Professor Luonan Chen

• Professor, Excutive director, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
• Present address (office): 500 Cao Bao Road, Shanghai 200233, China
• Phone (office): +86-21-6436-5937; Fax: +86-21-5497-2551.
• E-mail: lnchen@sibs.ac.cn
• Laboratory Homapage: http://www.sysbio.ac.cn/ , or
  http://www.sysbio.ac.cn/cb/chenlab/LuonanChen.htm , or http://www.sysbio.ac.cn/cb/chenlab , or http://www.sysbio.ac.cn/cb

Education

• September 1980- July 1984 : Department of Electrical Engineering, Huazhong University of Science and Technology (Wuhan, China). Received the BSEE degree.
• April 1986- March 1988 : Department of Electrical and Communication Engineering, Tohoku University (Sendai, Japan). Received the ME degree.
• April 1988- March 1991 : Department of Electrical and Communication Engineering, Tohoku University (Sendai, Japan). Received the Ph.D degree in February 1991.
  

Academic Activities (Editors of Journals)

• Section Editor, BMC Systems Biology,
• Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics,
• Associate Editor, Neural Processing Letters,
• Editorial Board Member, IET Systems Biology,
• Editorial Board Member, Mathematical Biosciences,
• Editorial Board Member, Journal of Theoretical Biology,
• Editorial Board Member, Journal of Royal Society Interface,
• Editorial Board Member, PLoS ONE,
• Editorial Board Member, International Journal of Systems and Synthetic Biology,
• Editorial Board Member, International Journal of Data Mining and Bioinformatics,
• Editorial Board Member, Frontier in Systems Physiology,
• Associate Editor, BMC Research Notes,
• Editorial Board Member, International Journal of Bioinformatics Research and Applications,
• Editorial Board Member, Journal of Systems Science and Complexity
  

Academic Activities (Societies)

• Chair, Technical Committee on Systems Biology, IEEE SMC Society (Systems, Man and Cybernetics Society),
• Committee Member, Life Science Systems of IEEE CAS (Circuits and Systems),
• President, Computational Systems Biology Society of ORS China.

Editors for Special Issues in Journals

• Editor, Journal of Molecular Cell Biology, Special Issue on Systems Biology for Complex Diseases, 2012.
• Co-editor, IEEE/ACM Trans. on Computational Biology and Bioinformatics, Special Issue on Bioinformatics and Biomedicine, 2011.
• Co-editor, Asian Journal of Control, Special Issue on Analysis and Control of Biological Networks, 2011.
• Co-editor, International Journal of Robust and Nonlinear Control, Special Issue on Systems Biology, 2011.
• Co-editor, Journal of Computational Biology and Bioinformatics, Special Issue on Genome Informatics, 2011.
• Co-editor, BMC Systems Biology, Special Issue on Computational Systems Biology, 2010.
• Editor, LET Systems Biology, Special Issue on Optimization and Systems Biology, Volume 3, Issue 6, 2009.
  

Academic Activities (Organizing international conferences)

• General Co-Chair, International Symposium of Optimization and Systems Biology (OSB 2007,2008,2009),
• General Co-Chair, International Conference on Intelligent Computing(ICIC2008),
• Co-Chair of International Committee, International Conference on Life System Modeling and Simulation (LSMS2008),
• General Co-Chair, International Conference on Bio-Science and Bio-Technology (BSBT 2008),
• Chair of Workshop, International Symposium on Bioinformatics Research and Applications (ISBRA 2009),
• Co-organizer and International coordinators, KITPC programs: Emergent behaviour of biomolecular ensembles and networks, 2010.
• General Co-Chair, Genome Informatics Workshop (GIW2010),
• General Co-Chair, International Conference on Computational Systems Biology (ISB2010),
• Co-Chair, Program Committee of the 2010 IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2010),
• General Co-Chair, 2011 IEEE International Conference on Systems Biology (ISB2011).

