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Xin, L., B. Ma, and K. Zhang, " A New Quartet Approach for Reconstructing Phylogenetic Trees: Quartet Joining Method", The 13th Annual International Computing and Combinatorics Conference. 40-50, 2007.
Xu, C., and B. Ma, "Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing", Computational System Bioinformatics Conference. 361-369, 2006.
Xu, J., L. Yu, and M. Li, "Consensus fold recognition by predicted model quality", APBC'05, Singapore, 2005.
Xu, E.W., D.G. Brown, and P. Kearney, "The use of functional domains to improve transmembrane protein topology prediction", Proceedings of APBC, 105-116, 2005.
Xu, J., D.G. Brown, M. Li, and B. Ma, " Optimizing Multiple Spaced Seeds for Homology Search", The 15th Symposium on Combinatorial Pattern Matching. 47-58, 2004.
Xu, J., M. Li, G. Lin, D. Kim, and Y. Xu, "Protein threading by linear programming", PSB'03, Hawaii, pp 264-275, 2003.
Xu, J., M. Li, D. Kim, and Y. Xu, "RAPTOR: optimal protein threading by linear programming", Journal of Bioinformatics and Computational Biology,1:1, 95-118, 2003.
Xu, J., D.G. Brown, M. Li, and B. Ma, " Optimizing Multiple Spaced Seeds for Homology Search", Journal of Computational Biology. 13(7): 1355-1368, 2006.
Xu, C., and B. Ma, " Review of software for computational peptide identification from MS/MS data", Drug Discovery Today 11(13/14): 595-600, 2006.
Xu, E.W., P. Kearney, and D.G. Brown, "The use of functional domains to improve transmembrane protein topology prediction", Journal of Bioinformatics and Computational Biology 4:109-113, 2006.
Xu, J., M. Li, and Y. Xu, "Protein Threading by Linear Programming: Theoretical Analysis and Computational Results", Journal of Combinatorial Optimization. 8:4, 403--418, 2004.
Xu, J., and M. Li, "Assessing RAPTOR's new linear programming approach for fold recognition in CAFASP3", PROTEINS: Structure, Function, and Genetics, 53(S6):579-584. Invited paper by CASP5 organizer, 2003.

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