Publications - Bioinformatics 2007


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Refereed Journal Articles

  1. Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen.
    Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
    PLoS ONE 2(11): e1207, 2007.
    Funding: NSFC(10631070), 973(2006CB503905)
  2. Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.
    Inferring transcriptional interactions and regulator activities from experimental data.
    Molecules and Cells, 24(3), 307-315, 2007
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
  3. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen and Xiang-Sun Zhang.
    Predicting Gene Ontology functions from protein's regional surface structures.
    BMC Bioinformatics, 8:475, 2007.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
  4. Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun Zhang, L.Chen.
    Discovering functions and revealing mechanisms at molecular level from biological networks.
    Proteomics, 7(16), 2856-2869, 2007.
    SCI; Funding: NSFC(10631070), 973(2006CB503905)
  5. Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang.
    Uncovering fuzzy community structure in complex networks.
    Physical Review E, 76, 046103, 2007
    SCI; Funding: NSFC(10631070), NSFC(10701080), 973(2006CB503905)
  6. Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen.
    Analysis on multi-domain cooperation for predicting protein-protein interactions.
    BMC Bioinformatics, 8:391, 2007
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
  7. Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
    Inferring transcriptional regulatory networks from high-throughput data.
    Bioinformatics, Vol. 23, pp. 3056-3064, 2007.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
  8. Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang.
    An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors.
    European J. of Operational research, 182, pp.413-427, 2007.
    SCI; Funding: NSFC(10471141), NSFC(60503004), NSFC(023101018)
  9. Zhenping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun.Zhang, Luonan Chen.
    Alignment of molecular networks by integer quadratic programming.
    Bioinformatics, Vol. 23, No. 13, 1631-1639, 2007.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10631070), NSFC(60503004), 973(2006CB503905)
  10. Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang.
    Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.
    Eur. Phys. J. B, 57, 67-74, 2007.
    SCI; Funding: NSFC(10631070)
  11. Yong Wang, Ling-Yun Wu, Luonan Chen and Xiang-Sun Zhang.
    Supervised classification of protein structures based on convex hull representation.
    International Journal of Bioinformatics Research and Applications, Vol. 3, No. 2, 123-144, 2007.
    Funding: NSFC(10471141), NSFC(60503004)
  12. Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang.
    Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering.
    Physica A, 2007, 374, 483–490..
    SCI; Funding: NSFC(10471141)

Proceedings Articles

  1. Zhong-Yuan Zhang, Tao Li, Chris Ding and Xiang-Sun Zhang.
    Binary matrix factorization with applications,
    Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007, page: 391-400.
    EI
  2. Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen.
    Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks,
    ICIC2007, Lecture Notes in Artificial Intelligence, 4682, 1090-1101, 2007
    EI, ISTP; Funding: 973(2006CB503905)
  3. Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
    Detecting community structure in complex networks by optimal rearrangement clustering,
    PAKDD 2007 workshop on Data Mining in Biomedical Applications, Lecture Notes in Artificial Intelligence, 4819,119-130, 2007
    EI, ISTP; Funding: NSFC(10701080), 973(2006CB503905)
  4. Zhong-Yuan Zhang and Xiang-Sun Zhang.
    Two Improvments of NMF Used for Tumor Clustering,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 242-249, World Publishing Corporation, Beijing, 2007.
    ISTP; Funding: NSFC(10631070), 973(2006CB503905)
  5. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen.
    An Approach for Clustering Protein Pockets into Similar Groups.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 204-212, World Publishing Corporation, Beijing, 2007.
    ISTP; Funding: NSFC(10631070), NSFC(60503004), 973(2006CB503905)
  6. Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen.
    New Insights into Network Motif Clusters from the Views of Cellular Localizations and Signal Pathways,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 100-109, World Publishing Corporation, Beijing, 2007.
    ISTP; Funding: NSFC(10631070), 973(2006CB503905)
  7. Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen.
    Establishing Protein Functional Linkage in a Systematic Way.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 75-88, World Publishing Corporation, Beijing, 2007.
    ISTP; Funding: NSFC(10471141), NSFC(60503004), 973(2006CB503905)
  8. Jinshan Li and Xiang-Sun Zhang.
    An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 35-41, World Publishing Corporation, Beijing, 2007.
    ISTP; Funding: NSFC(10631070), 973(2006CB503905)


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