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Shihua Zhang

Shihua Zhang is a second year Ph.D. student in Operations Research of the Institute
of Applied Mathematics, AMSS, at CAS. He also received the B.S. degree in Applied
Mathematics from the University of Yunnan, Kunming, China.

His general areas of research have been Operational research, Machine learning, and
Mathematical Programming with applications in Bioinformatics and Systems Biology,
Complex network. He has published over 15 technical papers in the refereed journals
and conference proceedings, such as Proteomics, Bioinformatics, Computational Biology
and Chemistry, BMC Structural Biology, Euro. Phys. J. B, Physica A. as well as

Institute of Applied Mathematics Academy of Mathematics and Systems Science, Chinese Academy of Science
Graduate University of Chinese Academy of Science, China

Educational Background

Research Areas and Interests


-Papers in Refereed International Journals and Conference Proceedings

  1. Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. Uncovering fuzzy community structure in complex networks. Submitted to Physical Review E.
  • Shihua Zhang, Guanxu Jin, Xiang-Sun Zhang and Luonan Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics, In press.
  • Zhenping Li*, Shihua Zhang*, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, In press. (*Co-first authors).
  • Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis. Eur. Phys. J. B 2007. In press.
  • Shihua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. Physica A: Statistical Mechanics and its Applications, 374(1), 483-490, 2007.
  • Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. Identification of functional modules in a PPI network by clique percolation clustering. Computational biology and chemistry, 30(6), 445-451, 2006.
  • Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang. A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks. ICDMW, 130-135, Sixth IEEE International Conference on Data Mining-Workshops (ICDMW'06), 2006. (Acceptance Ratio: 28.0%)
  • Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison. BMC Structural Biology, 2006, 6:18.
  • Shihua Zhang, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. ICIC06, LNCS, Lecture Notes in Bioinformatics, 4115, 514-524, 2006.
  • Zhenping Li, Yong Wang, Shihua Zhang, Xiang-sun Zhang and Luonan Chen. Alignment of Protein Interaction Networks by Integer Quadratic Programming. IEEE EMBC06, SaD03.4, 5527-5530, 2006.
  • Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. Comparison of Protein Structures by Multi-Objective Optimization. Genome Informatics, 16(2), 114-124, 2005.
  • Shihua Zhang, De-Gang Liu and Xiang-Sun Zhang. A framework for structural similarity search in proteins. ISORA05, Lecture Notes in Operations Research, 5, 285-295, 2005.

- Papers in Refereed Chinese Journals and Conference Proceedings
  1. Shihua Zhang and Xiang-Sun Zhang. Visualization of conformational space based on CA-CA distance. Chinese journal of Bioinformatics, 4, 153-156, 2006.

Index and Journals

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