Publications - Bioinformatics 2002-2005


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Refereed Journal Articles

  1. Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen.
    Unique optimal foldings of proteins on a triangular lattice.
    Applied Bioinformatics, Vol. 4, No. 2, pp. 105-116, 2005.
  2. Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shuihua Zhang and Xiang-Sun Zhang.
    Comparison of Protein Structures by Multi-Objective Optimization.
    Genome Informatics, Vol. 16, No. 2, pp. 114-124, 2005.
  3. Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang.
    A reconstruction algorithm to DNA sequencing by hybridization with target DNA length error.
    Acta Mathematicae Applicatae Sinica, Vol. 28, No. 3, pp. 385-395, 2005. (in Chinese)
  4. Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen.
    A parsimonious tree-grow method for haplotype inference.
    Bioinformatics, Vol. 21, No. 17, pp. 3475-3481, 2005.
  5. Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang.
    Haplotype assembly from aligned weighted SNP fragments.
    Computational Biology and Chemistry, Vol. 29, No. 4, pp. 281-287, 2005.
  6. Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang.
    Improved self-organizing map algorithm for protein folding and its realization.
    Journal of Systems Science and Mathematical Sciences, Vol. 25, No. 5, pp. 562-573, 2005. (In Chinese)
  7. Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang.
    Aligning multiple protein structures by deterministic annealing.
    Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, pp. 837-860, 2005.
  8. Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang.
    Haplotype reconstruction from SNP fragments by minimum error correction.
    Bioinformatics, Vol. 21, No. 10, pp. 2456-2462, 2005.
  9. Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen.
    Exploring protein's optimal HP configurations by self-organizing mapping.
    Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, pp. 385-400, 2005.
  10. Rui-Sheng Wang, Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang.
    Algorithms for the SNP haplotype assembly problem.
    Applied Mathematics, A Journal of Chinese Universities (Series A), Vol. 19, Supplement, pp. 515-528, 2004.
  11. Zhen-Ping Li, Yong Wang, Yu-Ying Zhao and Xiang-Sun Zhang.
    Haplotype inference and mating graphs.
    Applied Mathematics, A Journal of Chinese Universities (Series A), Vol. 19, Supplement, pp. 567-576, 2004.
  12. Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang.
    Reconstruction of DNA sequencing by hybridization.
    Bioinformatics, Vol. 19, No. 1, pp. 14-21, 2003.
  13. Xiang-Sun Zhang, Ji-Hong Zhang, and Ling-Yun Wu.
    A reconstruction algorithm to solve positional sequencing by hybridization.
    Journal of Systems Science and Mathematical Sciences, Vol. 22, No. 3, pp. 258-269, 2002. (In Chinese).

Proceedings Articles

  1. Xiang-Sun Zhang, Zhong-Wei Zhan, Yong Wang and Ling-Yun Wu.
    An attempt to explore the similarity of two proteins by their surface shapes.
    Operations Research and Its Applications, Lecture Notes in Operations Research, 5, pp. 276-284, World Publishing Corporation, Beijing, 2005.
  2. Shihua Zhang, De-Gang Liu and Xiang-Sun Zhang.
    A framwork for structural similarity search in protein.
    Operations Research and Its Applications, Lecture Notes in Operations Research, 5, pp. 285-295, World Publishing Corporation, Beijing, 2005.
  3. Rui-Sheng Wang, Xiang-Sun Zhang and Li Sheng.
    Haplotype inference by pure parsimony via genetic algorithm.
    Operations Research and Its Applications, Lecture Notes in Operations Research, 5, pp. 296-306, World Publishing Corporation, Beijing, 2005.
  4. Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, and Xiang-Sun Zhang.
    A Genetic algorithm for the individual haplotyping problem.
    Proceedings of ORSC 2004, 814-823, Global-Link Publishing Company, Hong Kong, 2004.
  5. Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, and Xiang-Sun Zhang.
    Haplotyping an individual from weighted SNPs fragments.
    Proceedings of ORSC 2004, 824-830, Global-Link Publishing Company, Hong Kong, 2004.
  6. Ji-Hong Zhang, Ling-Yun Wu, Yong Wang, Zheng-Ping Li, and Xiang-Sun Zhang.
    A statistical method based on markov chain for optimal reconstruction of haplotype from genotype data with SNP.
    Proceedings of ORSC 2004, 1268-1278, Global-Link Publishing Company, Hong Kong, 2004.
  7. Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang.
    Structure alignment of protein by mean field annealing.
    ICSB2003.
  8. Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang.
    Neural networks approach to DNA sequencing by hybridization.
    Operations Research and Its Applications, Lecture Notes in Operations Research, 4, pp. 312-320, World Publishing Corporation, Beijing, 2002.

Technical Reports

  1. Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Ji-Hong Zhang.
    A fast approach measure the protein structure similarity from the global shape view.
    Report of Research, IAM-R003, Institute of Applied Mathematics, AMSS, CAS, 2005.


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