Professor Luonan Chen
Professor Luonan Chen
Professor, Excutive director, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Present address (office): 320 YueYang Road, Shanghai 200031, China
Phone (office): +86-21-; Fax: +86-21-.
E-mail: lnchen@
Laboratory Homapage:
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,
Editorial Board Member, Journal of Molecular Cell Biology
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 09),
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
: Senior Engineer and Project manager at JPBS, Tokyo, Japan.
: Associate professor at the Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan.
: Visiting Professor at the Department of Computer Science, University of California, Los Angeles (UCLA), USA.
: Professor at the Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan.
: 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
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
Jie L Ting P Liang J Jia-Zuan Ni; Qiong L Luonan C Yan Zhang. Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Genome Biology and Evolution, doi: 10.1093/gbe/evv022, 2015.
Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang,Tao Zeng and Luonan Chen. Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015.
Wanwei Zhang, Tao Zeng, Xiaoping Liu, Luonan Chen. Diagnosing phenotypes of single-sample individuals by edge biomarkers. Journal of Molecular Cell Biology, 2015.
Xinan (Holly) Yang,Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan One , Jill de Jong, Jianjun Chen, Luonan Chen, John M. Cunningham. Systematic computation with functional gene-1 sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics, 2015.
Sharon E. Mitchell, Zan Hui Tang, Celine Kerbois, Camille Delville, Penelope Konstantopedos, Aurélie Bruel, Davina Derous, Cara Green, Richard M. Aspden, Luonan Chen, Jackie J.D. Han, Yingchun Wang, Daniel E.L. Promislow, David Lusseau, Alex Douglas and John R. Speakman.The effects of graded levels of calorie restriction: I. Impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse. Oncotarget, 2015.
Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura,Luonan Chen, and Kazuyuki Aihara. Clustered Model Reduction of Positive Directed Networks. Automatica, 2015.
Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen. Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. BMC Bioinformatics,2015.
Guoyun Cao, Luonan Chen, Kazuyuki Aihara. Power System Voltage Stability Assessment Based on Branch Active Powers. IEEE TRANSACTIONS ON POWER SYSTEMS, DOI: 10.1109/TPWRS., 2015.
Jiang Xie, Wang Ding, Luonan Chen, Qiang Guo and Wu Zhang. Advances in Protein Contact Map Prediction Based on Machine Learning. Medicinal Chemistry, 2015.
Xingming Zhao, Keqin Liu, Luonan Chen. Identifying cancer-related microRNAs based on gene expression data. Bioinformatics, doi:10.1093/bioinformatics/btu811, 2014.
Xiujun Zhang, Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao, and Luonan Chen. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research, doi: 10.1093/nar/gku.
Huanfei Ma, Kazuyuki Aihara, Luonan Chen. Detecting Causality from Nonlinear Dynamics with Short-term Time Series. Scientific Reports, doi:10.1038/srep0.
Yixue Li, Luonan Chen. Big Biological Data: Challenges and Opportunities. Genomics, Proteomics & Bioinformatics, 2014.
Tao Zeng, Diane Catherine Wang, Xiangdong Wang, Feng Xud, Luonan Chen. Prediction of dynamical drug sensitivity and resistance by module network rewiring-analysis based on transcriptional profiling. Drug Resistance Updates, DOI: 10.1016/j.drup., 2014.
Andrew E Teschendorff, Xiaoping Liu, Helena Caren, Steve Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen. The dynamics of DNA methylation covariation patterns in carcinogenesis. PLoS Computational Biology, 10(7): e1003709. doi:10.1371/journal.pcbi.14.
Zhenshu Wen, Luonan Chen. MCentridFS: a tool for identifying module biomarkers for multi-phenotypes from high-throughput data. Molecular BioSystems, DOI: 10.325J, 2014.
Huanfei Ma, Tianshou Zhou, Kazuyuki Aihara, Luonan Chen. Predicting Time-series from Short-term High-dimensional Data. International Journal of Bifurcation and Chaos, 2014.
Xiaodan Wu, Luonan Chen and Xiangdong Wang. Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clinical and Translational Medicine, 3:16, 2014.
Jiang Xie, Wang Ding, Luonan Chen, Qiang Guo and Wu Zhang. Advances in Protein Contact Map Prediction Based on Machine Learning.
Medicinal Chemistry, 2014.
