Shihua Zhang

Assistant Professor of Academy of Mathematics and Systems Science, CAS
Address: No.55, Zhongguancun East road, Beijing 100190, China
Tel: 86-10-62616670
Email: zsh@amss.ac.cn

Shihua Zhang was born on May, 1980 in Shandong Province, China. Now he is Assistant Professor of the Institute of Applied Mathematics, Academy of Mathematics and Systems Science, at CAS. His interests are within Bioinformatics and Systems Biology, particularly in Biological network-related issues. He has published over 30 technical papers in the refereed journals and conference proceedings such as in Proteomics, Bioinformatics, PLoS Comput. Bio., Plos ONE, Computational Biology and Chemistry, BMC Structural Biology, Physical Review E, European Physical Journal B, Physica A.

Positions

6/2008 - present, Assistant Professor.

Academy of Mathematics and Systems Science, Chinese Academy of Science (Beijing, China).

7/2008 - 12/2010, Postdoctoral Fellow.

Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California (Los Angeles, USA).

Educational Background

9/1999 - 7/2003, Bachelor of Science in Applied Mathematics,

School of Mathematics and Statistics, Yunnan University (Kunming, Yunnan, China)

9/2003 - 6/2008, PhD of Operational Research and Control (PhD-direct student),

Academy of Mathematics and Systems Science, Chinese Academy of Science (Beijing, China)

Research Interests

Bioinformatics/Systems Biology

Modeling and algorithms for molecular networks
Integrative analysis of molecular networks with other biological data
Algorithms for protein structures comparison and assemblies determination
Modeling and algorithms for integration of multiple 'omic' data
Computational methods for epigenomics

Complex networks/Network science

Community structure in complex networks
Structure and dynamics of networks

Selected Publications

Co-community Structure in Time-varying Networks.

Shihua Zhang, Junfei Zhao, Xiang-Sun Zhang.
Preprint: arXiv:1111.1365v2. In submission, 2012.

A joint matrix factorization framework for the integrative analysis of multi-dimensional genomic data.

Shihua Zhang, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter Laird, Xianghong Jasmine Zhou.
In submission, 2011.

A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.

Shihua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou
Bioinformatics (ISMB2011), 2011, 27:i401-i409. PDF

Discovering multi-dimensional regulatory modules by a sparse multi-block partial least square regression method.

Wenyuan Li*, Shihua Zhang*, Chun-Chi Liu, Xianghong Jasmine Zhou (*Co-first authors).
In submission, 2011.

Exploring the spatial and temporal organization of a cell’s proteome

Martin Beck, Maya Topf, Zachary Frazier, Harianto Tjong, Min Xu, Shihua Zhang and Frank Alber.
Journal of Structural Biology, 2011, 173(3):483-496. PDF

A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps.

Shihua Zhang, Daven Vasishtan, Min Xu, Maya Topf, Frank Alber.
Bioinformatics (ISMB2010), 2010, 26(12):i261-i268. Faculty of 1000 Biology

Determining modular organization of protein interaction networks by maximizing modularity density.

Shihua Zhang, Xue-Mei Ning, Chris Ding, Xiang-Sun Zhang.
BMC Systems Biology, 2010, 4:S10.

Detecting disease associated modules and prioritizing active genes based on high throughput data.

Yu-Qing Qiu*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen (*Co-first authors).
BMC Bioinformatics, 11:26, 2010. doi:10.1186/1471-2105-11-26. Highly accessed

Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

Ji-Guang Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
PLoS Computational Biology, 5(9): e1000521. doi:10.1371/journal.pcbi.1000521.

Identifying differentially expressed pathways based on a mixed integer linear programming model.

Qiu Yuqing, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen.
IET Systems Biology, 3(6), 475-486, 2009.

Quantitative function for community detection.

Zhenping Li*, Shihua Zhang*, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
Physical Review E, 77, 036109, 2008.
It has been selected by Virtual Journal of Biological Physics Research, 15(6), 2008.

