Publications - Bioinformatics 2011

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Books & Chapters


  1. Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen.
    Computational Models for Condition-Specific Gene and Pathway Inference
    Chapter 30 in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Mourad Elloumi and Albert Y. Zomaya (Editors). John Wiley & Sons, January, 2011.
  1. Ling-Yun Wu.
    Haplotype Inference Models and Algorithms
    Chapter 36 in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Mourad Elloumi and Albert Y. Zomaya (Editors). John Wiley & Sons, January, 2011.
  1. Zhong-Yuan Zhang
    Nonnegative Matrix Factorization: Models, Algorithms and Applications.
    Chapter in Data Minming: Foundations and Intelligent Paradigms 2, in press, 2011.


Refereed Journal Papers

  1. Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang.
    An Efficient Network Querying Method Based on Conditional Random Fields.
    Bioinformatics, 27 (22): 3173-3178, 2011. doi: 10.1093/bioinformatics/btr524.
    SCI; Funding: NSFC(60970091, 60873205), CAS(kjcx-yw-s7)
  1. Guangxu Jin, Changhe Fu, Hong Zhao, Kemi Cui, Jenny Chang, Stephen T.C. Wong
    A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy.
    Cancer Res, doi:10.1158/0008-5472.CAN-11-2333, 2011.
  1. Guangxu Jin, Hong Zhao, Xiaobo Zhou, Stephen T.C. Wong
    An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.
    Bioinformatics, 27(13):i310-6, 2011.
  1. Jiguang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Luonan Chen, and Xiang-Sun Zhang
    NOA: a novel Network Ontology Analysis method.
    Nucleic Acids Research, 39(13):e87, 2011.
    SCI; Funding: NSFC(60873205, 10801131, 60970091), CAS(kjcs-yw-s7)
  1. Shihua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou
    A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.
    Bioinformatics (ISMB2011), 27:i401-i409, 2011.
    SCI; Funding: NSFC(11001256), CAS(kjcs-yw-s7)
  1. Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang
    Two-stage flux balance analysis of metabolic networks for drug target identification.
    BMC Systems Biology, 5(Suppl 1):S11, 2011.
    SCI; Funding: NSFC(10631070, 60873205, 10701080)
  1. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang, Weiming Xia and Luonan Chen.
    Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients.
    Molecular Biosystems, 7(5):1441-1452, 2011.
  1. Yong Wang, Xiang-Sun Zhang, and Luonan Chen
    Computational systems biology: integration of sequence, structure, network, and dynamics.
    BMC Systems Biology, 5(Suppl 1):S1, 2011
  1. Yongcui Wang, Yong Wang, Zhixia Yang, Nai-Yang Deng
    Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context.
    BMC Systems Biology, 5(Suppl 1):S6, 2011.
    SCI; Funding: NSFC(10801131, 10801112, 10971223, 11071252)
  1. Ruoying Chen, Zhiwang Zhang, Di Wu, Peng Zhang, Xinyang Zhang, Yong Wang, and Yong Shi.
    Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming.
    Journal of Theoretical Biology, Vol. 269, pp. 174--180, 2011.
  1. Xianwen Ren, Yongcui Wang, Yong Wang, Nai-Yang Deng and Xiang-Sun Zhang.
    Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation
    BMC Bioinformatics 12:409, 2011.
    SCI; Funding: NSFC(60873205, 10801131, 10631070, 10971223, 11071252), CAS(kjcx-yw-s7)

Proceedings Papers


  1. Jun-Fei Zhao, Jiguang Wang, Xiang-Sun Zhang.
    A SVC-based Method to Detect Multi-scalar Noisy Communities in Complex Networks.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 133-143
  1. Yong Wang, Jiguang Wang, Chen Chen, Xiang-Sun Zhang.
    A Regularized Optimization Model for Community Identification in Complex Networks.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 147-156
  1. Hong-Wei Liu.
    A Non-monotone Adaptive Trust Region Algorithm For Nonlinear Equations.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 67-74
  1. Zhenping Li, Xianman Hu.
    The Team Orienteering Problem with Capacity Constraint and Time Window.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 157-163
  1. Xianwen Ren, Yong Wang, Xiang-Sun Zhang.
    A Flexible Convex Optimization Model for Semi-supervised Clustering with Instance-level Constraints.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 178-185
  1. Hong-Wei Liu.
    Linear Programming for Portfolio Selection Based on Fuzzy Decision-Making Theory.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 195-202
  1. Jin-Shan Li, San-qiang Wang, Jia-Rong Gao.
    Consumer’s Optimal Choice on lp Commodity.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 234-241
  1. Shoujun Xu, Jiguang Wang, Junhua Zhang, Xiang-Sun Zhang.
    Multiple Resolution Community Structure Analysis.
    The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 334-349
  1. Yong-Cui Wang, Xian-Wen Ren, Chun-Hua Zhang, Nai-Yang Deng, Xiang-Sun Zhang.
    Evaluating the Denoising Techniques in Protein-Protein Interaction Prediction.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 78-83
  1. Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen.
    Protein Interaction Prediction for Mouse PDZ Domains Using Dipeptide Composition Features.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 129-132
  1. Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto.
    Identification of Master Regulator Candidates for Diabetes Progression in Goto-Kakizaki Rat by a Computational Procedure.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 197-202
  1. Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang.
    A Linear Programming Model for Identifying Non-Redundant Biomarkers Based on Gene Expression Profiles.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 249-254
  1. Yong Wang, Qiao-Feng Wu, Chen Chen, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, Fan-Rong Liang.
    Identifying Biomarkers for Acupuncture Treatment via an Optimization Model.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 319-326
  1. Junhua Zhang, Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen.
    A Dynamical Method to Extract Communities Induced by Low or Middle-degree Nodes.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 340-344
  1. Qiang Huang, Ling-Yun Wu, Ji-Bin Qu, Xiang-Sun Zhang.
    Analyzing Time-Course Gene Expression Data Using Profile-State Hidden Markov Model.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 351-355
  1. Chen Chen, Jun-Fei Zhao, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang.
    Inferring Domain-Domain Interactions Using an Extended Parsimony Model.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 385-389
  1. Ji-Bin Qu, Xiang-Sun Zhang, Ling-Yun Wu, Yong Wang, Luonan Chen.
    Detecting Coherent Local Patterns from Time Series Gene Expression Data by a Temporal Biclustering Method.
    2011 IEEE International Conference on Systems Biology (ISB), pp. 399-404
  1. Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K.K. Leung, Xiang-Sun Zhang, Stephen K.W. Tsui and Luonan Chen.
    Inferring protein-protein interactions based on sequences and interologs in Mycobacterium tuberculosis.
    Leture Notes in Bioinformatics, 6840: pp. 91-96, 2011
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