Xiaoru Sun, Minghuan Zheng, Miaomiao Zhang, Mengjia Qian, Yonghua Zheng, Meiyi Li, Dragos Cretoiu, Chengshui Chen, Luonan Chen, Laurentiu M. Popescu and Xiangdong Wang. Differences in the expression of chromosome 1 genes between lung telocytes and other cells: mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells and lymphocytes. Journal of Cellular and Molecular Medicine, ):801-10. doi: 10.1111/jcmm.12302.
Xiaodan Wu, Luonan Chen and Xiangdong Wang. Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clinical and Translational Medicine
doi:10.26-3-16.
Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Rui Liu, Luonan Chen. Edge biomarkers for classification and prediction of phenotypes. SCIENCE CHINA Life Sciences, 2014.
Wanwei Zhang, Tao Zeng, Luonan Chen. EdgeMarker: identifying differentially correlated molecule pairs as edge-biomarkers. Journal of Theoretical Biology, DOI:10.1016/j.jtbi., 2014.
Rui Liu, Xiangtian Yu , Xiaoping Liu, Dong Xu, Kazuyuki Aihara and Luonan Chen. Identifying critical transitions of complex diseases based on a single sample. Bioinformatics, DOI:10.1093/bioinformatics/btu084, 2014.
B.Liu, Z.Yuan, K.Aihara, L.Chen. Reinitiation enhances reliable transcriptional responses in eukaryotes. J. R. Soc. Interface, 14.
Fang-Xiang Wu, Lin Wu, Jianxin Wang, Juan Liu, Luonan Chen. Transittability of complex networks and its applications to regulatory biomolecular networks. Scientific Reports, DOI: 10.1038/srep.
Tao Zeng, Chuan-chao Zhang, Wanwei Zhang, Rui Liu, Juan Liu, Luonan Chen. Deciphering early development of complex diseases by progressive module network. Methods, http://dx.doi.org/10.1016/j.ymeth., 2014.
Minchao Wang, Wu Zhang, Wang Ding, Dongbo Dai, Huiran Zhang, Hao Xie, Luonan Chen, Yike Guo and Jiang Xie. Parallel Clustering Algorithm for Large-scale Biological Data Sets. PLoS One, 2014.
Doss C. Priya George, Chiranjib Chakraborty, SA Syed Haneef, Nagarajan NagaSundaram, Luonan Chen, Hailong Zhu. Evolution- and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2). Theranostics, 4(4):366-385. doi: 10.7150/thno..
Zhang Pengjun, Zou Meng, Wen Xinyu, Gu Feng, Li Juan, Liu Gaixia, Dong Jingxiao, Deng Xinxin, Gao Jing, Li Xiaolong, Jia Xingwang, Dong Zhennan, Chen Luonan,Wang Yong, and Tian Yaping. Development of Serum Parameters Panels for Early Detection of Pancreatic Cancer. International Journal of Cancer, 134, , 2014.
Meng Zou, Peng-Jun Zhang, Xin-Yu Wen, Luonan Chen, Ya-Ping Tian and Yong Wang. Identifying multi-biomarkers to distinguish malignant from benign colorectal tumours by a mixed integer programming. Journal of the American Medical Informatics Association, 2014.
Chiranjib Chakraborty, George Priya Doss. C, Luonan Chen, Hailong Zhu.
Evaluating protein-protein interaction (PPI) networks using in silico pharmacology: to understand the diseases pathway, target discovery and drug-design. Current Protein and Peptide Science, 15, 561-571, 2014.
Xiangtan Yu, Guozheng Li, Luonan CHen. Prediction and early diagnosis of complex diseases by edge-network. Bioinformatics, doi:10.1093/bioinformatics/btt620，2013.
Tao Zeng, Shao-yan Sun, Yong Wang, Hailong Zhu, Luonan Chen. Network biomarkers reveal dysfunctional gene regulations during disease progression. FEBS Journal, doi:10.1111/febs.1.
Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology in the big data era. BMC Systems Biology, doi:10.09-7-S2-S1, 2013.
Rui Liu, Xiangdong Wang, Kazuyuki Aihara, Luonan Chen, Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers. Medicinal Research Reviews, DOI:10.1002/med.2.
Shao-Yan Sun, Zhi-Ping Liu, Tao Zeng, Yong Wang, and Luonan Chen. Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks. Scientific Reports, DOI: 10.1038/srep0.
