Publications - Bioinformatics 2006

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Refereed Journal Articles

  1. Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang.
    A dynamic programming algorithm for the k-haplotyping problem.
    Acta Mathematicae Applicatae Sinica, Vol.22, No.3, pp.405-412, 2006.
  2. Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang.
    Identification of functional modules in a PPI network by clique percolation clustering.
    Computational biology and chemistry, 30(6), 445-451, 2006.
  3. Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, and Wei Zhang.
    Minimum conflict individual haplotyping from SNP fragments and related genotype.
    Evolutionary Bioinformatics, 2006, 2, 271-280.
  4. Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen.
    A Markov Chain Model for Haplotype Assembly from SNP Fragments.
    Genome Informatics, Vol. 17, No. 2. 2006.
  5. Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang.
    Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
    BMC Structural Biology, 2006, 6:18, doi:10.1186/1472-6807-6-18.
  6. Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
    Inferring gene regulatory networks from multiple microarray datasets.
    Bioinformatics, 22(19):2413-2420; doi:10.1093/bioinformatics/btl396, 2006.
  7. Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang.
    Inferring Protein Interactions from Experimental Data by Association Probabilistic Method.
    Proteins: Structure, Function, and Bioinformatics, Vol. 62, pp. 833-837, 2006.
  8. Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen.
    Exploring the classification of protein structures on geometric patterns by neural networks.
    International Journal of Computational Intelligence Research, Vol. 2, No. 1, pp. 105-109, 2006.
  9. Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen.
    Models and algorithms for the haplotyping problem.
    Current Bioinformatics, Vol. 1, No. 1, pp. 105-114, 2006.
  10. Shi-Hua Zhang and Xiang-Sun Zhang.
    Visualization of conformational space based on CA-CA distance.
    Chinese journal of Bioinformatics. Vol. 4, No.4, pp. 153-156, 2006. (In Chinese)

Proceedings Articles

  1. Jinshan Li and Xiang-Sun Zhang.
    An Optimization Model for Achieving Sparsity of Gene Regulatory Networks.
    Operations Research and Its Applications, Lecture Notes in Operations Research, 6, pp. 368-379, World Publishing Corporation, Beijing, 2006.
  2. Yong Wang, Zhen-Ping Li, Xiang-Sun Zhang and Luonan chen.
    3D Structural Motif Finding in Protein Structures by Network Alignment,
    D. -S. Huang (Eds.): WICB2006, 2006.
  3. Shi-Hua Zhang, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang.
    Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods.
    ICIC06, LNCS, Lecture Notes in Bioinformatics, Vol. 4115, 514-524, 2006.
  4. Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang.
    A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks.
    ICDMW, 130-135, Sixth IEEE International Conference on Data Mining-Workshops (ICDMW'06), 2006. (Acceptance Ratio: 28.0%)
  5. Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen.
    Automatic classification of protein structures based on convex hull representation by integrated neural network.
    Theory and Applications of Models of Computation, J.-Y. Cai, S. B. Cooper, and A. Li, Eds., Vol. 3959, pp. 505--514, Springer-Verlag, 2006.
  6. Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen.
    Supervised Inference of Gene Regulatory Networks by Linear Programming.
    D. -S. Huang, K. Li and G. W. Irwin (Eds.): ICIC2006, LNBI, Vol. 4115, pp. 551-561, Springer-Verlag, 2006.
  7. Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen.
    Alignment of protein interaction networks by integer quadratic programming.
    28th IEEE EMBS Annual International Conference.
  8. Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen.
    Protein structure comparison by both structure and sequence data.
    IFMBE Proceedings, Vol. 14, 2006, 174-177, Springer Berlin Heidelberg.
  9. Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Shihua Zhang and Luonan Chen.
    Inferring Protein-Protein Interactions by Combinatorial Models.
    IFMBE Proceedings, Vol.14, 2006, 183--186, Springer Berlin Heidelberg.

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