Research and professional experience

• 1991-1997 : Senior Engineer and Project manager at JPBS, Tokyo, Japan.
• 1997-2000 : Associate professor at the Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan.
• 2000-2002 : Visiting Professor at the Department of Computer Science, University of California, Los Angeles (UCLA), USA.
• 2002- 2010 : Professor at the Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan.
• 2006-2009: Professor, Director, Institute of Systems Biology, Shanghai University, China.
• 2009-present: Research Professor, Institute of Industrial Science, The University of Tokyo, Japan.
• 2009-present: Professor, Executive Director, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China

SELECTED PUBLICATIONS

Books

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

Book Chapters

• Zhao Song, Luonan Chen, Dong Xu, Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome bioinformatics: Informatics for mass-spectrometry based protein science, the Human Press, 604:7-22, 2010.
• Yong Wang, Ruisheng Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring Gene Regulatory Networks from Genetical Genomics data. In Handbook of Research on Computational Methodologies in Gene Regulatory Networks, IGI Global, October, 2009.
• Xingming Zhao, Luonan Chen. Protein Function Prediction with Data Mining Techniques. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, John Wiley & Sons, June, 2010.
• Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Computational Models for Condition Specific Gene and Pathway Inference. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, John Wiley & Sons, 2010.

Edited Books

• Optimization and Systems Biology, Lecture Notes in Operations Research 7. Edited by X-S.Zhang, L.Chen, L-Y.Wu, Y.Wang. World Publishing Corporation, Beijing, 2007.
• Optimization and Systems Biology, Lecture Notes in Operations Research 8. Edited by X-S.Zhang, L.Chen, L-Y.Wu, Y.Wang. World Publishing Corporation, Beijing, 2008.
• Optimization and Systems Biology, Lecture Notes in Operations Research 9. Edited by L.Chen, L-Y.Wu, Y.Wang, X-S.Zhang. World Publishing Corporation, Beijing, 2009.
• Computational Systems Biology, Lecture Notes in Operations Research 13. Edited by L.Chen, X-S.Zhang, Bairong Shen, L-Y.Wu, Y.Wang. World Publishing Corporation, Beijing, 2010.
• Life System Modeling and Simulation, Supplementary volume to DCDIS series B: Applications and Algorithms. Edited by M.Fei, S.Ma, X.Li, L.Chen, Y.Ding. Watam Press, Waterloo, 2007.
• Combinatorial Optimization by Modern Heuristic Techniques, 1997, Nikan Publish, L.Chen (coauthor).
• Operation and Planning in Deregulated Power Systems, 2002, Tokyo DenKiDai Publish, L.Chen (coauthor).
• An Introduction to Environmental Systems, 2007, Denkishoin, L.Chen (coauthor).

