Publications - Bioinformatics 2008


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Refereed Journal Articles

  1. Jiguang Wang, Yuqing Qiu, Rui-Sheng Wang, Xiang-Sun Zhang.
    Remarks on network community properties,
    Jrl Syst Sci & Complexity, 21: 637-644, 2008.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070), 973(2006CB503905)
  2. Lin Wang, Yuqing Qiu, Jiguang Wang, Xiang-Sun Zhang.
    Recognition of structure similarities in proteins,
    Jrl Syst Sci & Complexity, 21: 665-675, 2008.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10631070)
  3. Ji-Hong Zhang, Ling-Yun Wu, Jian Chen, Xiang-Sun Zhang.
    A fast haplotype inference method for large population genotype data,
    Computational Statistics and Data Analysis, 52(11): 4891-4902, 2008.
  4. Guangxu Jin, Xiaobo Zhou, Honghui Wang, Hong Zhao, Kemi Cui, Xiang-Sun Zhang, Luonan Chen, Stanley L. Hazen, King Li, and Stephen T. C. Wong.
    The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events.
    J Proteome Res. 7(9): 4013-4021, 2008.
  5. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    Protein cavity clustering based on community structure of pocket similarity network.
    International Journal of Bioinformatics Research and Applications, Vol. 4, No. 4, pp.445–460, 2008.
    Funding: NSFC(60503004), NSFC(10631070), 973(2006CB503905)
  6. Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
    Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures.
    Neurocomputing, 72, 134–141, 2008.
    SCI; Funding: NSFC(10701080), NSFC(10631070), 973(2006CB503905)
  7. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen.
    Bridging protein local structures and protein functions.
    Amino Acids, 35(3): 627-650, 2008.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), 973(2006CB503905)
  8. Zhenping Li, Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen.
    Quantitative function for community detection.
    Physical Review E, 77, 036109, 2008.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070), NSFC(60503004), 973(2006CB503905)
  9. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen.
    Analysis of Protein Surface Patterns by Pocket Similarity Network.
    Protein and Peptide Letters, 15:448-455, 2008.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), 973(2006CB503905)
  10. Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang.
    Detecting community structure in complex networks based on a measure of information discrepancy.
    Physica A, 2008, 387(7), 1675-1682.
    SCI; Funding: NSFC(10701080), NSFC(10631070)
  11. Shihua Zhang, Xiang-Sun Zhang and Luonan Chen.
    Biomolecular network querying: a promising approach in systems biology.
    BMC Systems Biology, 2008, 2:5.
    SCI; Funding: NSFC-JSPS(10711140116), 973(2006CB503905)
  12. Shu-Qin Zhang, Wai-Ki Ching, Yue Jiao, Ling-Yun Wu, and Raymond H. Chan.
    Construction and control of genetic regulatory networks: A multivariate Markov chain approach.
    Journal of Biomedical Science and Engineering, Vol. 1, pp. 15-21, 2008.

Proceedings Articles

  1. Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen.
    Reconstruction of regulator activity in E. coli post-transcription processes.
    IEEE International Conference on Bioinformatics and Biomedicine, 2008 (IEEE BIBM'08), 339-342.
    EI; NSFC (10701080), NSFC(10631070), NSFC-JSPS(10711140116)
  2. Xiang-Sun Zhang and Rui-Sheng Wang.
    Optimization analysis of modularity measures for network community detection.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 13-20, World Publishing Corporation, Lijiang, 2008.
    ISTP
  3. Yu-Qing Qiu, Shihua Zhang.
    Uncovering Differentially Expressed Pathways with Protein Interaction and Gene Expression Data.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 74-82, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10631070), 973(2006CB503905)
  4. Lin Wang, Wen-Juan Zhang.
    A New Algorithm for Sequential and Non-sequential Protein Multiple Structure Alignment.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 83-90, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC-JSPS(10711140116), NSFC(10631070), NSFC(60503004)
  5. Guangxu Jin, Xiaobo Zhou, Kemi Cui, Stephen T.C. Wong.
    The Network Biomarker Discovery in Prostate Cancer from Both Genomics and Proteomics Levels.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 144-151, World Publishing Corporation, Lijiang, 2008.
    ISTP
  6. Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang.
    Mass Flow Model and Essentiality of Enzymes in Metabolic Networks.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 182-190, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(60873205), NSFC(10631070), NSFC(60503004), NSFC(10701080)
  7. Ling-Yun Wu, Ji-Hong Zhang, Raymond Chan.
    Improved Approach for Haplotype Inference Based on Markov Chain.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 212-223, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10631070), NSFC(60503004)
  8. Ling-Yun Wu, Xiaobo Zhou, Chung-Che Chang, Stephen T.C. Wong.
    Model Based Probe Fitting and Selection for SNP Array.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 224-231, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(60503004)
  9. Zhi-Ping Liu, Weiming Xia, Luonan Chen.
    Analysis of Domain Interactions Among Gamma-secretase Substrates.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 232-241, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC-JSPS(10711140116), NSFC(10631070), 973(2006CB503905)
  10. Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang.
    Comparative Study on A Class of Evaluation Indices for Community Detection.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 294-303, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10631070), 973(2006CB503905)
  11. Junhua Zhang, Weihua Yue, and Xiang-Sun Zhang.
    Multilocus analysis of case-control data to schizophrenia based on measures of information discrepancy,
    Operations Research and Its Applications,Lecture Notes in Operations Research, vol. 8,pp. 442-449,World Publishing Corporation,2008
    ISTP
  12. Yong Wang, Yu Xia.
    Condition Specific Subnetwork Identification Using an Optimization Model.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 333-340, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10801131), 973(2006CB503905)
  13. Shu-Qin Zhang, Wai-Ki Ching, Yue Jiao, Ling-Yun Wu, and Raymond H. Chan.
    A simplified multivariate Markov chain model for the construction and control of genetic regulatory networks.
    Proceedings of the 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), pp. 569--572, Shanghai, China, 2008.
  14. Zhi-Xia Yang.
    A Multi-class Algorithm Model Based on p-class Support Vector Ordinal Regression Machine.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 54-61, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10801112), NSFC(70601033), NSFC(10631070)
  15. Jun-Yan Tang, Zhi-Xia Yang.
    Incorporating Gene Similarity into Support Vector Machine for Microarray Classification and Gene Selection.
    Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 350-357, World Publishing Corporation, Lijiang, 2008.
    ISTP; Funding: NSFC(10801112), NSFC(70601033), NSFC(10631070)



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