Publications - Bioinformatics 2010

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Books & Chapters


  1. Ling-Yun Wu, Xiaobo Zhou, and Stephen T. C. Wong.
    Computational Imaging and Modeling for System Biology
    Chapter 17 in Elements of Computational Systems Biology, Huma M. Lodhi and Stephen H. Muggleton (Editors). John Wiley & Sons, February, 2010.


Refereed Journal Papers


  1. Yan Xu, Xiao-Bo Wang, Jun Ding, Ling-Yun Wu, and Naiyang Deng.
    Lysine acetylation sites prediction using an ensemble of support vector machine classifiers
    Journal of Theoretical Biology, 264(1):130-135, 2010.
    SCI;
  1. Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia.
    Protein evolution in yeast transcription factor subnetworks
    Nucleic Acids Research, 38(18): 5959–5969, 2010.
    SCI; Funding: NSFC(10801131, 10631070)
  1. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    Prediction of protein-RNA binding sites by a random forest method with combined features
    Bioinformatics, 26(13):1616-1622, 2010.
    SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
  1. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen.
    Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
    BMC Systems Biology, 4(Suppl 2):S11.
    SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
  1. Yongcui Wang, Zhixia Yang, Yong Wang, and Nai-Yang Deng.
    Computationally probing drug-protein interactions via support vector machine
    Letters In Drug Design & Discovery, 7(5), 370-378, 2010.
    SCI;
  1. Zhong-Yuan Zhang, Tao Li, Chris Ding, Xian-Wen Ren, and Xiang-Sun Zhang.
    Binary matrix factorization for analyzing gene expression data
    Data Mining and Knowledge Discovery, 20(1), 28-52, 2010.
    SCI;
  1. Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu, and Xiang-Sun Zhang.
    An information-flow-based model with dissipation, saturation and direction for active pathway inference
    BMC Systems Biology, 4:72, 2010.
    SCI; Funding: NSFC(60873205), 973(2006CB503905)
  1. Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen.
    Detecting disease associated modules and prioritizing active genes based on high throughput data.
    BMC Bioinformatics. 11:26, 2010.
    SCI; Funding: 973(2006CB503905), NSFC(60873205, 10801131), CAS(kjcx-yw-s7)
  1. Zheng Xia, Ling-Yun Wu, Xiaobo Zhou, and Stephen TC Wong.
    Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces.
    BMC Systems Biology, Vol. 4, Suppl 2, S6, 2010.
    SCI;
  1. Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    Optimization Meets Systems Biology.
    BMC Systems Biology, Vol. 4, Suppl 2, S1, 2010.
    SCI;
  1. Tingting Gao, Zhixia Yang, Yong Wang, Ling Jing.
    Identifying translation initiation sites in prokaryotes using support vector machine.
    Journal of Theoretical Biology, Vol. 262, No. 4, 644-649, 2010.
    SCI; Funding: NSFC(10631070, 10801131)
  1. Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    SANA: an algorithm for sequential and non-sequential protein structure alignment
    Amino Acids, Vol. 39, No. 2, 417-425, 2010.
    SCI; Funding: NSFC(10631070, 60503004), JSPS-NSFC (10711140116).
  1. Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, and Luonan Chen.
    Self-organizing map of complex networks for community detection
    Journal of Systems Science and Complexity, 23(5), 931-941, 2010.
    SCI; Funding: NSFC(10631070, 60873205, 10701080), BNSFC(1092011)
  1. Xianwen Ren, Xiang-Sun Zhang.
    A linear programming model based on network flow for pathway inference
    Journal of Systems Science and Complexity, 23(5), 971-977, 2010.
    SCI; Funding: NSFC(10631070, 60873205)
  1. Junhua Zhang, Yuqing Qiu, Xiang-Sun Zhang.
    Detecting community structure: From parsimony to weighted parsimony
    Journal of Systems Science and Complexity, 23(5), 1024-1036, 2010.
    SCI; Funding: NSFC(60873205),CAS(kjcx-yw-s7)


Proceedings Papers


  1. Zhi-Ping Liu, Xiang-Sun Zhang and Luonan Chen.
    Inferring gene regulatory networks from expression data with prior knowledge by linear programming.
    Proceedings of the 9th International Conference on Machine Learning and Cybernetics. pp. 3067-3072, Qingdao, China, 2010.
    EI; Funding: 973(2006CB503905), NSFC(10631070, 10801131)
  1. Yong Wang, Xiang-Sun Zhang, Katsuhisa Horimoto, and Luonan Chen.
    System Identification Models for Gene Regulation System.
    Proceedings of The 29th Chinese Control Conference (CCC), pp. 6239-6244, Beijing, 2010.
    EI; Funding: NSFC(10801131)
  1. Ruisheng Wang, Zhenping Li, Xiang-Sun Zhang, and Luonan Chen.
    Optimization and Control of Metabolic Networks.
    Proceedings of The 29th Chinese Control Conference (CCC), pp. 6251-6255, Beijing, 2010.
    EI; Funding: NSFC(10631070,10701080,60873205)
  1. Xiaorong Yang, Xianwen Ren, Xiaobo Zhou.
    Transcriptional Regulatory Network Discovery via Information Mining Approach in Rett Syndromes Study.
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 109-118
  1. Zhi-Ping Liu, Xiang-Sun Zhang.
    Effects of Multiple Probesets in Affymetrix GeneChips on Identifying Differentially Expressed Genes in iPS Cells.
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 187–195
  1. Jiguang Wang, Yong Wang, Xianwen Ren, Wei Guo, Luonan Chen.
    Uncover the Transient Transcriptional Regulations by a Novel Sliding Window Correlation Strategy.
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 235–242
  1. Jibin Qu, Michael Ng, Luonan Chen.
    Constrained Subspace Clustering for Time Series Gene Expression Data.
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 323–330
  1. Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang.
    Drug Target Identification Based on Flux Balance Analysis of Metabolic Networks.
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 331–338
  1. Yu-Qing Qiu, Xing-Ming Zhao, Zikai Wu, Chaochao Wu, Rong Zeng, Luonan Chen.
    Network Flow Model Based Analysis of Mouse Hepatocarcinogenesis
    The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 355–362
  1. Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang.
    An Optimization Model for Fuzzy Binary Clustering.
    The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 422-432
  1. Junhua Zhang, Xiang-Sun Zhang.
    On Resolution Limit of the Modularity in Community Detection.
    The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 492-499

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