Zhao Jing's homepage

ZHAO JING

PhD, Professor

Department of mathematics, Logistical Engineering University, Chongqing, China

Email: zhaojanne@gmail.com

Research Interests

The application of mathematics and information sciences to understand complex networks in biological, social, and technological systems

Funding

National Natural Science Foundation of China (10971227), 2010-2012.

Publications

Papers

1）Zhao J, Chen J, Yang TH, Holme P, Pathogenesis of Axial Spondyloarthropathy in a Network Perspective. 2011 IEEE Conference on Systems Biology, 2011, P41-46

2）Zhao J, Yang TH, Huang YX, Holme P, Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PLoS One 2011, 6(9):e24306. [PDF]

3）Zeng H, Dou S, Zhao J, Fan S, Yuan X, Zhu S, Li L, Zhang W, Liu R, The inhibitory activities of the components of Huang-Lian-Jie-Du-Tang (HLJDT) on eicosanoid generation via lipoxygenase pathway. Journal of Ethnopharmacology 2011 135:561-568. [PDF]

4）Yuan X, Yan SK, Zhao J, Shi D, Yuan B, Dai W, Jiao B, Zhang W, Miao M, Lipid metabolism pathway and peroxisome proliferator-activated receptor signaling pathway participated in late-phase liver regeneration. Journal of Proteomics Research 2011, 10(3): 1179-1190 [PDF]

5）Zhao J, Zhang WD, Systems biological based study of multi-target and multi-component drugs. Chin Pharm J 2010, 45(15): 1121-1126 (in Chinese) [PDF]

6）Zhao J, Holme P, Three faces of metabolites: pathways, localizations and network positions. Lecture Notes in Operations Research 2010, 13:13-21.[PDF]

7）Yu W-G, Zhou K-Q, Wu Z-Z, YangT-H, Zhao J: Simulation of Novel NEMS Contact Switch Using MRTD with Alterable Steps. Journal of Nanotechnology 2010: 492074 [PDF]

8）Zhao J, Geng C, Tao L, Zhang D-F, Jiang Y, Tang K-L, Zhu R-X, Yu H, Zhang W-D, He F-C et al: Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data. Journal of Proteomics Research 2010, 9(4):1648-58 [PDF]

9）Zhao J, Jiang P, Zhang WD: Molecular networks for the study of TCM pharmacology. Briefings in Bioinformatics 2010, 11(4): 417-430 [PDF]

10） Yan SK，Zhao J, Dou SS，Jiang P，Liu RH, Zhang WD, Systems Biology and Bioinformatics Based Methodology: Modernization Research on the Composite Formula of Traditional Chinese Medicine. Chin J Nat Med 2009, 7(4) (in Chinese)

11） Ding G, Yu Z, Zhao J, Wang Z, Li Y, Xing X, Wang C, Liu L, Li Y: Tree of Life Based on Genome Context Networks. PLoS ONE 2008, 3(10):e3357 [PDF]

12） Zhao J, Ding G-H, Tao L, Yu H, Yu Z-H, Luo J-H, Cao Z-W, Li Y-X: Modular co-evolution of metabolic networks. BMC Bioinformatics 2007, 8:31 [PDF]

13） Zhao J, Tao L, Yu H, Luo J-H, Cao Z-W, Li Y-X: The effects of degree correlations on network topologies and robustness. Chinese Physics 2007, 16:3571-3580 [PDF]

14） Holme P, Zhao J, Exploring the assortativity-clustering space of a network's degree sequence, Phys. Rev. E 75, 046111 (2007) [PDF]

15） Zhao J, Tao L., Yu H, Luo JH, Cao Z.W., Li YX，Bow-tie topological features of metabolic networks and functional significance, Chinese Science Bulletin 2007, 52:1036-1045[PDF]

16） Wei W, Wang WH, Cao ZW, Yu H, Wang XJ, Zhao J, Tan H, Xu H, Jiang WH, Li YX, Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes, Acta Biochim Biophys Sinica 2007, 39: 317-325 [PDF]

17） Zhao J, Yu H, Luo JH, Cao Z.W., Li YX, Hierarchical modularity of nested bow-ties in metabolic networks，BMC bioinformatics,2006:7:386. [PDF]

18） Zhao J, Yu H, Luo JH, Cao Z.W., Li YX, Complex networks theory for analyzing metabolic networks, Chinese Science Bulletin, 2006 Vol.51, No. 13, 1529-1537. [PDF]

19） Zhang X，Zhao J ，Wang QK，Cao ZW, Study of an efficient alternative splicing searching algorithm, High Technology Letters, 2006, 16: 1051-1055(in Chinese). [PDF]

20） Zhao J, Zhu YM, Song PM, Fang Q, Luo JH，Recognition of gene acceptor site based on multi-objective optimization，Acta Biochimica et Biophysica Sinica 37 (7): 435-439,2005. [PDF]

