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Chen, Luonan
CAS Key Laboratory of System Biology
http://www.sysbio.ac.cn/cb/chenlab , or, http://www.sysbio.ac.cn/cb/chenlab/LuonanChen.htm

Research Focus
systems biology, computational biology, and nonlinear dynamics. 


Chen, Luonan received the M.E. and Ph.D. degrees in the electrical engineering, from Tohoku University, Sendai, Japan, in 1988 and 1991, respectively. From 1997, he was an associate professor of the Osaka Sangyo University, Osaka, Japan, and then a full Professor. Since 2010, he has been a professor and executive director at Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. He was the founding director of Institute of Systems Biology, Shanghai University, and currently is the founding president of Computational Systems Biology Society of ORS China. From 2009, he also holds the affiliate professorship in the University of Tokyo. He serves as Chair of Technical Committee of Systems Biology at IEEE SMC Society, and serves as editor or editorial board member for major systems biology related journals, e.g. BMC Systems Biology, IEEE/ACM Trans. on Computational Biology and Bioinformatics, Journal of Theoretical Biology, IET Systems Biology, Mathematical Biosciences, Journal of Royal Society Interface, Neural Processing Letters, Int. J. of Systems and Synthetic Biology, and J. of Systems Science and Complexity. His fields of interest are systems biology, computational biology, and nonlinear dynamics. In recent five years, he published over 100 journal papers and two monographs (books) in the area of systems biology.

Selected Publications

(Recent four years)

1. L. Chen, R-S.Wang, X-S.Zhang, Biomolecular Networks: Methods and Applications in Systems Biology, John Wiley & Sons, 2009.
2. L. Chen, R-Q.Wang, C. Li, K. Aihara, Modelling Biomolecular Networks in Cells: Structures and Dynamics, Springer-Verlag, London, 2010.

Journal Papers: 

