Publications - Bioinformatics 2009

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Books & Chapters


  1. Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.
    Biomolecular Networks: Methods and Applications in Systems Biology.
    John Wiley & Sons, Hoboken, New Jersey. July, 2009.
  1. Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia.
    A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data,
    Chapter XIX in Computational Methodologies in Gene Regulatory Networks, Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009.
  1. Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen
    Fuzzy system methods in modeling gene expression and analyzing protein networks
    Chapter 9 in Fuzzy Systems in Bioinformatics and Computational Biology, edited by Y. Jin, L. Wang, pp:165-189, Springer Berlin/Heidelberg, 2009

Refereed Journal Papers


  1. Guangxu Jin, Xiaobo Zhou, Kemin Cui, Xiang-Sun Zhang, Luonan Chen, and Steve T.C. Wong.
    Cross-platform method for identifying candidate network biomarkers for prostate cancer.
    IET Systems Biology, 3(6), 505-512, 2009
  1. Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen.
    Identifying differentially expressed pathways via a mixed integer linear programming model.
    IET Systems Biology, 3(6), 475-486, 2009
  1. Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen.
    Detecting drug targets with minimum side effects in metabolic networks.
    IET Systems Biology, 3(6), 523-533, 2009
  1. Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.
    Evaluating protein similarity from coarse structures.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 4, pp. 583-593, 2009.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
  1. Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.
    Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.
    Protein Engineering, Design, and Selection, Vol. 22, No. 11, pp. 707-712, 2009.
  1. Yong Wang, Xiang-Sun Zhang, and Yu Xia.
    Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.
    Nucleic Acids Research, Vol. 37, No. 18, pp. 5943-5958, 2009.
    SCI; Funding: NSFC(10631070), NSFC(60873205), NSFC(10801131), CAS(kjcx-yw-s7)
  1. Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang.
    Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.
    PLoS Computational Biology, 9(5), e1000521, 2009.
    SCI; Funding: NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)
  1. Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen.
    Modularity optimization in community detection of complex networks.
    Europhysics Letters, 87, 38002, 2009.
    SCI; Funding: NSFC(10701080), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905), CAS(kjcx-yw-s7)
  1. Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    A network biology study on circadian rhythm by integrating various omics data.
    OMICS: A Journal of Integrative Biology, Vol. 13, No. 4, 2009.
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)
  1. Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.
    Self-organizing map approaches for the haplotype assembly problem.
    Mathematics and Computers in Simulation, 79(10), 3026-3037, 2009
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), NSFC(60873205)
  1. Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.
    Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.
    BMC Bioinformatics, 2009, 10(Suppl 4):S6
    SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070)
  1. W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.
    Multiple distinct clones may co-exist in different lineages in myelodysplastic syndromes.
    Leukemia Research, 33(6), 847-853, 2009
  1. Xiaojian Shao, Yingjie Tian, Lingyun Wu, Yong Wang, Naiyang Deng.
    Predicting DNA-and RNA-binding proteins from sequences with kernel methods.
    Journal of Theoretical Biology, 258 (2009) 289–293.
  1. Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T.C. Wong.
    Conditional random pattern algorithm for LOH inference and segmentation.
    Bioinformatics, Vol. 25, No. 1, 61-67, 2009.
  1. Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.
    Exploring the constrained maximum edge-weight connected graph problem.
    Acta Mathematicae Applicatae Sinica (E), 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
    SCI; NSFC(60873205)
  1. Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.
    A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.
    International Journal of Data Mining in Bioinformatics, 3(1), 68-84, 2009.
    SCI; NSFC(10631070), CAS(kjcx-yw-s7)
  1. Xiaorong Yang, Xiaobo Zhou, Wan-Ting Huang, Lingyun Wu, Federico A. Monzon, Chung-Che Chang, and Stephen T.C. Wong.
    Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays.
    PLoS One, Vol. 4, No. 4, e5054, 2009.
    SCI


Proceedings Papers


  1. Naiyang Deng, Ling-Yun Wu, Xiaobo Wang.
    The Prediction of Protein Post-translational Modification Sites,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Zhong-Yuan Zhang.
    NMF-based Models for Tumor Clustering: A Systematic Comparison,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Zhenping Li, Rui-Sheng Wang, Luonan Chen.
    Extracting Community Structure of Complex networks by Self-Organizing Maps,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu.
    Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang.
    A Constrained Optimization Method for Community Detection,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Xuemei Ning, Shihua Zhang.
    A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Zhi-Ping Liu, Luonan Chen.
    Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Lin Wang, Ji-Guang Wang, Luonan Chen.
    Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang.
    Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Shihua Zhang, Xuemei Ning, Chris Ding.
    Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Junhua Zhang, Xiang-Sun Zhang.
    A Weighted Parsimony Model for Community Detection in Complex Networks,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Xianwen Ren, Xiang-Sun Zhang.
    A Novel Approach for Pathway Inference Based on Network Flow,
    Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.
    ISTP
  1. Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen.
    Dynamically dysfunctional protein interactions in the development of Alzheimer's disease.
    IEEE International Conference on Systems, Man and Cybernetics, pp. 4262-4267. San Antonio, TX, USA, 2009.
    EI


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