Jiguang Wang, Yidan Sun, Si Zheng, Xiang-Sun Zhang, Huarong Zhou, and Luonan Chen. APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems. Scientific Reports, DOI: 10.1038/srep0.
Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Xiang-Sun Zhang, Alexander R. Pico. NOA: A Cytoscape Plugin for Network Ontology Analysis. Bioinformatics, doi:10.1093/bioinformatics/btt334, 2013.
Xiaoping Liu, Xiaodong Zhang, Wei-Hua Tang, Luonan Chen and Xing-Ming Zhao. eFG: an electronic resource for Fusarium graminearum. Database, doi:10.1093/database/bat042, 2013.
Mingzhu Zhao, Hao-Teng Chang, Zhiping Liu, Luonan Chen, Dongqing Wei. Predicting Protein--Ligand Interactions Based on Chemical Preference Features with its Application to New D--Amino Acid Oxidase Inhibitor Discovery. Current Pharmaceutical Design, DOI: 10.114902 , 2014.
Jiang Xie, Zhonghua Zhou, Kai Lu, Luonan Chen, Wu Zhang. Visualization of Biomolecular Networks Comparison on Cytoscape. Tsinghua Science and Technology, 2013.
Zikai Wu, Yong Wang, Luonan Chen. A New Framework for Drug Repositioning by Incorporating Functional Information. IET Systems Biology, 7(5):188-94, doi: 10.1049/iet-syb., 2013.
Meiyi Li, Tao Zeng, Yong Wang, Luonan Chen. Detecting tissue-specific early-warning signals for complex diseases based on dynamical network biomarkers: study of type-2 diabetes by cross-tissue analysis. Briefings in Bioinformatics, DOI:10.1093/bib/bbt027, 2013.
Rui Liu, Kazuyuki Aihara, Luonan Chen. Dynamical network biomarkers for identifying critical transitions of biological processes. Quantitative Biology, DOI 10.-013-13.
Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen. A Sequence-based Computational Approach to Predicting PDZ Domain-Peptide Interactions. BBA - Proteins and Proteomics, 2013.
Zikai Wu, Yong Wang, Luonan Chen. Network-Based Drug Repositioning. Molecular BioSystems, DOI:10.382A, 2013.
Chenglei Sun, Zheng-Zheng Shi, Xiaobo Zhou, Luonan Chen, Xing-Ming Zhao. Prediction of S-Glutathionylation Sites Based on Protein Sequences. PLoS ONE 8(2): e55512. doi:10.1371/journal.pone.13.
George Priya Doss C, Nagasundaram N, Chiranjib Chakraborty, Luonan Chen and Hailong Zhu. Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: A Molecular dynamics approach, Human Genomics, 7:10, /content/7/1/10, 2013.
Zhiyuan Yang, Yan Zhang, and Luonan Chen. Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat. BMC Systems Biology, 2013.
Zhi-Ping Liu, Wanwei Zhang, Katsuhisa Horimoto, and Luonan Chen. A Gaussian Graphical Model for Identifying Significantly Responsive Regulatory Networks from Time Course High-Throughput Data. IET Systems Biology, 2013.
Peipei Zhou, Shuiming Cai, Zengrong Liu, Luonan Chen, Ruiqi Wang. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems. Chaos, Solitons & Fractals, .
Rui Liu, Meiyi Li, Zhi-Ping Liu, Jiarui Wu, Luonan Chen, Kazuyuki Aihara. Identifying critical transitions and their leading networks in complex diseases. Scientific Reports, DOI: 10.1038/srep0.
Xiaoping Liu, Rui Liu, Xing-Ming Zhao, Luonan Chen. Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Medical Genomics, doi:10.94-6-S2-S8, 2013.
Xiaoping Liu, Jiguang Wang, Luonan Chen. Whole-exome sequencing reveals recurrent somatic mutation networks in cancer. Cancer Letters, http://dx.doi.org/10.1016/j.canlet., 2012.
Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang and Qi Jin. ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. Nucleic Acids Research, 41, 4 e53, doi:10.1093/nar/gks.
Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, and Luonan Chen. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, DOI:10.1093/bioinformatics/bts619, 2012.
Ying Wang, Xiaowei Chen, Zhi-Ping Liu, Qiang Huang, Yong Wang, Xiang-Sun Zhang, Runsheng Chen, Luonan Chen. De novo prediction of RNA-protein interactions from sequence information. Molecular BioSystems, DOI: 10.292a, 2012.