1. Luonan Chen, Rui Liu, Zhiping Liu, Meiyi Li, Kazuyuki Aihara. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Scientific Reports, 2012.
2. 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 (PEDS), doi:10.1093/protein/gzr066, 2012.
3. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen: Network-based analysis of complex diseases. IET Systems Biology, doi: 10.1049/iet-syb.2010.0052, 2012.
4. Hui-Jia Li, Yong Wang, Ling-Yun Wu, Zhi-Ping Liu, Luo-Nan Chen and Xiang-Sun Zhang. Community structure detection based on Potts model and network’s spectral characterization. Europhysics Letters, 2012.
5. Tao Zeng and Luonan Chen. Tracing dynamic biological processes during phase transition. BMC Systems Biology, accepted, 2012.
6. Guanyin Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu2, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto. A computational procedure for identifying master regulator candidates for diabetes progression in Goto-Kakizaki rat. BMC Systems Biology, accepted, 2012.
7. Danning He, Zhi-Ping Liu, Luonan Chen. Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. BMC Genomics, 12:592, 2011.
8. Xiaoping Liu, Zhiping Liu, Xingming Zhao, Luonan Chen. Identifying disease genes and module biomarkers with differential interactions. Journal of the American Medical Informatics Association, doi:10.1136/amiajnl-2011-000658, 2011.
9. Xiujun Zhang, Xingming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhiping Liu, Luonan Chen. Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information. Bioinformatics, doi: 10.1093/bioinformatics/btr626, 2011.
10. Ruiqi Wang, Kaihui Liu, Luonan Chen and Kazuyuki Aihara. Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling. Bioinformatics, doi:10.1093/bioinformatics/btr551, 2011.
11. Achyut Sapkota, Xiaoping Liu, Xingming Zhao, Yongwei Cao, Jingding Liu, Zhiping Liu, Luonan Chen. DIPOS: Database of Interacting Proteins in Oryza Sativa. Molecular BioSystems, DOI: 10.1039/C1MB05120B, 2011.
12. 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, doi: 10.1093/nar/gkr251, 2011.
13. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Detecting and analyzing differentially activated pathways in brain regions of Alzheimer’s disease patients. Molecular BioSystems, DOI: 10.1039/C0MB00325E, 2011.
14. Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S1, 2011.
15. Graziano Chesi, Luonan Chen. Systems Biology. Int. J. Robust. Nonlinear Control, 21:1729, 2011.
16. D. Liu, X. Chang, Z.Liu, L.Chen, R.Wang. Bistability and oscillations in gene regulation mediated by small noncoding RNAs. PLoS ONE 6(3): e17029. doi:10.1371/journal.pone.0017029, 2011.
17. X. Chang, D.Liu, Z.Liu, L.Chen, R.Wang. Adaptation of simple molecular networks to time dependent stimulus. Asian Journal of Control, Volume 13, Issue 5, pages 701C712, September 2011.
18. Zhenping Li, Ruisheng Wang, Xiang-Sun Zhang, Luonan Chen. Drug target identification based on flux balance analysis in metabolic network. BMC Systems Biology, accepted, 2011.
19. Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen. Detecting thermophilic proteins through selecting amino acid and dipeptide composition features. Amino Acids, DOI 10.1007/s00726-011-0923-1, 2011.
20. Hongbo Lei, Jifeng Zhang, Luonan Chen. Property of Multiple Equilibria for SSI Metabolic Module. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S15, 2011.
21. Huarong Zhou, Zhiping Liu, Kazu Horimoto, Luonan Chen. Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S16, 2011.
22. Hong-Bo Lei, Xin Wang, Ruiqi Wang, Xin-Guang Zhu, Luonan Chen, Ji-Feng Zhang. A parameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism. Asian Journal of Control, Volume 13, Issue 5, pages 611C624, September 2011.
23. Luonan Chen, James Lam, Zidong Wang. ANALYSIS AND CONTROL OF BIOLOGICAL NETWORKS. Asian Journal of Control, DOI: 10.1002/asjc.424, 2011.
24. Graziano Chesi1, Luonan Chen and Kazuyuki Aihara. On the robust stability of time varying uncertain genetic regulatory networks. Int. J. Robust. Nonlinear Control, DOI:10.1002/rnc.1775, 2011.
25. Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, Volume 13, Issue 5, pages 738C748, September 2011
26. Hongbo Lei, Jifeng Zhang, Luonan Chen. Multi-equilibrium property of metabolic networks: Exclusion of multi-stability for SSN metabolic modules. International Journal of Robust and Nonlinear Control, DOI: 10.1002/rnc.1718, 2011.
