Publications

Refereed Journal Publications:
17. J. Wang, X. Wang, Q. Wang, X. You, Y. Li, and X. Gao. Non-negative matrix factorization by maximizing correntropy for cancer clustering. Submitted. Corresponding Author. [Source code]
16. M. Fan, K. Wong, T. Ryu, T. Ravasi, and X. Gao. SECOM: a novel hash seed and community detection-based approach for genome-scale protein domain identification. Submitted. Corresponding Author. [PDF][Source code]
15. A. Ramanathan, S. Moitra, X. Gao, and C. Langmead. Mechanistic insights of the ubiquitin binding energy landscape. Submitted.
14. J. Wang, X. Gao, Q. Wang, Y. Zhang, Y. Li, J. Zhang, H. Pei, C. Fan, and J. He. IterPropMCS: semi-supervised hot spot residue prediction visa transductive learning working on multiple assumptions. Submitted.
13. Z. Liu, B. Jing, and X. Gao. WaVPeak: picking NMR peaks through wavelet transform and volume-based filtering. Bioinformatics. doi: 10.1093/bioinformatics/bts078. Corresponding Author. [PDF] [Source code]
12.J. Wang, Y. Li, Q. Wang, J. Zhang, X. You, J. Man, C. Wang, and X. Gao. ProClusEnsem: predicting membrane protein types by fusing different models of pseudo amino acid composition. Computers in Biology and Medicine. In press. Corresponding Author.
11. J. Wang, X. Gao, Q. Wang, Y. Zhang, and Y. Li. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval. BMC Bioinformatics (Invited submission). Corresponding Author.
10. R. Jang, X. Gao, and M. Li. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. BMC Bioinformatics (2012), 12(S3):S4.
9. Md. S. Bhuyan, and X. Gao. A protein-dependent side-chain rotamer library. BMC Bioinformatics (2011), 12(S14): S10. Corresponding Author. [PDF]
8. J. Wang, Y. Li, Y. Zhang, C. Wang, H. Xie, G. Chen, and X. Gao. Bag-of-features based medical image retrieval via multiple assignment and visual words weighting. IEEE Transactions on Medical Imaging, vol. 6(1), (2011). [PDF]
7.  R. Jang, X. Gao, and M. Li. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks, Journal of Computational Biology, vol. 18(3), (2011), pp 347-363. Equally Contributed First Author.  [PDF]
6.  B. Alipanahi, 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, Journal of Bioinformatics and Computational Biology, vol. 9, (2011), pp 15-41. Equally Contributed First Author.  [PDF]
5.  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]
4.  X. Gao, D. Bu, J. Xu, and M. Li. Improving consensus contact prediction via server correlation reduction. BMC Structural Biology, 2009, 9:28. [PDF]
3.  B. Alipanahi, X. Gao, E. Karakoc, L. Donaldson, A. Gutmanas, C. Arrowsmith, and M. Li. PICKY: a novel SVD-based NMR spectra peak picking method. Bioinformatics, vol. 25, no. 12, (2009), pp. i268-i275. Equally Contributed First Author.  [PDF]
2.  S. C. Li, D. Bu, X. Gao, J. Xu, and M. Li. Designing succinct structural alphabets. Bioinformatics, vol. 24, no. 13, (2008), pp. i182-i189. [PDF]
1.  X. Gao, D. Bu, S. C. Li, J. Xu, and M. Li. FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Informatics, vol. 19, no. 1, (2007), pp. 27-39. [PDF]


Refereed Conference Publications:
10. Md. S. Bhuyan, and X. Gao. A protein-dependent side-chain rotamer library. The 22nd International Conference on Genome Informatics (GIW2011). Busan, Korea, December 2011. Corresponding Author.
9. H. Kuwahara, and X. Gao. An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. The 9th International Conference on Computational Methods in Systems Biology (CMSB2011). Paris, September 2011. Corresponding Author. [PDF]
8. R. Jang, X. Gao, and M. Li. Combined structure-based backbone and NOE assignment from N-HSQC chemical shift mapping and N-NOESY NMR spectra. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011. Chicago, August 2011. (Acceptance rate 19%).
7.  R. Jang, X. Gao, and M. Li. Towards automated structure-based NMR resonance assignment, The Fourteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB2010). Portugal, April 2010. (Acceptance rate 20%). Equally Contributed First Author.  [PDF]
6.  B. Alipanahi, X. Gao, E. Karakoc, L. Donaldson, A. Gutmanas, C. Arrowsmith, and M. Li. PICKY: a novel SVD-based NMR spectra peak picking method. The Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2009), accepted. (Acceptance rate 18%). Equally Contributed First Author.  [PDF]
5.  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%). [PDF]
4.  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%).  Equally Contributed First Author.  [PDF]
3.  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%). Best Paper Award. [PDF]
2.  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]
1.  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]


Book Chapters:
1.  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.


Non-refereed Conference Publications:
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.


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