Journal Papers

• [1] 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.
• [2] 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.
• [3] 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.
• [4] Tao Zeng and Luonan Chen. Tracing dynamic biological processes during phase transition. BMC Systems Biology, accepted, 2012.
• [5] 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.
• [6] 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.
• [7] 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.
• [8] 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.
• [9] 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.
• [10] 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.
• [11] 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.
• [12] 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.
• [13] 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.
• [14] Graziano Chesi, Luonan Chen. Systems Biology. Int. J. Robust. Nonlinear Control, 21:1729, 2011.
• [15] 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.
• [16] 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
• [17] 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.
• [18] 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.
• [19] 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.
• [20] 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.
• [21] 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.
• [22] Luonan Chen, James Lam, Zidong Wang. ANALYSIS AND CONTROL OF BIOLOGICAL NETWORKS. Asian Journal of Control, DOI: 10.1002/asjc.424, 2011.
• [23] 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.
• [24] Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, Volume 13, Issue 5, pages 738C748, September 2011
• [25] 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.
• [26] 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.
• [27] 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.
• [28] Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.
• [29] 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.
• [30] 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.
• [31] 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.
• [32] 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.
• [33] 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.
• [34] 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.
• [35] 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.
• [36] 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.
• [37] 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.
• [38] 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.
• [39] 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.
• [40] Zhao Song, Luonan Chen, Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.
• [41] 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.
• [42] 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.
• [43] 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.
• [44] 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.
• [45] 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.
• [46] 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.
• [47] 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.
• [48] 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.
• [49] 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.
• [50] 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.
• [51] 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.
• [52] 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.
• [53] H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:026107, 2009.
• [54] 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.
• [55] Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.
• [56] 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.
• [57] 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.
• [58] 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.
• [59] 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.
• [60] 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.
• [61] 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.
• [62] 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.
• [63] 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.
• [64] B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 28006, 2008.
• [65] 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.