21） Zhao J, Song PM, Fang Q, Luo JH， Protein secondary structure prediction using dynamic programming， Acta Biochimica et Biophysica Sinica 37 (3): 167-172, 2005. [PDF]

22） Zhao J, Chen W, Luo JH， Feedforward wavelet neural network and multi-variable functional approximation， Lecture Notes in Computer Science 3314: 32-37 2004. [PDF]

23） Zhao J, Song PM, Xie LS, Luo JH，The structural classes of proteins predicted by multi-resolution analysis， Lecture Notes in Computer Sscience 3314: 645-651 2004. [PDF]

24） Zhao J, Chen W, Luo JH, Predicting Protein Structural Features with Wavelet Packet, Proceedings of 3^rd International Conference on Wavelet Analysis and Its Applications, World Scientific Publishing, 2003.

25） Zhao J, Yang X, Li J, Tang Y, DNA Sequences Classification Based on Wavelet Packet Analysis. Proceedings of the 2^nd International Conference on Wavelet Analysis and Its Applications, Lecture Notes in Computer Science 2251，Springer-Verlag Heidelberg,2001. [PDF]

26） Yang X, Zhao J, Li J, Liu J, Zeng S, The Application of the Wavelet Transformation to the Prediction of Gas Zones, Proceedings of the 2^nd International Conference on Wavelet Analysis and Its Applications, Lecture Notes in Computer Science 2251,Springer-Verlag Heidelberg, 2001. [PDF]

Submitted manuscripts

1. Lu BN, Zhao J, Wang XN, Hu MM, Peng JY, Liu KX, I nvestigation of the cytotoxic effect of berberine on human cervix adenocarcinoma HeLa cells by proteomics experiments, network analysis and in-silico target prediction.

PhD Thesis

Research on structure, function and evolution of cellular metabolic networks

Chinese version

English version

Textbooks and proceedings

1) Zhao J.,Dan Q., Mathematical Modeling and Mathematical Experiments,3^rd Edition. Higher Education Press, Beijing,China, 2008.

2) Zhao J.,Dan Q., Mathematical Modeling and Mathematical Experiments,2^nd Edition. Higher Education Press, Beijing,China, 2003.

3) Zhao J.,Dan Q., Mathematical Modeling and Mathematical Experiments,1^st Edition. Higher Education Press, Beijing,China, and Springer-Verlag Heidelberg, 2000.

4) Zhao J.,Lin Q., Dan Q., Engineering Mathematical Experiments, Higher Education Press, Beijing,China, 2002.

5) Li J., Wickerhauser V., Tang Y., Daugman J., Peng L., Zhao J., Proceedings of the third international conference on wavelet analysis and its applications, Vol.1 and Vol.2, World Scientific, Singapore, 2003.

6) Li J., Liu J., Zhong N., Yen J., Zhao J., Proceedings of the second international conference on active media technology, World Scientific, Singapore, 2003.

Presentations

1) Ranking candidate disease genes from gene expression and protein interaction, The Fifth International Conference on Computational Systems Biology (ISB 2011), September 2-4, 2011, Zhuhai, China.

2) Biological Network Based Pharmacology for Traditional Chinese Medicine, IceLab, Umea University, Sweden, Aug 25, 2011.

3) Complex Networks and Interdisciplinary Studies, Basic Department, Logistical Engineering University, July 22, 2011.

4) Network-based Pharmacology for Traditional Chinese Medicine. Interdisciplinary Applications of Statistical Physics & Complex Networks, Kavli Institute for Theoretical Physics China (KITPC), Chinese Academy of Sciences, Beijing, March 1-April 1, 2011.

5) Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data. The 6th Chinese Conference of Complex Networks，October 15-18, 2010. Suzhou, China.

6) Three faces of metabolites: pathways, localizations and network positions. The Fourth International Conference on Computational Systems Biology (ISB 2010) , September 9-11, 2010 Suzhou, China.

7) Network-based TCM pharmacology. Sino-German Workshop on Computational systems biology approaches for cancer research and biomarker discovery, January 12-15, 2010, Zhejiang University, Hangzhou, China.

8) Topology and function of metabolic networks. Spring school on multiscale methods and modeling in biophysics and system biology, May 18-29, 2009, Tongji University, Shanghai, China. [Part I] [Part II]

9) Modular Co-evolution of metabolic networks (In Chinese) . PhD students’ Forum on Bioinformation, May 12-16,2008, Fudan University, Shanghai, China.

10) Topology, functionality and evolution of metabolic networks. ComBio 2007 meeting, September 24 - October 04, 2007, Shanghai, China.

11) Hierarchical modularity of nested bow-ties in metabolic networks. PICB workshop on the Organization and Control of Metabolism, August 4- August 6, 2007, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

12) Modular Co-evolution of metabolic networks. May 27, 2007. Shanghai Center for Bioinformation and Technology.

13) An introduction of complex networks. Nov. 26, 2006, Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.