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 Homepage: http://www.sysbio.ac.cn/cb/chenlab/, or, http://www.sysbio.ac.cn/cb, or, http://www.sysbio.ac.cn/cb/chenlab/LuonanChen.htm
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.
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 Fellow and 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
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,
Associate Editor, BMC Research Notes,
Editorial Board Member, IET Systems Biology,
Editorial Board Member, Mathematical Biosciences,
Editorial Board Member, Journal of Theoretical Biology,
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,
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),President, Computational Systems Biology Society of ORS China.
Editors for Special Issues in Journals
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).
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] 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. MolecularBioSystems, DOI: 10.1039/C0MB00325E, 2011.
[2] Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Systems Biology, accepted, 2011.
[3] 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.
[4] Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, accepted, 2011.
[5] Huarong Zhou, Zhiping Liu, Kazu Horimoto, Luonan Chen. Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Systems Biology,
accepted, 2011.
[6] Hongbo Lei, Jifeng Zhang, Luonan Chen. Property of Multiple Equilibria for SSI Metabolic Module. BMC Systems Biology, accepted, 2011.
[7] 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, accepted, 2011.
[8] Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen: Network-based analysis of complex diseases. IET Systems Biology, accepted, 2011.
[9] D. Liu, X. Chang, Z.Liu, L.Chen, R.Wang. Bistability and oscillations in gene regulation mediated by small noncoding RNAs. PLoS One, 2011.
[10] 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.
[11] Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.
[12] 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.
[13 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.
[14 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, 942–950, 2010.
[15] 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.
[16] 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.
[17] 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.
[18] 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.
[19] 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.
[20] 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.
[21] 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.
[22] 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.
[23] 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.
[24] Zhao Song, Luonan Chen, Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.
[25] 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.
[26] 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.
[27] 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.
[28] 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.
[29] 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.
[30] 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.
[31] 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.
[32] 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.
[33] 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.
[34] 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.
[35] 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.
[36] H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:026107, 2009.
[37] 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.
[38] Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.
[39] 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.
[40] 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.
[41] 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.
[42] 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.
[43] 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.
[44] 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.
[45] 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.
[46] 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.
[47] B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 28006, 2008.
[48] 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.
[49] T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 037126, 2008.
[50] Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community detection. Physical Review E, 77, 036109, 2008.
[51] 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.
[52] 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.
[53] G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network. Neurocomputing, 71, 2794-2805, 2008.
[54] 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, 10.1109/TCBB.2007.70250, 2008.
[55] 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.
[56] 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.
[57] 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.
[58] 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.
[59] 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.
[60] 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.
[61] 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
[62] 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.
[63] 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.
[64] 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.
[65] 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.
[66] R. Wang, Y.Wang, X-S. Zhang, L.Chen. Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics, 23(22):3056-3064, 2007.
[67] X.Zhao, L.Chen, K.Aihara. Protein classification with imbalanced data. Proteins: Structure, Function, and Bioinformatics, Vol.70, 1125 - 1132, 2007.
[68] 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.
[69] C. Li, L. Chen, K. Aihara. Stochastic Stability of Genetic Networks with Disturbance Attenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.
[70] Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639, 2007.
[71] 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.
[72] R.Wang, L.Chen, K.Aihara. Detection of Cellular Rhythms and Global Stability within Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.
[73] C.Li, L.Chen, K.Aihara. Stochastic Synchronization of Genetic Oscillator Networks. BMC Systems Biology, doi:10.1186/1752-0509-1-6, 2007.
[74] 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.
[75] 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.
[76] 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.
[77] 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.
[78] 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.
[79] 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.
[80] 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.
[81] 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.
[82] Y.Wang, X-S.Zhang, L.Chen. Supervised Classification of Protein Structures, International Journal of Bioinformatics Research and Applications, Vol.3, No.2, 2006.
[83] 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.
[84] Y.Wang, T.Joshi, D.Xu, X-S.Zhang, L.Chen, Inferring Gene Regulatory Networks from Multiple Microarray Datasets, Bioinformatics, 22, 2413 - 2420, 2006.
[85] 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.
[86] 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.
[87] 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.
[88] R.Wang, L.Chen,K.Aihara, Synchronizing a Multicellular System by External Input: An Artificial Control Strategy,Bioinformatics, 22, 1775 - 1781, 2006.
[89] R.Wang, L.Chen, K.Aihara, ”Construction of Genetic Oscillators with Interlocked Feedback Networks”, Journal of Theoretical Biology, Vol.242, 454-463, 2006.