• [66] T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 037126, 2008.
• [67] Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community detection. Physical Review E, 77, 036109, 2008.
• [68] 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.
• [69] 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.
• [70] G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network. Neurocomputing, 71, 2794-2805, 2008.
• [71] 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.
• [72] 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.
• [73] 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.
• [74] 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.
• [75] 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.
• [76] 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.
• [77] 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.
• [78] 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
• [79] Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen and Xiang-Sun Zhang. Predicting Gene Ontology Functions from Protein’s Regional Surface Structures. BMC Bioinformatics, 8:475, doi:10.1186/1471-2105-8-475, 2007.
• [80] Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS ONE, 2(11): e1207, doi: 10.1371/journal.pone.0001207, 2007.
• [81] Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen. Inferring transcriptional interactions and regulator activities from experimental data. Molecules and Cells, vol.24, 307-315, 2007.
• [82] R.Wang, Y.Wang, L-Y.Wu, X-S.Zhang, L.Chen. Analysis on Multi-domain Cooperation for Predicting Protein-Protein Interactions. BMC Bioinformatics, 8:391, doi:10.1186/1471-2105-8-391, 2007.
• [83] R. Wang, Y.Wang, X-S. Zhang, L.Chen. Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics, 23(22):3056-3064, 2007.
• [84] X.Zhao, L.Chen, K.Aihara. Protein classification with imbalanced data. Proteins: Structure, Function, and Bioinformatics, Vol.70, 1125 - 1132, 2007.
• [85] L.Chen, Y.Wang, M.Fei, Z.Liu. Systems Biology from Theoretical and Engineering Perspective. SCIENCE & TECHNOLOGY REVIEW, Vol.25, No.10, 5-10, 2007.
• [86] C. Li, L. Chen, K. Aihara. Stochastic Stability of Genetic Networks with Disturbance Attenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.
• [87] Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639, 2007.
• [88] S. Zhang, G. Jin, X-S. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks, Proteomics, Vol.7, 2856-2869, 2007.
• [89] R.Wang, L.Chen, K.Aihara. Detection of Cellular Rhythms and Global Stability within Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.
• [90] C.Li, L.Chen, K.Aihara. Stochastic Synchronization of Genetic Oscillator Networks. BMC Systems Biology, doi:10.1186/1752-0509-1-6, 2007.
• [91] Z.Wu, Y.Wang, E.Feng, L.Chen. A new geometric-topological method to measure protein fold similarity. Chemical Physics Letters, Vol.433,432-438, 2007.
• [92] Z.Wu, E.Feng, Y.Wang, L.Chen. Discrimination of Outer Membrane Proteins by a New Measure of Information Discrepancy. Protein & Peptide Letters, 14, 37-44, 2007.
• [93] C.Li, L.Chen, K.Aihara. A systems biology perspective on signal processing in genetic network motifs. IEEE Signal Processing Magazine, Vol.24, No.2, 136-147, 2007.
• [94] Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-FengWan, Laurent Brechenmacher, Nengbing Tao, David Emerich, Gary Stacey, Dong Xu. Development and Assessment of Scoring
Functions for Protein Identification Using Peptide Mass Fingerprinting Data. ELECTROPHORESIS, 28, 864-870, 2007.
• [95] S,Fukutome, H. Azuma, N. Honjou, L. Chen, Development of Generation-Transmission Expansion Planning Method Based on A Hierarchical Model, Transactions IEE of Japan, Vol.127-B, No.1, 130-136, 2007.
• [96] S.Fan, C.Mao, L.Chen, Next-Day Electricity Price Forecasting Using a Hybrid Network. IET Generation, Transmission & Distribution, Vol.1, No.1, 176-182, 2007.
• [97] R-S. Wang, L-Y.Wu, X-S.Zhang, L.Chen. A Markov Chain Model for Haplotype Assembly from SNP Fragments. Genome Informatics, Vol.17,No.2. 2006.
• [98] Y.Wang, L-Y.Wu, X-S.Zhang and L.Chen. Exploring the classification of protein structures on geometric patterns by neural networks. International Journal of Computational Intelligence Research, Vol. 2, No. 1, pp. 105-109, 2006.
• [99] Y.Wang, X-S.Zhang, L.Chen. Supervised Classification of Protein Structures, International Journal of Bioinformatics Research and Applications, Vol.3, No.2, 2006.
