Publications - Bioinformatics 2012


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Books & Chapters



Accepted Papers




Refereed Journal Papers

  1. Xiang-Sun Zhang, Zhenping Li, Rui-Sheng Wang, and Yong Wang
    A combinatorial model and algorithm for globally searching community structure in complex networks
    Journal of Combinatorial Optimization, 23(4): 425-442, 2012.
    SCI; Funding: NSFC(10631070, 60873205, 10801131, 10701080), CAS(kjcx-yw-s7)
  2. Hui-Jia Li, Yong Wang, Ling-Yun Wu, Junhua Zhang and Xiang-Sun Zhang
    Potts model based on a Markov process computation solves the community structure problem effectively
    Physical Review E, 86: 016109, 2012.
    SCI; Funding: NSFC(11131009, 60970091, 61171007, 91029301, 61072149, 31100949, 61134013), CAS(kjcx-yw-s7)
  3. Hui-Jia Li, Yong Wang, Ling-Yun Wu, Zhi-Ping Liu, Luonan Chen and Xiang-Sun Zhang
    Community structure detection based on Potts model and network's spectral characterization
    Europhysics Letters, 97: 48005, 2012.
    SCI; Funding: NSFC(11131009, 60970091, 61171007, 91029301, 61072149, 31100949, 61134013), CAS(kjcx-yw-s7)
  4. Hui-Jia Li, Junhua Zhang, Zhi-Ping Liu, Luonan Chen and Xiang-Sun Zhang
    Identify overlapping communities in social networks using multi-scale local information expansion
    European Physical Journal B, 85(6): 190, 2012.
    SCI; Funding: NSFC(11131009, 60970091, 61171007, 91029301, 61072149, 31100949, 61134013), CAS(kjcx-yw-s7)
  5. Zhi-Ping Liu, Yong Wang. Xiang-Sun Zhang, Luonan Chen.
    Network-based analysis of complex diseases
    IET Systems Biology, 6(1): 122-133, 2012.
  6. Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K.K. Leung, Xiang-Sun Zhang, Stephen K.W. Tsui and Luonan Chen.
    Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs.
    BMC Bioinformatics, 13(Suppl 7): S6, 2012.
    SCI; Funding: NSFC(31100949, 61072149, 91029301)
  7. Lin Wang, Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen.
    Prediction of hot spots in protein interfaces using a random forest model with hybrid features
    Protein Engineering Design and Selection, 25(3):119-126, 2012.
    SCI; Funding: NSFC(31100949, 60873205, 61134013, 61072149, 91029301)
  8. Xianwen Ren, Yong Wang, Jiguang Wang and Xiang-Sun Zhang.
    A unified computational model for revealing and predicting subtle subtypes of cancers
    BMC Bioinformatics 13:70, 2012.
    SCI; Funding: NSFC(61171007, 11131009)
  9. Zhong-Yuan Zhang
    Divergence Functions of Nonnegative Matrix Factorization: A Comparison Study.
    Communications in Statistics - Simulation and Computation, 40: 1594-1612, 2012.
  10. Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
    Modelling biological systems from molecules to dynamical networks.
    BMC Systems Biology, 6(Suppl 1):S1, 2012.
  11. Chen Chen, Jun-Fei Zhao, Qiang Huang, Rui-Sheng Wang, and Xiang-Sun Zhang.
    Inferring domain-domain interactions from protein-protein interactions in the complex network conformation.
    BMC Systems Biology, 6(Suppl 1):S7, 2012.
    SCI; Funding: NSFC(60873205)
  12. Yong Wang, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, and Fan-Rong Liang.
    Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection.
    BMC Systems Biology, 6(Suppl 1):S15, 2012.
    SCI; Funding: NSFC(61171007, 11131009, 60970091), CAS(kjcx-yw-s7)
  13. Yongcui Wang, Xianwen Ren, Chunhua Zhang, Naiyang Deng, Xiang-Sun Zhang.
    Interrogating noise in protein sequences from the perspective of protein–protein interactions prediction
    Journal of Theoretical Biology 315(21): 64-70, 2012.
    SCI; Funding: NSFC(10801131, 10971223)


Proceedings Papers

  1. Duren Zhana, Yong Wang, Shigeru Saito, Katsuhisa Horimoto.
    Inferring Gene Regulatory Network for Cell Reprogramming.
    . Proceedings of The 31th Chinese Control Conference (CCC), pp. 7437-7442, Anhui, 2012.
  2. Zhi-Ping Liu, Wanwei Zhang, Katsuhisa Horimoto, Luonan Chen.
    A Gaussian Graphical Model for Identifying Significantly Responsive Regulatory Networks from Time Series Gene Expression Data.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 142-147.
  3. Xinjian Zhuo.
    Analysis of a HBV Infection Model With Non-cytolytic Cure Process.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 148-151.
  4. Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang.
    CNetA: Network alignment by combining biological and topological features.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 220-225.
  5. Changhe Fu, Ling Jing, Su Deng, Guangxu Jin.
    Identification of Oncogenic Genes for Colon Adenocarcinoma from Genomics Data.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 263-266.
  6. Junhua Zhang, Shihua Zhang, Yong Wang, Junfei Zhao, Xiang-Sun Zhang.
    Identifying Mutated Core Modules in Glioblastoma by Integrative Network Analysis.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 304-309.
  7. Xinxin Wang, Zhana Duren, Chao Zhang, Lin Chen, Yong Wang.
    Clinical Data Analysis Reveals Three Subytpes of Gastric Cancer.
    2012 IEEE International Conference on Systems Biology (ISB), pp. 315-320.
  8. Hui-Jia Li, Zhi-Ping Liu, Luonan Chen and Xiang-Sun Zhang
    Identification of overlapping communities in protein interaction networks using multi-scale local information expansion.
    2012 10th World Congress on Intelligent Control and Automation (WCICA), pp. 5071-5076
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