. Zi, Y. Zhou. Protein exibility prediction by an all-atom mean-field statistical theory. Protein Science (2005); 14:1772-1777.
• H. Zhou, Chi Zhang, S. Liu, Y. Zhou. Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis, and comparative analysis of domain combinations. Nucl. Acids. Res. (2005); (Server issue) 33:W193-W197. 
• S.V. Gardner, V. Bernard, Ulf-G. Meissner, Chi Zhang. Radiative Neutron-Decay in effective field theory. Journal of Research of the NIST (2005); 110:411-414. 
• S. Liu, Chi Zhang, H. Zhou, Y. Zhou. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins (2004); 56:93-101. 
• Chi Zhang, S. Liu, H. Zhou, Y. Zhou. The Dependence of Statistical Potentials on Training Structural Database. Biophysical Journal (2004); 86:3349-3358. 
• Y. Zhou, H. Zhou, Chi Zhang, S. Liu. Toward a Physical Energy Function for Intra- and Inter-protein Interactions by Combining Structural Knowledge with Physical Principles. Biophysical Journal (2004); 86:306A-307A, Part 2 Suppl.
• Chi Zhang, S. Liu, H. Zhou, Y. Zhou. An Accurate, Residue-level, Pair Potential of Mean Force for Folding and Binding Based on the Distance-scaled, Ideal-gas Reference State. Protein Science (2004); 13:400-411. 
• Chi Zhang, S. Liu, H. Zhou, Y. Zhou. Accurate and Efficient Loop Selections by the DFIREbased All-atom Statistical Potential. Protein Science (2004); 13:391-399. 
• Y. Zhou, Chi Zhang, G. Stell, J. Wang. Temperature Dependence of the Distribution of the First Passage Time: Results from Discontinuous Molecular Dynamics Simulations of an All-atom Model of the Second Beta-hairpin Fragment of Protein G. Journal of the American Chemical Society (2003); 125:6300-6305. 
• D. Manivannan, Chi Zhang. Performance of Communication-Induced Checkpointing Algorithms. International Journal of Computer Systems Science and Engineering (2003); 18(3):129-136.  
• V. Bernard, S.V. Gardner, Ulf-G. Meissner, Chi Zhang. Radiative Neutron-decay in Effective Field Theory. Physics Letters B (2004); 593:105-114. 
• S.V. Gardner, Chi Zhang. Sharpening Low-Energy, Standard-Model Tests via Correlation Coefficients in Neutron Beta-Decay. Phys. Rev. Lett. (2001); 86(25):5666-5669.