• [100] L.Chen, L-Y.Wu, Y.Wang, S.Zhang, X-S.Zhang, Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison, BMC Structural Biology, doi:10.1186/1472-6807-6-18, 2006.
• [101] Y.Wang, T.Joshi, D.Xu, X-S.Zhang, L.Chen, Inferring Gene Regulatory Networks from Multiple Microarray Datasets, Bioinformatics, 22, 2413 - 2420, 2006.
• [102] S.Fan, C.Mao, L.Chen, Electricity Peak Load Forecasting with Self-Organizing Map and Support Vector Regression, Transactions IEE of Japan, Vol.1, 330-336, 2006.
• [103] C.Li, L.Chen, K.Aihara, Transient Resetting: a novel mechanism for biological synchrony, PLoS Computational Biology, DOI:10.1371/journal.pcbi.0020103.eor, 2006.
• [104] Y.Wang, L-Y.Wu, X-S.Zhang, L.Chen, Automatic Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. Lecture Notes in Computer Science, Springer Berlin Heidelberg, Vol.3959, 505-514,2006.
• [105] R.Wang, L.Chen,K.Aihara, Synchronizing a Multicellular System by External Input: An Artificial Control Strategy,Bioinformatics, 22, 1775 - 1781, 2006.
• [106] R.Wang, L.Chen, K.Aihara, ”Construction of Genetic Oscillators with Interlocked Feedback Networks”, Journal of Theoretical Biology, Vol.242, 454-463, 2006.
• [107] C.Li, L.Chen, K.Aihara, ”Synchronization of Coupled Nonidentical Genetic Oscillators”, Physical Biology, 3, 37-44, 2006.
• [108] R.Li, L.Chen, R.Yokoyama, ”A Pricing Method for Transmission Loss Based on Sensitivity Analysis”, IEEE Trans. on Power Systems, Vo.21, No.3, pp.1201 - 1208, 2006.
• [109] X-S.Zhang, R-S. Wang, L-Y. Wu, L. Chen, ”Models and Algorithms for Haplotyping Problem,”Current Bioinformatics, 1, 105-114, 2006.
• [110] L.Chen, L-Y. Wu, Y.Wang, X-S. Zhang, ”Inferring Protein Interactions from Experimental Data by Association Probabilistic Method,” Proteins, 62, 833-837, 2006.
• [111] T.Wachi, S.Fukutome, L.Chen, Y.Makino, ”Decomposition of Market Clearing Price in Electricity Markets,” Transactions IEE of Japan, Vol. 126-B, No.3, pp.297-307, 2006.
• [112] L.Chen, R.Wang, ”Designing Gene Regulatory Networks with Specified Functions,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications, Vol.53, No.11, 2444-2450, 2006.
• [113] C.Li, L.Chen, K.Aihara, ”Stability of Genetic Networks with SUM Regulatory Logic,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications, Vol.53, No.11, 2451-2458, 2006.
• [114] Z. Jing, R. Wang, L.Chen, J.Deng, ”Attractive Regions in Power Systems by Singular Perturbation Analysis,” DOI 10.1007/3-7643-7429-28, Differential Equations with Symbolic Computation, 2006.
• [115] S.Fan, L.Chen, ”Short-Term Load Forecasting Based on an Adaptive Hybrid Method,” IEEE Trans. on Power Systems, 21, 392- 401, 2006.
• [116] S.Fan, C.Mao, L.Chen, ”Optimal coordinated PET and generator excitation control for power systems,” International Journal of Electrical Power & Energy Systems, 28, No.3, 158-165, 2006.
• [117] L.Chen, L-Y.Wu, R.Wang, Y.Wang, S.Zhang, X-S.Zhang, ”Comparison of Protein Structures by Multi-Objective Optimization,” Genome Informatics, Vol.16, No.2, pp.114-124, 2005.
• [118] T. Zhou,L.Chen, K.Aihara, ”Molecular Communication through Stochastic Synchronization Induced by Extracellular Fluctuations,” Physical Review Letter, 95, 178103, 2005.
• [119] R.Li, R.Yokoyama, L.Chen, ”Pricing for Load and Wheeling Charge Considering Transmission Paths in Deregulated Power Markets” International Journal of Electrical Power & Energy Systems, Vol.27, pp.496-505, 2005.
• [120] T.Zhou, L.Chen, R.Wang, ”A mechanism of synchronization in interacting multi-cell genetic systems,” Physica D, 211, 107-127, 2005.
• [121] Z.Li, W.Zhou, X.Zhang, L.Chen, ”A Parsimonious Tree-Grow Method for Haplotype Inference,”Bioinformatics, 21, 3475-3481, 2005.
• [122] T.Zhou, L.Chen, R.Wang, ”Excitation functions of coupling,” Physical Review E, 71, 066211, 2005.
• [123] R.Wang, L.Chen, ”Synchronizing genetic oscillators by signalling molecules,”Journal of Biological Rhythms, 20, 257-269, 2005.
• [124] L.Chen, R.Wang, T.Zhou, K.Aihara,”Noise-induced Cooperative Behavior in a Multi-Cell System,” Bioinformatics, Vol.21, 2722-2729, 2005.
• [125] T.Zhou, L.Chen, Y.Tang, X.Zhang,”Aligning Multiple Protein Structures by Deterministic Annealing,” Journal of Bioinformatics and Computational Biology, Vol.3, No.4, 837-860, 2005.