27. D.Liu, X.Chang, Z.Liu, L.Chen, R.Wang. The effect of coupled feedback on noise filtering in signal transduction networks. J. Syst. Sci. Complex, vol.23, 942C950, 2010.
28. Xiaoping Liu, Wei-Hua Tang, Xingming Zhao, Luonan Chen. A Network Approach to Predict Pathogenic Genes for Fusarium graminearum. PLoS One, 5(10): e13021, 2010.
29. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.
30. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, Vol. 26, 1616C1622, 2010.
31. Zikai Wu, Xing-Ming Zhao, Luonan Chen. A systems biology approach to identify effective cocktail drugs. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S7, 2010.
32. Zhiping Liu, Weiming Xia, Xiang-Sun Zhang, Luonan Chen. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimers’ disease brains. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S11, 2010.
33. Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen. FGsub: Fusarium graminearum protein subcellular localization prediction from primary structures. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S12, 2010.
34. Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen. SANA: an algorithm for sequential and non-sequential protein structure alignment. Amino Acids, 39(2):417-25, 2010.
35. Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics, 11:26, 2010.
36. Yi Ding, Peng Wang, L. Goel1, Luonan Chen, Poh Chiang Loh. A Penalty Scheme for Reducing Electricity Price Volatility. IEEE Transactions on Power Systems, 25(1): 223-233, 2010.
37. Zhao Song, Luonan Chen, Dong Xu, Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome bioinformatics: Informatics for mass-spectrometry based protein science, Methods in Molecular Biology, 604:7-22, 2010.
38. Xingming Zhao, Kazuyuki Aihara, Luonan Chen. A discriminative approach to identifying domain-domain interactions from protein-protein interactions. PROTEINS: Structure, Function, and Bioinformatics, 78(5), 1243-1253, 2009.
39. Xingming Zhao, Xiao-Wei Zhang, Weihua Tang, Luonan Chen. FPPI: Fusarium graminearum protein-protein interaction database. Journal of Proteome Research, DOI: 10.1021/pr900415b, 2009.
40. Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, Xiang-Sun Zhang. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology, PLoS Comput Biol 5(9): e1000521. doi:10.1371journal.pcbi.1000521, 2009.
41. Zhao Song, Luonan Chen, Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.
42. Y. Li, Z. Liu, J. Zhang, R. Wang, L. Chen. Synchronisation mechanisms of circadian rhythms in the suprachiasmatic nucleus. IET Systems Biology, 3(2), 100-112, 2009.
43. X. S. Zhang, R. S. Wang, Y. Wang, J. Wang, Y. Qiu, L. Wang and L. Chen. Modularity optimization in community detection of complex networks. Europhysics Letters, 87:38002, 2009.
44. R.Wang, G.Jin, X-S. Zhang, L.Chen. Modelling post-transcriptional regulation of microRNAs in E.coli. BMC Bioinformatics, 10(Suppl 4):S6, 2009.
45. Y.Wang, X-S.Zhang, L.Chen. A network biology study on circadian rhythm by integrating various omics data. OMICS, 13(4):313-24, 2009.
46. Y.Wang, J.Shen, B.Niu, Z.Liu, L.Chen. Robustness of interval gene networks with multiple time-varying delays and noise. Neurocomputing, doi:10.1016/j.neucom.2009.02.012, 2009.
47. Y.Wang, Z.Ma, J.Shen, Z.Liu, L.Chen. Periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbations. Mathematical Biosciences, doi:10.1016/j.mbs.2009.03.010, 2009.
48. Y.Qiu, S.Zhang, X-S.Zhang, L.Chen. Identifying differentially expressed pathways via a mixed integer linear programming model. IET Systems Biology, 3, 475-486, 2009.
49. Jianwei Shen, Zengrong Liu, Weixing Zheng, Fengdan Xu, Luonan Chen. Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs. Physica A: Statistical Mechanics and its Applications. 388(14), 2995-3000, 2009.
50. Guangxu Jin, Xiaobo Zhou, Kemin Cui, Xiang-Sun Zhang, Luonan Chen, and Steve T.C. Wong. Cross-platform method for identifying candidate network biomarkers for prostate cancer. IET Systems Biology, 3(6), 505-512, 2009.
51. B.Wang, L.Chen, K.Aihara. Limited ability driven phase transitions in the coevolution process in Axelrod’s model. Physics Letters A, 373(17), 1519-1523, 2009.
52. L-Y.Wu, Z.Li, R.Wang, X-S.Zhang, L.Chen. Self-organizing map approaches for the haplotype assembly problem Mathematics and Computers in Simulation. Mathematics and Computers in Simulation,79(10), 3026-3037, 2009.