Bengong Zhang, Luonan Chen, Kazuyuki Aihara. Incremental stability analysis of stochastic hybrid systems. Nonlinear Analysis (Series B: Real World Applications), 14, , 2012.
Hailong Zhu, R. Shyama Prasad Rao, Jiming Liu, Tao Zeng, Luonan Chen. Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. Nucleic Acids Research, doi:10.1093/nar/gks860, 2012.
Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen. An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. Journal of the American Medical Informatics Association, doi:10.1136/amiajnl-, 2012.
Zhenshu Wen, Zhi-Ping Liu, Yiqing Yan, Guanying Piao, Zhengrong Liu, Jiarui Wu and Luonan Chen. Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One, 7(7), e4.
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, 2, 342; DOI:10.1038/srep0.
Zhiping Liu, Luonan Chen. Proteome-wide prediction of protein-protein interactions from high-throughput data.
Protein & Cell, 2012.
Hee Sook Lee, Taejeong Bae, Ji-Hyun Lee, Dae Gyu Kim, Young Sun Oh, Yeongjun Jang, Ji-Tea Kim, Jong-Jun Lee, Alessio Innocenti, Claudiu T Supuran, Luonan Chen, Kyoohyoung Rho and Sunghoon Kim. Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Systems Biology, 2012.
Ke-Qin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao. Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics, 13:126 doi:10.05-13-126, 2012.
Wei Song, Jiguang Wang, Ying Yang, Nai-He Jing, Xiang-Sun Zhang, Luonan Chen, Jia-Rui Wu. Rewiring drug-activated p53-regulatory network from suppressing to promoting tumorigenesis. Journal of Molecular Cell Biology, 4(4), 197-206, 2012.
Jiajun Zhang,Luonan Chen,and Tianshou Zhou. Analytical Distribution and Tunability of Noise in a Model of Promoter Progress. Biophysical Journal, Vol.102, , 2012.
Luonan Chen, Jiarui Wu. Systems biology for complex diseases. Journal of Molecular Cell Biology, doi:10.1093/jmcb/mjs022, 2012.
H.J. Li, J.H. Zhang, Z.P. Liu, L. Chen, X.S. Zhang. Identify overlapping communities in social networks using multi-scale local information expansion. The European Physical Journal B, 85: 190, DOI: 10.1140/epjb/e-5, 2012.
Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Modelling biological systems from molecules to dynamical networks. BMC Systems Biology, doi:10.09-6-S1-S1, 2012.
Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross KK Leung, Xiang-Sun Zhang, Stephen KW Tsui and Luonan Chen. Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. doi:10.05-13-S7-S6, BMC Bioinformatics, 2012.
Danning He, Zhiping Liu, Masao Honda, Shuichi Kaneko, Luonan Chen. Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma. Journal of Molecular Cell Biology, 4(3), 140-152, 2012.
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.
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., 2012.
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, 97 (48005), doi:10.75/97/4.
Tao Zeng and Luonan Chen. Tracing dynamic biological processes during phase transition. BMC Systems Biology, doi:10.09-6-S1-S12, 2012.
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, doi:10.09-6-S1-S2, 2012.
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.
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.
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.
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.
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: 10.120B, 2011.
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.
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: 10.325E, 2011.
Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Systems Biology, doi:10.09-5-S1-S1, 2011.
Graziano Chesi, Luonan Chen. Systems Biology. Int. J. Robust. Nonlinear Control, 21:.
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.11.
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.
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.
Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen. Detecting thermophilic proteins through selecting amino acid and dipeptide composition features. Amino Acids, DOI 10.-011-11.
Hongbo Lei, Jifeng Zhang, Luonan Chen. Property of Multiple Equilibria for SSI Metabolic Module. BMC Systems Biology, doi:10.09-5-S1-S15, 2011.
Huarong Zhou, Zhiping Liu, Kazu Horimoto, Luonan Chen. Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Systems Biology, doi:10.09-5-S1-S16, 2011.
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.
Luonan Chen, James Lam, Zidong Wang. ANALYSIS AND CONTROL OF BIOLOGICAL NETWORKS. Asian Journal of Control, DOI: 10.1002/asjc.424, 2011.
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..
Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, Volume 13, Issue 5, pages 738C748, September 2011
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..
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.