• [126] X.Zhang, Y.Wang, Z. Zhan, L.Wu, L.Chen,”Exploring Protein’s Optimal HP Configurations by Self-Organizing Mapping,” Journal of Bioinformatics and Computational Biology, Vol.3, No.2, 385-400, 2005.
• [127] P.Wei, L. Chen, H-D. Chiang, ”Bidding price analysis for competitive generators and large consumers,” International Journal of Electrical Power & Energy Systems, Vol.27, 169-176, 2005.
• [128] S.Fan, C.Mao, L.Chen, ”Peak load forecasting using the self-organizing map”, 640-647, Advances in Neural Networks, Springer, 2005.
• [129] Geerli, L.Chen, I.Kurihara, K.Takahasi, ”Cooperative Game Theory Applied to Transmission Expansion Cost Allocation for Congestion Relief,” International Journal of Electrical Power & Energy Systems, Vol.27, 61-67, 2005.
• [130] Z.Li, X.Zhang,L.Chen, ”Unique Optimal Foldings of Protein on a Triangular Lattice,” Journal of Applied Bioinformatics, Vol.4, 105-116, 2005.
• [131] L.Chen, T.Zhou, Y.Tang, ”Protein Structure Alignment by Deterministic Annealing,” Bioinformatics, Vol.21, 51-62, 2005.
• [132] R. Wang, Z.Jing, L.Chen, ”Modelling Periodic Oscillation in Gene Regulatory Networks by Cyclic Feedback Systems,” Bulletin of Mathematical Biology, Vol.67, 339-367, 2005.
• [133] T. Wachi, S.Fukutome, L. Chen, Y. Makino, G. Koshimizu, ”Application for Single Price Auction Model (SPA) in AC Network,” Transactions IEE of Japan, Vol.125-B, 81-89, 2005.
• [134] T.Zhou, L.Chen, R.Wang, K.Aihara, Intercellular Communications Induced by Random Fluctuations, Genome Informatics, Vol.15, No.2, 223-233, 2004.
• [135] R. Wang, Z. Jing, L.Chen, ”Periodic oscillators in genetic networks with negative feedback loops,” WSEAS Trans. on Mathematics, Vol.3, No.1, pp.150-156, 2004.
• [136] R. Wang, T. Zhou, Z. Jing, L. Chen, ”Modelling Periodic Oscillation of Biological Systems with Multiple Time Scale Networks, ” Systems Biology, Vol.1, No.1, pp.71-84,2004.
• [137] L. Chen, R. Wang, T. Kobayashi, K.Aihara, ”Dynamics of gene regulatory networks with cell division cycle,” Physical Review E, Vol. 70, 011909, 2004.
• [138] P.Charusanti, X.Hu, L.Chen, D.Neuhauser, J.Distefano, A mathematical model of BCRABL autophosphorylation, signaling through the CRKL pathway, and gleevec dynamics in chronic myeloid leukemia, Discrete and Continuous Dynamical Systems - Series B, Vol.4, No.1, pp.99-114,2004.
• [139] T.Zhou, J.Lu, L.Chen, Z.Jing, Y.Tang, ”On the optimal solutions for power flow equations,”International Journal of Electrical Power & Energy Systems, Vol.25, pp.533-541, 2003.
• [140] Z.Jing, D.Xu, Y.Chang, L.Chen, ”Bifurcations, chaos, and system collapse in a three node power system,” International Journal of Electrical Power & Energy Systems, Vol.25, No.6, pp.443-461, 2003.
• [141] T.Kobayashi, L.Chen, K.Aihara, ”Modeling Genetic Switches with Positive Feedback Loops,”Journal of Theoretical Biology, Vol.221, pp.379-399, 2003.
• [142] S.Fukutome, H.Azuma, T. Saishoji, M.Yasuda, H.Saito, K.Ogimoto, L.Chen ,”Fast power system reliability evaluation by Monte Carlo method,” Transactions IEE of Japan, Vol.122-B, No.3, pp.369-374, 2002.
• [143] R. Yuan, Z.Jing, L.Chen, ”UNIFORM ASYMPTOTIC STABILITY OF HYBRID DYNAMICAL SYSTEMS WITH DELAY,” IEEE Trans. on Automatic Control, Vol.48, No.2, pp.344-348, 2003.
• [144] L.Chen, K.Aihara, ”A Model of Periodic Oscillation for Genetic Regulatory Systems,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.10, pp.1429-1436,2002.
• [145] Z.Jing, J.Wang, L.Chen, ”Computation of Limit Cycle via Higher Order Harmonic Balance Approximation and Its Application to a 3-Bus Power System,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.9, pp.1360-1370, 2002.
• [146] L.Chen, K.Aihara, ”Stability of Genetic Regulatory Networks with Time Delay,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.5, pp.602-608, 2002.
• [147] L.Chen, H.Suzuki, K.Wachi, Y.Shimura, ”Components of Nodal Prices For Electric Power Systems,” IEEE Trans. on Power Systems. Vol.17, no.1, pp.41-49, 2002.
• [148] S. Fukutome, M. Yasuda, L. Chen, ”Fast power system reliability evaluation by Monte Carlo method,” Transactions IEE of Japan, Vol. 122-B, No.3, pp. 369-374, 2002.
• [149] L.Chen, K.Aihara, ”Chaotic dynamics of neural networks and its application to combinatorial optimization,” Journal of Dynamical Systems and Differential Equations, invited review paper, vol.9, no.3, pp.139-168, 2001.
