Recent Publications

    2008

  1. "Fast and accurate search for non-coding RNA pseudoknot structures in genomes", Bioinformatics, (with Z. Huang, Y. Wu, J. Robertson, F. Liang, and R. Malmberg), accepted, 2008. [pdf]

  2. "Fixed-parameter approximation: conceptual framework and approximability results", Algorithmica, (with X. Huang), accepted, 2008. [pdf]

  3. "Parameterized complexity and biopolymer sequence comparison", The Computer Journal, Special Issue in Parameterized Complexity, 51(3): 270-291, (with X. Huang, C. Liu, F. Rosamond, and Y. Song), 2008. [pdf]

  4. "Fast de novo peptide sequencing and spectral alignment via tree decomposition", International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, (with C. Liu, Y. Song, B. Yan, and Y. Xu), accepted, 2008. [pdf]

  5. "Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition", Journal of Mathematical Biology, Special Issue in RNA, Vol 56, No: 1-2, pp. 145-159, (with J. Zhao, R. Malmberg), 2008. [pdf]

    2007

  6. "Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition", Proceedings of Pacific Symposium on Biocomputing (PSB 2007) 12:496-507, Hawaii, (with J. Zhao and D. Che), 2007. [pdf]

  7. "Operon prediction in microbial genomes using decision tree approach", Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), pp 135-142, also to appear in International Journal of Information Technology and Intelligent Computing, (with D. Che, J. Zhao, and Y. Xu), 2007.

  8. "Comparative pathway prediction with structural genomic information via a unified graph Model", Proceedings of 2007 International Symposium on Bioinformatics Research and Applications (ISBRA 2007), pp 627-637, (with J. Zhao and D. Che).[pdf]

  9. "Protein tertiary structure prediction by protein threading: a survey", Plant Biotechnology Journal, to appear, (with X. Huang and E. Hood), 2007.

  10. "The complexity of polynomial-time approximation", Theory of Computing Systems (formerly Mathematical Systems Theory), Vol 41, No 3, pp. 459-477, (with M. Fellows, D. Juedes, F. Rosamond), 2007. [pdf]

    2006

  11. "Tag-based blind PTM identification with point process model", Proceedings of International Symposium on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, also in Bioinformatics, Vol 22, No 14, (with C. Liu, B. Yan, Y. Song and Y. Xu), pp. 307-313, 2006. [pdf]

  12. "Efficient parameterized algorithms for biopolymer structure-sequence align ment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 3, No. 4, pp. 423-431, (with Y. Song, C. Liu, X. Huang, R. Malmberg, Y. Xu), 2006. [pdf]

  13. "Efficient annotation of non-coding RNA structures including pseudoknots via automated filters", Proceedings of Life Science Society Computational Systems Biology Conference (CSB 2006), Palo Alto, California, pp. 99-110, (with C. Liu, Y. Song, P. Hu, R. Malmberg), 2006. [pdf]

  14. "Protein structure prediction by protein threading", in Computational Methods for Protein Structure Prediction and Modeling, Vols I&II, Xu, Xu and Liang (eds), 389-430, Springer, (with Y. Xu, Z. Liu, D. Xu), 2007. [pdf]

  15. "Rapid ab initio RNA folding including pseudoknots via graph tree decomposition", Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI 2006), Lecture Notes in Bioinformatics 4175, Zurich, Switzerland, pp. 262-273 (with J. Zhao and R. Malmberg), 2006. [pdf]

  16. "Phylogenetic network inferences through efficient haplotyping", Proceedings of Workshop on Algorithms in Bioinformatics (WABI 2006), Lecture Notes in Bioinformatics 4175, Zurich, Switzerland, pp. 68-79 (with Y. Song, C. Liu and R. Malmberg), 2006. [pdf]

  17. "Fixed-parameter approximation: conceptual framework and approximability results", Proceedings of the 2nd International Workshop on Parameterized and Exact Computation, Zurich, Switzerland, Lecture Notes in Computer Science 4169, pp. 96-108, (with X. Huang), 2006. [pdf]

  18. "Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots", International Journal of Bioinformatics Research and Applications, Vol. 2, No. 3, pp. 289-304, (with Y. Song, C. Liu, R. Malmberg and C. He), 2006. [pdf]

  19. "Learning the parameters of stochastic grammar models for RNA structures with pseudoknots", Proceeding of IEEE International Conference on Granular Computing (IEEE GrC 2006), Atlanta, pp. 170-175 (with J. Zhao, R. Malmberg), 2006. [pdf]

  20. "Fast de novo peptide sequencing and spectral alignment via tree decomposition", Proceedings of Pacific Symposium on Biocomputing (PSB 2006), pp. 255-266, Hawaii, (with C. Liu, Y. Song, B. Yan, Y. Xu), 2006. [pdf]

    2005

  21. "Tree decomposition-based fast RNA pseudoknot search in genomes", Proceedings of IEEE Computer Society Computational Systems Bioinformatics Conference, (CSB 2005) pp. 223-234, Palo Alto, California, (with Y. Song, C. Liu, R. Malmberg, F. Pan), 2005. [pdf]

  22. "Profiling and searching for RNA pseudoknot structure in genomes", Transactions on Computational Systems Biology 2: pp. 37-47 (with C. Liu, Y. Song, R. Malmberg), 2005. [pdf]

  23. "BEST: Binding-site estimation suite of tools", Bioinformatics 21(12): pp. 2909-2911, (with D. Che, S. Jensen, J.S. Liu), 2005.

  24. "Efficient parameterized algorithms for biopolymer structure-sequence alignment", Proceedings of Workshop on Algorithms in Bioinformatics (WABI 2005), Mallorca, Spain, Lecture Notes in Bioinformatics 3692: pp. 376-388, (with Y. Song, C. Liu, X. Huang, R. Malmberg, Y. Xu), 2005. [pdf]

  25. "RNA structural homology search with a succinct stochastic grammar model", Journal of Computer Science and Technology Vol.20, No.4, Special Issue in Bioinformatics, pp. 454-464, (With Y. Song, J. Zhao, C. Liu, K. Liu, and R. Malmberg), Springer, 2005. [pdf]

  26. "Profiling and searching for RNA pseudoknot structure in genomes", Proceedings of International Workshop in Bioinformatics Research and Applications (IWBRA 2005), Lecture Notes in Computer Science 3515: pp 968-975, (with C. Liu, Y. Song, R. Malmberg), 2005. [pdf]