Journals
1. X. Deng and J. Cheng. Enhancing HMM-Based Protein Profile-Profile Alignment with Structural Features and Evolutionary Coupling Information. BMC Bioinformatics, July, 2014.
2. G.A. Khoury, A. Liwo, F. Khatib, H. Zhou, G. Chopra, J. Bacardit, L.O. Bortot, R.A. Faccioli, X. Deng, Y. He, P. Krupa, J. Li, M.A. Mozolewska, A.K. Sieradzan, J. Smadbeck, T. Wirecki, S. Cooper, J. Flatten, K. Xu, D. Baker, J. Cheng, A.C.B. Delbem, C.A. Floudas, C. Keasar, M. Levitt, Z. Popovic, H.A. Scheraga, J. Skolnick, S.N. Crivelli, and Foldit Players. WeFold: A Coopetition for Protein Structure Prediction. Proteins, in press.
3. X. Deng, J.Li and J. Cheng. (2013) Predicting protein model quality from sequence alignments by support vector machines. Journal of Proteomics and Bioinformatics, 10:S9, 2013.
4. J. Li, X. Deng, J. Eickholt, J. Cheng. (2013) Designing and Benchmarking the MULTICOM Protein Structure Prediction System.BMC Structural Biology,13:2.
5. M. Zhu, X. Deng, T. Joshi, D. Xu, G. Stacey, J. Cheng. (2012) Reconstructing Differentially Co-expressed Gene Modules and Regulatory Networks of Soybean Cells. BMC Genomics, 13:434, 2012.
6. J. Cheng, J. Li, Z. Wang, J. Eickholt, and X. Deng. (2012) The MULTICOM Toolbox for Protein Structure Prediction. BMC Bioinformatics, 13:65, April, 2012.
7. J. Cheng, J. Eickholt, Z. Wang, and X. Deng. (2012) Recursive Protein Modeling: a Divide and Conquer Strategy for Protein Structure Prediction and its Case Study in CASP9. ournal of Bioinformatics and Computational Biology, vol. 10, no. 3, 2012.
8. X. Deng and J. Cheng. (2011) MSACompro: Protein Multiple Sequence Alignment Using Predicted Secondary Structure, Solvent Accessibility, and Residue-Residue Contacts. BMC Bioinformatics, 12:472, 2011.
9. X. Deng, J. Eickholt and J. Cheng. (2011) A Comprehensive Overview of Computational Protein Disorder Prediction Methods.Molecular BioSystems, DOI:10.1039/C1MB05207A.
10. J. Eickholt, X. Deng and J. Cheng. (2011) DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinformatics, February, 2011.
11. X. Deng, J. Eickholt and J. Cheng. (2009) PreDisorder: Ab Initio Sequence-based Prediction of Protein Disordered Regions. BMC Bioinformatics, 10:436, 2009.
12. R.W. Yu, L.N. Wang, D.J. Wang, and X. Deng. (2009) Study on security enhancement technology for disaster tolerant system.Wuhan University Journal of Natural Sciences, Volume 14, Number 1 / February, 2009.
13. X. Deng. (2006) Brief dissertation of SIP protocol and its security problems. Science and technology of west china, 2006.
14. X. Deng. (2006) Policies to strengthen the professional English teaching in the area of computer science in undergraduate university. Journal of ZhongNan University of economics and law, No.1 2006(Serial No.154).
15. X. Deng, (2015) J. Gumm, S. Karki, J. Eickholt, and J. Cheng. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions. Int. J. Mol. Sci, 2015, 16(7).
Conference Papers
1. J. Cheng, J. Eickholt, Z. Wang, and X. Deng (2011) Recursive Protein Modeling: a Divide and Conquer Strategy for Protein Structure Prediction and its Case Study in CASP9. Computational Structural Bioinformatics Workshop, Atlanta, Georgia, 2011.
2. B. Adhikari, D. Bhattacharya, X. Deng, J. Li, J. Cheng. (2013) A Contact-Assisted Approach to Protein Structure Prediction and Its Assessments in CASP10. The Workshop on Artificial Intelligence and Robotics Methods in Computational Biology of the 27th AAAI Conference, Bellevue, WA, USA.
Book Chapters
1. X. Deng and J. Cheng. (2013) MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features. in press.
2. J. Li, D. Bhattacharya, R. Cao, B. Adhikari, X. Deng, J. Eickholt, J. Cheng. (2013) The MULTICOM Protein Tertiary Structure Prediction System. in press.