• [150] L.Chen, K.Aihara, ”Stability and Bifurcation Analysis of Differential-Difference-Algebraic Equations,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications. Vol.48, No.3, pp.308-326,2001.
• [151] L.Chen, Y.Tada, H.Okamoto, R.Tanabe, A.Ono, ”Optimal Operation Solutions of Power Systems with Transient Stability Constraints,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications. Vol.48, No.3, pp.327-339,2001.
• [152] Geerli, L.Chen, R.Yokoyama, ”Pricing and operation in deregulated electricity market by noncooperative game,” Electrical Power Systems Research, Vol.57, pp.133-139, 2001.
• [153] J.Wang, L.Chen, Z.Jing, ”Chaos and asymptotical stability in discrete-time recurrent neural networks with generalized input-output function,” Science in China, vol.44, no.2, pp.193-200, 2001.
• [154] L.Chen, K.Aihara, ”Strange Attractors in Chaotic Neural Networks,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications, Vol.47, No.10, pp. 1455-1468, 2000.
• [155] L.Chen, et al., ”Optimal Operation of Power Systems Constrained by Transient Stability,”Transactions IEE of Japan, Vol. 120-B, No.12, pp. 1582-1594, 2000.
• [156] L.Chen, et al., ”Analysis of Nodal Prices for Power Systems,” Transactions IEE of Japan, Vol.120-B, No.5, pp.686-693, 2000.
• [157] Geerli, L.Chen, et al., ”Negotiation Models for Electric Pricing and Load Dispatch in Electricity Market,” Transactions IEE of Japan, Vol.120-B, No.2, pp.219-226, 2000.
• [158] L.Chen, H.Tanaka, K.Katou, Y.Nakamura, ”Stability analysis for digital controls of power systems,” Electric Power Systems Research, Vol. 55, pp.79-86, 2000.
• [159] L.Chen, K.Aihara, ”Global Searching Ability of Chaotic Neural Networks,” IEEE Transactions on Circuits and Systems- I: Fundamental Theory and Applications, Vol.46, No.8,pp.974-993, 1999.
• [160] L.Chen, S.Matoba, et al., ”Surrogate Constraint Method for Optimal Power Flow,” IEEE Transactions on Power Systems, Vol.13, No.3, pp.1084-1089,1998.
• [161] L.Chen, H.Susuki, et al., ”Mean Field Theory for Optimal Power Flow,” IEEE Transactions on Power Systems,Vol.12, No.4, pp.1481-1486, 1997.
• [162] L.Chen, K.Aihara, ”Chaos and Asymptotical Stability in discrete-time neural networks”, Physica D, Vol.104, pp.286-325, 1997.
• [163] L.Chen, et al ”A Comparison of Reliability Evaluation Techniques for Power Systems,”Transactions of IEE Japan, Vol.116-B,No.3, 1996.
• [164] L.Chen, K.Aihara, ”Chaotic Simulated Annealing by a Neural Network Model with Transient Chaos,” Neural Networks, Vol.8, No.6, pp.915-930, 1995.
• [165] L.Chen, K.Aihara, ”Chaotic Simulated Annealing for Combinatorial Optimization,” N.Aoki, et al (Eds.), Dynamic Systems and Chaos, World Scientific, Vol.1, pp.319-322, 1995.
• [166] L.Chen, K.Aihara, ”Chaotic simulated annealing and combinatorial optimization,” Journal of Computation Technology, Vol.25, No.2, pp.20-28, 1994.
• [167] L.Chen, K.Aihara, ”Transient Chaotic Neural Networks and Chaotic Simulated Annealing,”M. Yamaguti(Editor), Towards the Harnessing of Chaos, Elsevier Science B.V., pp.347-352, 1994.
• [168] L. Chen, et al, ” Optimal Electric Generation Planning for Interconnected Systems by Benders Decomposition,” Transactions of IEE Japan,, Vol.B-113, No.6, pp.643-652, 1993.
• [169] L. Chen, J. Toyoda, ”Optimal Generating Unit Maintenance Scheduling for Multi-Area System with Network Constraints,” IEEE Transactions on Power Systems, Vol.PWRS-6, No.3, pp.1168-1174, August 1991.
• [170] L. Chen, J. Toyoda, ”Power Arrival Evaluation of Bulk System Including Network Constraints Based on Linear Programming Approach,” IEEE Transactions on Power Systems, Vol.PWRS-6, No.1, pp.37-42, February 1991.
• [171] L. Chen, J. Toyoda, ”Maintenance Scheduling Based on Two Level Hierarchical Structure to Equalize Incremental Risk ,” IEEE Transactions on Power Systems, Vol.PWRS-5, No.4, pp.1510-1516, November 1990.
• [172] L. Chen, J. Toyoda, ”Optimal Unit Commitment Scheduling of Thermal Power System Based on the Monte Carlo Method, ” Transactions of IEE Japan, Vol.B-109, No.3, pp.73-80, 1989.
• [173] L. Chen, J.Toyoda, ”A New Approach to Maintenance Scheduling Based on Incremental Reliability Index,” Transactions of IEE Japan, Vol.B-108, No.5, pp.205-212, 1988.
  

Conference Papers

• (More than 200 conference papers), omission.