[90] C.Li, L.Chen, K.Aihara, ”Synchronization of Coupled Nonidentical Genetic Oscillators”, Physical Biology, 3, 37-44, 2006.
[91] 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.
[92] X-S.Zhang, R-S. Wang, L-Y. Wu, L. Chen, ”Models and Algorithms for Haplotyping Problem,” Current Bioinformatics, 1, 105-114, 2006.
[93] 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.
[94] 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.
[95] 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.
[96] 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.
[97] 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.
[98] S.Fan, L.Chen, ”Short-Term Load Forecasting Based on an Adaptive Hybrid Method,” IEEE Trans. on Power Systems, 21, 392- 401, 2006.
[99] 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.
[100] 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.
[101] T. Zhou,L.Chen, K.Aihara, ”Molecular Communication through Stochastic Synchronization Induced by Extracellular Fluctuations,” Physical Review Letter, 95, 178103, 2005.
[102] 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.
[103] T.Zhou, L.Chen, R.Wang, ”A mechanism of synchronization in interacting multi-cell genetic systems,” Physica D, 211, 107-127, 2005.
[104] Z.Li, W.Zhou, X.Zhang, L.Chen, ”A Parsimonious Tree-Grow Method for Haplotype Inference,” Bioinformatics, 21, 3475-3481, 2005.
[105] T.Zhou, L.Chen, R.Wang, ”Excitation functions of coupling,” Physical Review E, 71, 066211, 2005.
[106] R.Wang, L.Chen, ”Synchronizing genetic oscillators by signalling molecules,” Journal of Biological Rhythms, 20, 257-269, 2005.
[107] L.Chen, R.Wang, T.Zhou, K.Aihara,”Noise-induced Cooperative Behavior in a Multi-Cell System,” Bioinformatics, Vol.21, 2722-2729, 2005.
[108] 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.
[109] 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.
[110] 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.
[111] S.Fan, C.Mao, L.Chen, ”Peak load forecasting using the self-organizing map”, 640-647, Advances in Neural Networks, Springer, 2005.
[112] 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.
[113] Z.Li, X.Zhang,L.Chen, ”Unique Optimal Foldings of Protein on a Triangular Lattice,” Journal of Applied Bioinformatics, Vol.4, 105-116, 2005.
[114] L.Chen, T.Zhou, Y.Tang, ”Protein Structure Alignment by Deterministic Annealing,” Bioinformatics, Vol.21, 51-62, 2005.
[115] 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.
[116] 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.
[117] T.Zhou, L.Chen, R.Wang, K.Aihara, Intercellular Communications Induced by Random Fluctuations, Genome Informatics, Vol.15, No.2, 223-233, 2004.
[118] 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.
[119] 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.
[120] L. Chen, R. Wang, T. Kobayashi, K.Aihara, ”Dynamics of gene regulatory networks with cell division cycle,” Physical Review E, Vol. 70, 011909, 2004.
[121] 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.
[122] 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.
[123] 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.
[124] T.Kobayashi, L.Chen, K.Aihara, ”Modeling Genetic Switches with Positive Feedback Loops,” Journal of Theoretical Biology, Vol.221, pp.379-399, 2003.
[125] 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.
[126] 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-
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[127] 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.
[128] 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.
[129] 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.
[130] 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.
[131] 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.
[132] 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.
[133] 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.
[134] 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.
[135] 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.
[136] 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.
[137] 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.
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[139] L.Chen, et al., ”Analysis of Nodal Prices for Power Systems,” Transactions IEE of Japan, Vol.120-B, No.5, pp.686-693, 2000.
[140] 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.
[141] 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.
[142] 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.
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[144] 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.
[145] L.Chen, K.Aihara, ”Chaos and Asymptotical Stability in discrete-time neural networks”, Physica D, Vol.104, pp.286-325, 1997.
[146] L.Chen, et al ”A Comparison of Reliability Evaluation Techniques for Power Systems,” Transactions of IEE Japan, Vol.116-B,No.3, 1996.
[147] 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.
[148] 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.
[149] L.Chen, K.Aihara, ”Chaotic simulated annealing and combinatorial optimization,” Journal of Computation Technology, Vol.25, No.2, pp.20-28, 1994.
[150] 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.
[151] 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.
[152] 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.
[153] 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.
[154] 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.
[155] 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.
[156] 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.
