11. L. Larson, M. Zhang, K. Kosaka, V. Kovacevic, A. Lamsa, J. Cheng, P. Baldi, G.W. Hatfield, and S. Sandmeyer. Ty3 Capsid Scanning Mutations Reveal Early and Late Functions of the Amino-Terminal Domain. Journal of Virology. Accepted, 2006.

10. J. Cheng and P. Baldi. A Machine Learning Information Retrieval Approach to Protein Fold Recognition. Bioinformatics, vol. 22, no. 12, pp. 1456-1463, 2006. [PDF][PDF at Bioinformatics website] . FOLDpro and 3Dpro are the No. 2 and No. 3 Servers for High-Accuracy Protein Structure Prediction in the Seventh Edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7).

9. J. Cheng, M. Sweredoski, and P. Baldi. DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Mining and Knowledge Discovery, vol. 13, no. 1, pp. 1-10, 2006. [PDF] [DAMI advance online] . FOLDpro-DOMpro is the No. 1 Server for Automated Protein Domain Prediction in CASP7.

8. S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, R. K. Brachmann, and R. H. Lathrop. Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants. IEEE Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 114-125, 2006. [PDF]

7. J. Cheng, A. Randall, and P. Baldi. Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines. Proteins: Structure, Function, Bioinformatics, vol. 62, no. 4, pp. 1125-1132, 2006. [PDF][PDF at Proteins website]

6. J. Cheng, H. Saigo, and P. Baldi. Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.Proteins: Structure, Function, Bioinformatics, vol 62, no. 3, pp. 617-629, 2006. [PDF][PDF at Proteins website]

5. J. Cheng, M. Sweredoski, and P. Baldi. Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data, Data Mining and Knowledge Discovery, vol. 11, no. 3, pp. 213-222, 2005. [PDF] [PDF at DAMI website] DISpro is No. 2 server in disorder prediction in CASP7 (No. 5 in both human and server predictors).

4. J. Cheng, A. Randall, M. Sweredoski, and P. Baldi, SCRATCH: a Protein Structure and Structural Feature Prediction Server. Nucleic Acids Research, vol. 33 (web server issue), w72-76, 2005. [PDF][PDF at NAR website]

3. J. Cheng, L. Scharenbroich, P. Baldi, and E. Mjolsness. Sigmoid: Towards a Generative, Scalable, Software Infrastructure for Pathway Bioinformatics and Systems Biology. IEEE Intelligent Systems, vol. 20, no. 3, pp. 68-75, 2005.[PDF][PDF at IEEE website]

2. J. Cheng and P. Baldi. Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms. Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 2005). Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005. [PDF][PDF at Bioinformatics website][ISMB Talk]. BETApro is one of the Best Residue Contact Predictors in CASP7.

1. P. Baldi, J. Cheng, and A. Vullo. Large-Scale Prediction of Disulphide Bond Connectivity . Advances in Neural Information Processing Systems 17 (NIPS 2004), L. Saul,Y. Weiss, and L. Bottou editors, MIT press, pp.97-104, Cambridge, MA, 2005. [PDF][PDF at NIPS website]

Theses

2. J. Cheng. Machine Learning Algorithms for Protein Structure Prediction. PhD Dissertation. University of California Irvine, Irvine, CA, 2006. [PDF]

1. J. Cheng. A Comparative Study of the Similarity Measures of Text Categorization. Master Thesis. Utah State University, Logan, UT, 2001.