Biomolecular network querying: a promising approach in systems biology.

Shihua Zhang, Xiang-Sun Zhang and Luonan Chen.
BMC Systems Biology, 2008, 2:5. doi:10.1186/1752-0509-2-5. (Complementary). Highly accessed

Discovering functions and revealing mechanisms at molecular level from biological networks.

Shihua Zhang, Guanxu Jin, Xiang-Sun Zhang and Luonan Chen.
Proteomics, 7(16), 2856-69, 2007.

Alignment of molecular networks by integer quadratic programming.

Zhenping Li*, Shihua Zhang*, Yong Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
Bioinformatics, 23(13):1631-1639, 2007; doi:10.1093/bioinformatics/btm156.

A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.

Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang.
International Journal of Data Mining and Bioinformatics, 3(1), 68-84, 2009.

Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.

Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
PLoS ONE 2(11): e1207, 2007. doi:10.1371/journal.pone.0001207.

Uncovering fuzzy community structure in complex networks

Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang
Physical Review E, 76, 046103, 2007.
It has been selected by Virtual Journal of Biological Physics Research, 14(8), 2007.

Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.

Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang.

European Physical Journal B, 57, 67-74, 2007.

Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures

Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen
Neurocomputing, 72, 134-141, 2008.

Identification of overlapping community structure in complex networks using fuzzy c-means clustering

Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang
Physica A: Statistical Mechanics and its Applictions, 2007, 374, 483–490

Detecting community structure in complex networks based on a measure of information discrepancy.

Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang
Physica A: Statistical Mechanics and its Applictions, 2008, 387(7), 1675-1682. doi:10.1016/j.physa.2007.10.061.

Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks

Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
Lecture Notes in Artificial Intelligence, 4682, 1090-1101, 2007.

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang.
BMC Structural Biology, 2006, 6:18. Highly accessed

Identification of functional modules in a PPI network by clique percolation clustering.

Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang.
Computational biology and chemistry, 30(6), 445-451, 2006.

Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods.

Shihua Zhang, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang.
Lecture Notes in Bioinformatics, 4115, 514-524, 2006.

Honors and Awards

National Excellent PhD thesis Award, 2010.
Excellent PhD thesis Award of Chinese Academy of Science, 2009.
Top Grade Presidential Award of Chinese Academy of Science, 2008.
BHPB Scholarship of Graduate University of Chinese Academy of Science, 2007.
Baojie Excellent PhD student Scholarship of Chinese Academy of Science, 2007.
Baogang Scholarship, 2003.

Research Projects

Research on Some Important Problems in Bioinformatics (2005-2008)

Important Direction Research Grant, Chinese Academy of Sciences (CAS), Joint Investigator.

Research on Models and Algorithms of Haplotype Inference Problem in Bioinformatics (2006-2008).

National Natural Science Foundation of China (NSFC), Grant No. 60503004, Joint Inverstigator

Research on theory and algorithms of community detection in complex networks (2008-2010)

National Natural Science Foundation of China (NSFC), Grant No. 10701080, Joint Investigator

"The whole of science is nothing more than a refinement of everyday thinking." —— Albert Einstein (1879-1955)

"In science, the important thing is to modify and change one’s ideas as science advances." —— Herbert Spencer (1820–1903)

"The good life is one inspired by love and guided by knowledge." —— Betrand Russell

"The difficulty lies, not in the new ideas, but in escaping the old ones, which ramify, for those brought up as most of us have been, into every corner of our minds.." ——John Maynard Keynes (1883 - 1946)

"Life is like riding a bicycle. To keep your balance, you must keep moving." —— Albert Einstein (1879-1955)

"It's not your aptitude but your attitude that determines your altitude in life." —— Jesse Jackson

"People can be divided into three classes, the few who make things happen, the many who watch things happen, and the overwhelming majority who have no idea what has happened."

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