My group focuses on developing computational tools to tackle biological problems, such as protein structure prediction, protein interaction, protein function prediction, biological sequence alignments, inference and simulation of biological networks, and genomics.  Currently, my group is actively working to

1. predict protein structure from protein sequence;
2. evaluate the quality of protein structure models;
3. develop tools to simulate and infer biological pathways with applications to plant development (iPlant collaborative project);
4. apply systems biology techniques to epigenomics and cancer research (collaborative project);
5. develop a protein structure and function database for the soybean genome (collaborative project);
6. apply bioinformatics methods to analyze the maize genome (collaborative project)
7. predict and analyze protein domain structure and domain evolution (collaborative project);
8. predict protein interaction;
9. build a computer-aided protein design (collaborative project);
10. develop tools to integrate multi-source data, including gene expression, SNP, protein structure, protein interaction, protein function, and biological pathway to discover the mechanism of a disease (collaborative project).

The bioinformatics tools produced by our group are used in a variety of biomedical research by life scientists from around the world.

• ASPB members lead new plant genome research program awards (Nov 2010)
• System that predicts protein structures could help researchers design drugs (May 2010)
• Sequencing of soybean genome adds potential to research (Mar 2010)
• Genome sequencing shows past genetics events made soybeans rich in versatile gene families (Jan 2010)
• New protein prediction software put to the test (Jan 2009)
• In race to predict protein structure, computers take lead (Jan 2009)

• National Science Foundation CAREER Award (2012)
• 2nd in Automated High-Accuracy 3D Protein Structure Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006
• 1st in Automated Protein Domain Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006.
• 2nd in Automated Residue Contact Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006
• 2nd in Automated Protein Disorder Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7), 2006.
• Two campus awards during 2005 University of California Data Mining Contests
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008)
• Panelist, National Science Foundation Cyber-Enabled Discovery and Innovation (CDI) program (2008)
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM, 2008)
• Program Committee, International Joint Conference on Neural Networks (IJCNN) (2008)
• Program Committee, International Conference on Biomedical Engineering and Informatics (BMEI 2008)
• Editorial Board Member, Journal of Computational Intelligence in Bioinformatics and Systems Biology (since 2007)
• Editorial Board Member, International Journal of Computational Biology and Drug Design (since 2007)
• Program Committee and Session Chair, IEEE 7th Symposium on Bioinformatics and Bioengineering (BIBE 2007)
• Program Committee, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)
• Chair of the Genomics Session, International Conference on Bioinformatics and Computational Biology (BIOCOMP 2007)

Wang Z, Eickholt J, and Cheng J. APOLLO: A quality assessment service for single and multiple protein models. Bioinformatics 2011;27(12):1715-1716.

Tanaka K, Nguyen CT, Libault M, Cheng J, and Stacey G. Enzymatic activity of the soybean ecto-apyrase GS52 is essential for stimulation of nodulation. Plant Physiology 2011; 155(4):1988-1998.

Wang Z, Zhang XC, Le MH, Xu D, Stacey G, and Cheng J. A protein domain Co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS ONE 2011;6(3) art. no. e17906.

Eickholt J, Deng X, and Cheng J. DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinformatics 2011;12, art. no. 43.

Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen H, Xu D, Stacey G and Cheng J. SoyDB: A knowledge database of soybean transcription factors. BMC Plant Biology 2010;14.

Libault M, Brechenmacher L, Cheng J, Xu D and Stacey G. Root hair systems biology. Trends in Plant Science 2010;15(11):641-650.

Wang Z, Eickholt J and Cheng J. MULTICOM: A multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 2010;26(7):882-888.

Lin GN, Wang Z, Xu D and Cheng J. SeqRate: Sequence-based protein folding type classification and rates prediction. BMC Bioinformatics 2010;11(SUPPL. 3):art. no S1.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC and Jackson SA. Genome sequence of the palaeopolyploid soybean. Nature 2010;463(7278):178-183.

Wang Z, Tegge AN and Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins: Structure, Function and Bioformatics 2009;75(3):638-647.

Tegge AN, Wang Z, Eickholt J and Cheng J. NNcon: Improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Research 2009;37(SUPPL. 2):

Stagner EE, Bouvrette DJ, Cheng J and Bryda EC. The polycystic kidney disease-related proteins Bicc1 and SamCystin interact. Biochemical and Biophysical Research Communications 2009;383(1):16-21.

Lin GN, Wang Z, Xu D and Cheng J. Sequence-based prediction of protein folding rates using contacts, secondary structures and support vector machines. 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 2009;3-8.

Deng X, Eickholt J and Cheng J. PreDisorder: Ab initio sequence-based prediction of protein disordered regions. BMC Bioinformatics 2009;10(

Cheng J, Wang Z, Tegge AN and Eickholt J. Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 2009;77 Suppl 9(181-184.

Randall A, Cheng J, Sweredoski M and Baldi P. TMBpro: Secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins. Bioinformatics 2008;24(4):513-520.

Hecker J, Yang JY and Cheng J. Protein disorder prediction at multiple levels of sensitivity and specificity. BMC Genomics 2008;9(SUPPL. 1):

Dai J and Cheng J. HMMEditor: A visual editing tool for profile hidden Markov model. BMC Genomics 2008;9(SUPPL. 1):

Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC Structural Biology 2008;8(

Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Baker D, Chivian D, Kim D and Ezkurdia L. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins: Structure, Function and Genetics 2007;69(SUPPL. 8):137-151.

Larsen LSZ, Zhang M, Beliakova-Bethell N, Bilanchone V, Lamsa A, Nagashima K, Najdi R, Kosaka K, Kovacevic V, Cheng J, Baldi P, Hatfield GW and Sandmeyer S. Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. Journal of Virology 2007;81(13):6957-6972.

Cheng J and Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007;8(

Cheng J. DOMAC: an accurate, hybrid protein domain prediction server. Nucleic Acids Research 2007;35(Web Server issue):

Danziger SA, Swamidass SJ, Zeng J, Dearth LR, Lu Q, Chen JH, Cheng J, Hoang VP, Saigo H, Luo R, Baldi P, Brachmann RK and Lathrop RH. Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2006;3(2):114-124.

Cheng J, Sweredoski MJ and Baldi P. DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Mining and Knowledge Discovery 2006;13(1):1-10.

Cheng J, Saigo H and Baldi P. Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins: Structure, Function and Genetics 2006;62(3):617-629.

Cheng J, Randall A and Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins: Structure, Function and Genetics 2006;62(4):1125-1132.

Cheng J and Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006;22(12):1456-1463.

Cheng J, Sweredoski MJ and Baldi P. Accurate prediction of protein disordered regions by mining protein structure data. Data Mining and Knowledge Discovery 2005;11(3):213-222.

Cheng J, Scharenbroich L, Baldi P and Mjolsness E. Sigmoid: A software infrastructure for pathway bioinformatics and systems biology. IEEE Intelligent Systems 2005;20(3):68-75.

Cheng J, Randall A, Sweredoski M and Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research 2005;33(W72-W76.

Cheng J and Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005;21(SUPPL. 1):