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Refereed Papers

    27. J. Schmutz, S. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. Hyten, Q. Song, J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. May, Y. Yu, T. Sakurai, T. Umezawa, M. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, J. Dr, Z. Tian, L. Zhu, N. Gill, J. Trupti, M. Libault, A. Sethuraman, X. Zhang, S. Shinozaki, H. Nguyen, R. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R. Shoemaker and S. Jackson. Genome sequence of the paleopolylid soybean (Glycine max (L.). Nature, in press.

    26. G. Lin, Z. Wang, D. Xu, and J. Cheng. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington D.C., 2009. [PDF]

    25. J. Cheng, Z. Wang, A.N. Tegge and J. Eickholt. Prediction of Global and Local Quality of CASP8 Models by MULTICOM series. Proteins, vol. 77, pp. 181-184, 2009. [at Proteins web site] CASP8 invited contribution

    24. A.N. Tegge, Z. Wang, J. Eickholt, and J. Cheng. NNcon: Improved Protein Contact Map Prediction Using 2D-Recursive Neural Networks. Nucleic Acids Research , vol. 37, pp. w515-w518, 2009. [at NAR web site]. NNcon was ranked among the best contact map prediction methods in CASP8.

    23. E.E. Stagner, D.J. Bouvrette, J. Cheng, and E.C. Bryda. The Polycystic Kidney Disease-related Proteins Bicc1 and SamCystin Interact. Biochemical and Biophysical Researh Communications. 383(1):16-21, 2009. [PDF]

    22. A. N. Tegge, Z. Wang, and J. Cheng. Integrative Protein Fold Recognition by Alignments and Machine Learning. in Protein Structure Prediction: Method and Algorithms (editors: H. Rangwala and G. Karypis), Wiley, 2009.

    21. Z. Wang, A. N. Tegge, and J. Cheng. Evaluating the Absolute Quality of a Single Protein Model Using Support Vector Machines and Structural Features. Proteins, vol. 75, no. 3, 638-647, 2009. [at Proteins website] ModelEvaluator was ranked among the best model evaluation methods in CASP8. [CASP8 model quality assessment talk]

    20. J. Cheng. A Multi-Template Combination Algorithm for Protein Comparative Modeling. BMC Structural Biology.8:18, 2008. [Open Access at BMC website] MULTICOM was ranked among the best template-based and template-free structure prediction methods in CASP8. [CASP8 template-based modeling talk]; [CASP8 template_free modeling talk]

    19. J. Cheng, Z. Wang, and G. Pollastri. A Neural Network Approach to Ordinal Regression. International Joint Conference on Neural Networks (IJCNN), Hongkong, 2008. [PDF]

    18. J. Dai and J. Cheng. HMMEditor: A Visual Editing Tool for Profile Hidden Markov Model. BMC Genomics. 9(S1):S8, 2008. [Open Access at BMC website]

    17. J. Hecker, J. Yang, and J. Cheng. Protein Disorder Prediction at Multiple Levels of Sensitivity and Specificity. BMC Genomics. 9(S1):S9, 2008. [Open Access at BMC website] PreDisorder was ranked among the best disorder predictors in CASP8. [CASP8 disorder prediction talk]

    16. A. Randall, J. Cheng, M. Sweredoski, and P. Baldi. TMBpro: Secondary Structure, Beta-Contact, and Tertiary Structure Prediction of Transmembrane Beta-Barrel Proteins. Bioinformatics, vol. 24, pp. 513-520, 2008. [Bioinformatics website] [PDF]

    15. J. Cheng, A. N. Tegge, and P. Baldi. Machine Learning Methods for Protein Structure Prediction. IEEE Reviews in Biomedical Engineering. 1:41-49, 2008. [PDF]

    14. J. Cheng. DOMAC: An Accurate, Hybrid Protein Domain Prediction Server. Nucleic Acids Research, vol. 35, pp. w354-w356, 2007. [PDF] [Open Access at NAR website] DOMAC was ranked among the best domain predictors in CASP8

    13. J. Cheng and P. Baldi. Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set. BMC Bioinformatics. 8:113, 2007. [PDF][Free access at BMC Bioinformatics website] SVMcon is one of the best contact map predictors in CASP7 and CASP8.

    12. M. Tress, J. Cheng, P. Baldi, K. Joo, J. Lee, J.H. Seo, J. Lee, D. Baker, D. Chivian, D. Kim, A. Valencia, and I. Ezkurdia. Assessment of Predictions Submitted for the CASP7 Domain Prediction Category. Proteins: Structure, Function and Bioinformatics, vol. 68 (S8):137-151, 2007. [CASP7 Invited Contribution] [PDF] [Paper at Proteins Website]

    11. L. Larson, M. Zhang, N. Beliakova-Bethell, V. Bilanchone, A. Lamsa, K. Nagashima, R. Najdi, 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, vol. 81, pp. 6957-6972, 2007. [PDF] [Free Access at Journal of Virology website]

    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][Free Access 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). Recommended by Faculty of 1000 Biology.

    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][Free Access at Bioinformatics website][ISMB Talk]. BETApro is one of the Best Residue Contact Predictors in CASP7 and CASP8.

    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, 2004. [PDF][Free Access 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.