Xiaoping Liu, Wei-Hua Tang, Xingming Zhao, Luonan Chen. A Network Approach to Predict Pathogenic Genes for Fusarium graminearum. PLoS One, 5(10): e1.
Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.09-4-S2-S1, 2010.
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, , 2010.
Zikai Wu, Xing-Ming Zhao, Luonan Chen. A systems biology approach to identify effective cocktail drugs. BMC Systems Biology, doi:10.09-4-S2-S7, 2010.
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:10.09-4-S2-S11, 2010.
Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen. FGsub: Fusarium graminearum protein subcellular localization prediction from primary structures. BMC Systems Biology, doi:10.09-4-S2-S12, 2010.
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.
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.
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.
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.
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), , 2009.
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.
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.09.
Zhao Song, Luonan Chen, Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), , 2009.
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.
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, 87:3.
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.
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.
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.
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.
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.
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), , 2009.
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.
B.Wang, L.Chen, K.Aihara. Limited ability driven phase transitions in the coevolution process in Axelrod&s model. Physics Letters A, 373(17), , 2009.
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), , 2009.
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.
H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:09.
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.
Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.
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. , 2009.
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.
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), , 10.1021/pr08.
S.Zhang, X-S.Zhang, L.Chen. Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology, 2:5, doi:10.09-2-5, 2008.
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.
Z.Liu, L.Wu, Y.Wang, X-S. Zhang, L.Chen. Bridging protein local structures and protein functions. Amino Acids, DOI 10.-008-08.
X.Zhao, K.Aihara, L.Chen. Protein function prediction with high-throughput data. Amino Acids, Vol.35, pp.517-530, DOI 10.-008-0077-y, 2008.
Y.Xie, L.Chen, Y.Kang, K. Aihara. Controlling the onset of Hopf bifurcation in the Hodgkin-Huxley model. Physical Review E. 77, 08.
B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 2.
C. Li, L. Chen, K.Aihara. Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks. Chaos. Vol.18, 08.
T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 08.
Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community detection. Physical Review E, 77, 08.
X.Zhao, Y.Wang, L.Chen, K.Aihara. Gene function prediction using labeled and unlabeled data. BMC Bioinformatics, 9:57, doi:10.05-9-57, 2008.
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.
G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network. Neurocomputing, 71, , 2008.
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., 2008.
R.Wang, C.Li, L.Chen, K.Aihara. Modeling and Analyzing Biological Oscillations in Molecular Networks. Proceedings of The IEEE, Vol.96, , 2008.
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.
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.
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.
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.
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.
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. , 2008
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:10.05-8-475, 2007.
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.07.
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.
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:10.05-8-391, 2007.
R. Wang, Y.Wang, X-S. Zhang, L.Chen. Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics, 23(22):, 2007.
X.Zhao, L.Chen, K.Aihara. Protein classification with imbalanced data. Proteins: Structure, Function, and Bioinformatics, Vol.70, 1125 - .
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.
C. Li, L. Chen, K. Aihara. Stochastic Stability of Genetic Networks with Disturbance Attenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.
Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, , 2007.
S. Zhang, G. Jin, X-S. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks, Proteomics, Vol.7, , 2007.
R.Wang, L.Chen, K.Aihara. Detection of Cellular Rhythms and Global Stability within Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.
C.Li, L.Chen, K.Aihara. Stochastic Synchronization of Genetic Oscillator Networks. BMC Systems Biology, doi:10.09-1-6, 2007.
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.
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.
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.
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.
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.
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.
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.
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.
Y.Wang, X-S.Zhang, L.Chen. Supervised Classification of Protein Structures, International Journal of Bioinformatics Research and Applications, Vol.3, No.2, 2006.
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:10.07-6-18, 2006.
Y.Wang, T.Joshi, D.Xu, X-S.Zhang, L.Chen, Inferring Gene Regulatory Networks from Multiple Microarray Datasets, Bioinformatics, 22, 2413 - .
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.
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.
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.4,2006.
R.Wang, L.Chen,K.Aihara, Synchronizing a Multicellular System by External Input: An Artificial Control Strategy,Bioinformatics, 22, 1775 - .
R.Wang, L.Chen, K.Aihara, &Construction of Genetic Oscillators with Interlocked Feedback Networks&, Journal of Theoretical Biology, Vol.242, 454-463, 2006.
C.Li, L.Chen, K.Aihara, &Synchronization of Coupled Nonidentical Genetic Oscillators&, Physical Biology, 3, 37-44, 2006.
