15. A protocol for automated NMR protein structure determination. In preparation.

14. A. Babak, X. Gao, E. Karakoc, F. Balbach, S. C. Li, G. Feng, L. Donaldson, and M. Li. Error tolerant NMR backbone resonance assignment for automated structure generation. The Eighteenth Annual International Conference on Intelligent System for Molecular Biology (ISMB2010) , submitted. Equally contributed first author.

13. R. Jang, X. Gao, and M. Li. Towards automated structure-based NMR assignment. The Fourteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB2010) , ACCEPTED. Portugal, April 2010. Equally contributed first author.

12. X. Gao. Towards automating protein structure determination from NMR data. Ph.D. Thesis, University of Waterloo, Waterloo, Canada. September, 2009.

11. X. Gao, J. Xu, S. C. Li, and M. Li. Predicting local quality of a sequence-structure alignment. Journal of Bioinformatics and Computational Biology, vol. 7, (2009), pp. 789-810. [PDF]

10. X. Gao, D. Bu, J. Xu, and M. Li. Improving consensus contact prediction via server correlation reduction. BMC Structural Biology, 2009, 9:28. [Open Access at BMC Structural Biology website]

9. B. Alipanahi, X. Gao, E. Karakoc, L. Donaldson, A. Gutmanas, C. Arrowsmith, and M. Li. PICKY: an SVD-based spectra peak picking method. The Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2009), accepted. (Acceptance rate 18%). Bioinformatics, vol. 25, no. 12, (2009), pp. i268-i275.. Equally contributed first author. [Open Access at Bioinformatics website]

8. S. C. Li, D. Bu, X. Gao, J. Xu, and M. Li. Designing succinct structural alphabets. The Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July 2008. (Acceptance rate 15%). Bioinformatics, vol. 24, no. 13, (2008), pp. i182-i189. [Open Access at Bioinformatics website]

7. J. Zhang, X. Gao, J. Xu, and M. Li. Rapid and accurate protein side chain prediction with local backbone information. The Twelfth Annual International Conference on Research in Computational Molecular Biology (RECOMB2008), Singapore, April 2008. (Acceptance rate 15%). Lecture Notes in Computer Science, vol. 4955, (2008), pp. 285-299. Equally contributed first author. [PDF]

6. X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. FragQA: predicting local fragment quality of a sequence-structure alignment. The Eighteenth International Conference on Genome Informatics (GIW 2007), Singapore, December 2007. (Acceptance rate 29%). Genome Informatics, vol. 19, no. 1, (2007), pp. 27-39. Best Paper Award. [Open Access at Genome Informatics website]

5. X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. Consensus contact prediction by linear programming, in Proceedings of the Sixth Annual International Conference on Computational Systems Bioinformatics (CSB 2007), pp. 323-334, San Diego, USA, August 2007. (Acceptance rate 22%). [PDF]

4. X. Gao, S. C. Li, and Y. Lu. New algorithms for the spaced seeds. International Frontiers of Algorithmics Workshop 2007 (FAW 2007), LanZhou, P.R. China, August 2007. (Acceptance rate 23%). Lecture Notes in Computer Science, vol. 4613, (2007), pp. 50-61. [PDF]

3. D. Bu, S. C. Li, X. Gao, L. Yu, J. Xu, and M. Li. Consensus approaches to protein structure prediction. Invited book chapter, in Machine Learning in Bioinformatics, Chapter 8, Eds: Yanqing Zhang and Jagath C. Rajapakse, John Wiley & Sons, 2007.

2. X. Gao, M. Li, and J. Xu. RAPTORESS: an atom-level refinement approach for protein structure prediction. The 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), pp. 96-97. Long abstract, Pacific Grove, USA, November 2007.

1. L. Yu, D. Bu, S. C. Li, X. Gao, J. Xu, and M. Li. RAPTOR-ACE: an integer linear programming based consensus fold recognition method, The 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), pp. 94-95. Long abstract, Pacific Grove, USA, November 2007.