53. Z.Li, R.Wang, X-S.Zhang, L.Chen. Detecting drug targets in metabolic networks by integer linear programming. IET Systems Biology, Vol. 3, No.6, pp. 523-533, 2009.
54. H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:026107, 2009.
55. Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara. Automatic modeling of signaling pathways by network flow model. Journal of Bioinformatics and Computational Biology, 7(2):309-22, 2009.
56. Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.
57. S.Fan, L.Chen, W. J. Lee. Short-term Load Forecasting Using Comprehensive Combination based on Multi- Meteorological Information. IEEE Trans. on Industry Application. Vol. 45, No. 4, pp. 1460-1466, 2009.
58. S.Fan, Y.Yokoyama, L.Chen. Forecasting the Wind Generation Using A Two-stage Network Based on Meteorological Information. IEEE Transactions on Energy Conversion. Vol. 24, No. 2, pp. 474-482, 2009.
59. G. Jin, X.Zhou, H.Wang, H.Zhao, K.Cui, X. Zhang, L. Chen, S. Hazen, K. Li, S. Wong. The knowledge-integrated network biomarkers discovery for Major Adverse Cardiac Events. Journal of Proteome Research, 7 (9), 4013-4021, 10.1021/pr8002886, 2008.
60. S.Zhang, X-S.Zhang, L.Chen. Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology, 2:5, doi:10.1186/1752-0509-2-5, 2008.
61. X. Zhao, R.Wang, L. Chen, K.Aihara. Uncovering signal transduction networks from highthroughput data by integer linear programming. Nucleic Acids Research, Vol.36, No.9, e48, doi:10.1093/nar/gkn145, 2008.
62. Z.Liu, L.Wu, Y.Wang, X-S. Zhang, L.Chen. Bridging protein local structures and protein functions. Amino Acids, DOI 10.1007/s00726-008-0088-8, 2008.
63. X.Zhao, K.Aihara, L.Chen. Protein function prediction with high-throughput data. Amino Acids, Vol.35, pp.517-530, DOI 10.1007/s00726-008-0077-y, 2008.
64. Y.Xie, L.Chen, Y.Kang, K. Aihara. Controlling the onset of Hopf bifurcation in the Hodgkin-Huxley model. Physical Review E. 77, 061921, 2008.
65. B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 28006, 2008.
66. C. Li, L. Chen, K.Aihara. Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks. Chaos. Vol.18, 023132, 2008.
67. T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 037126, 2008.
68. Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community detection. Physical Review E, 77, 036109, 2008.
69. X.Zhao, Y.Wang, L.Chen, K.Aihara. Gene function prediction using labeled and unlabeled data. BMC Bioinformatics, 9:57, doi:10.1186/1471-2105-9-57, 2008.
70. X.Zhao, Y.Wang, L.Chen, K.Aihara. Protein domain annotation with integration of heterogeneous information sources. Proteins: Structure, Function, and Bioinformatics, Vol.72, no.1, 461 - 473, 2008.
71. G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network. Neurocomputing, 71, 2794-2805, 2008.
72. Y.Wang, L-Y.Wu, J.Zhang, Z.Zhan, X-S.Zhang, L.Chen. Evaluating Protein Similarity From Coarse Structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi:10.1109/TCBB.2007.70250, 2008.
73. R.Wang, C.Li, L.Chen, K.Aihara. Modeling and Analyzing Biological Oscillations in Molecular Networks. Proceedings of The IEEE, Vol.96, 1361-1385, 2008.
74. R.-S. Wang, S. Zhang, Y. Wang, X.-S. Zhang, L. Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. Neurocomputing, 72, 134-141, 2008.
75. X.-M. Zhao, Y. Wang, L. Chen, and K. Aihara. Protein domain annotation with predicted domain-domain interaction networks. Protein & Peptide Letters, 15, 456-462, 2008.
76. X.-M. Zhao, L. Chen, and K. Aihara. Protein function prediction with the shortest path in functional linkage graph and boosting. International Journal of Bioinformatics Research and Applications, 4, 375 - 384, 2008.
77. Z.-P. Liu, L.-Y. Wu, Y. Wang, X.-S. Zhang, L. Chen. Protein cavity clustering based on community structure of pocket similarity network. International Journal of Bioinformatics Research and Applications, 4, 445-460, 2008.
78. Z.Liu, L-Y.Wu, X-S.Zhang, L.Chen. Analysis of protein surface patterns by pocket similarity network in a systems biology framework. Protein & Peptide Letter, 15, 448-455, 2008.
79. S. Fan, L. Chen, W. J. Lee. Machine Learning Based Switching Model for Electricity Load Forecasting. Energy Conversion and Management, Vol. 49, No. 6, pp. 1331-1344, 2008
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