|
Refereed Papers
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.
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, CASP7 suppl.. In press, 2007. [CASP7
Invited Contribution]
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.
In press, 2007.
[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.
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][Free
Access
at NIPS website]
Non-Refereed Papers
1. J. Hecker and J. Cheng.
Protein Disorder Prediction at Multiple Levels of Sensitivity
and Specificity. Journal of Computational Intelligence in
Bioinformatics. In press, 2007.
2. J. Cheng. A Neural Network Approach to
Ordinal Regression. arXiv:0704.1028, 2007
[PDF][Free Access at arXiv]
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.
|
|
|