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 - .
X-S.Zhang, R-S. Wang, L-Y. Wu, L. Chen, &Models and Algorithms for Haplotyping Problem,&Current Bioinformatics, 1, 105-114, 2006.
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.
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.
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, , 2006.
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, , 2006.
Z. Jing, R. Wang, L.Chen, J.Deng, &Attractive Regions in Power Systems by Singular Perturbation Analysis,& DOI 10.3-7429-28, Differential Equations with Symbolic Computation, 2006.
S.Fan, L.Chen, &Short-Term Load Forecasting Based on an Adaptive Hybrid Method,& IEEE Trans. on Power Systems, 21, 392- 401, 2006.
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.
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.
T. Zhou,L.Chen, K.Aihara, &Molecular Communication through Stochastic Synchronization Induced by Extracellular Fluctuations,& Physical Review Letter, 95, 05.
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.
T.Zhou, L.Chen, R.Wang, &A mechanism of synchronization in interacting multi-cell genetic systems,& Physica D, 211, 107-127, 2005.
Z.Li, W.Zhou, X.Zhang, L.Chen, &A Parsimonious Tree-Grow Method for Haplotype Inference,&Bioinformatics, 21, , 2005.
T.Zhou, L.Chen, R.Wang, &Excitation functions of coupling,& Physical Review E, 71, 05.
R.Wang, L.Chen, &Synchronizing genetic oscillators by signalling molecules,&Journal of Biological Rhythms, 20, 257-269, 2005.
L.Chen, R.Wang, T.Zhou, K.Aihara,&Noise-induced Cooperative Behavior in a Multi-Cell System,& Bioinformatics, Vol.21, , 2005.
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.
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.
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.
S.Fan, C.Mao, L.Chen, &Peak load forecasting using the self-organizing map&, 640-647, Advances in Neural Networks, Springer, 2005.
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.
Z.Li, X.Zhang,L.Chen, &Unique Optimal Foldings of Protein on a Triangular Lattice,& Journal of Applied Bioinformatics, Vol.4, 105-116, 2005.
L.Chen, T.Zhou, Y.Tang, &Protein Structure Alignment by Deterministic Annealing,& Bioinformatics, Vol.21, 51-62, 2005.
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.
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.
T.Zhou, L.Chen, R.Wang, K.Aihara, Intercellular Communications Induced by Random Fluctuations, Genome Informatics, Vol.15, No.2, 223-233, 2004.
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.
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.
L. Chen, R. Wang, T. Kobayashi, K.Aihara, &Dynamics of gene regulatory networks with cell division cycle,& Physical Review E, Vol. 70, 04.
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.
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.
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.
T.Kobayashi, L.Chen, K.Aihara, &Modeling Genetic Switches with Positive Feedback Loops,&Journal of Theoretical Biology, Vol.221, pp.379-399, 2003.
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.
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.
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.02.
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., 2002.
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.
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.
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.
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.
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.
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.
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.
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.
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. , 2000.
L.Chen, et al., &Optimal Operation of Power Systems Constrained by Transient Stability,&Transactions IEE of Japan, Vol. 120-B, No.12, pp. , 2000.
L.Chen, et al., &Analysis of Nodal Prices for Power Systems,& Transactions IEE of Japan, Vol.120-B, No.5, pp.686-693, 2000.
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.
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.
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.
L.Chen, S.Matoba, et al., &Surrogate Constraint Method for Optimal Power Flow,& IEEE Transactions on Power Systems, Vol.13, No.3, pp.98.
L.Chen, H.Susuki, et al., &Mean Field Theory for Optimal Power Flow,& IEEE Transactions on Power Systems,Vol.12, No.4, pp., 1997.
L.Chen, K.Aihara, &Chaos and Asymptotical Stability in discrete-time neural networks&, Physica D, Vol.104, pp.286-325, 1997.
L.Chen, et al &A Comparison of Reliability Evaluation Techniques for Power Systems,&Transactions of IEE Japan, Vol.116-B,No.3, 1996.
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.
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.
L.Chen, K.Aihara, &Chaotic simulated annealing and combinatorial optimization,& Journal of Computation Technology, Vol.25, No.2, pp.20-28, 1994.
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.
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.
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., August 1991.
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.
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., November 1990.
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.
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 250 conference papers), omission.