陈洛南 教授

文章出处: 作者: 发布时间: 2015-02-13 访问次数: 673

Name : Luonan CHEN

Current position:

Research Professor, Executive Director, Key Laboratory of Systems Biology, Shanghai

Institutes for Biological Sciences, Chinese Academy of Sciences, China

Address: Yueyang Road 320, Shanghai 200031, China.

Phone (office): (China) TEL: +86-21-5492-0100; Fax: +86-21-5492-0120.

E-mail: lnchen@sibs.ac.cn

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, IEEE Transactions on Systems, Man, and Cybernetics: Systems,

Associate Editor, Neural Processing Letters,

Associate Editor, BMC Research Notes,

Editorial Board Member, IET Systems Biology,

Editorial Board Member, Journal of Molecular Cell Biology,

Editorial Board Member, Mathematical Biosciences,

Editorial Board Member, Journal of Theoretical Biology,

Editorial Board Member, Journal of Royal Society Interface,

Editorial Board Member, Quantitative Biology,

Associate Editor, 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, International Journal of Bioinformatics Research and Applications,

Editorial Board Member, Journal of Systems Science and Complexity

Editor, Encyclopedia of Systems Biology, Springer.

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

  Editor, Methods, Special Issue on Systems Biology with Omics Data, 2014.

  Editor, Journal of Theoretical Biology, Special Issue on Network Biomarkers, 2014.

  Co-editor, BMC Systems Biology, Special Issue-3 on Computational Systems Biology, 2013.

  Editor, Journal of Molecular Cell Biology, Special Issue on Systems Biology for Complex

  Diseases, 2012.

  Co-editor, BMC Systems Biology, Special Issue-2 on Computational Systems Biology, 2012.

  Co-editor, IEEE/ACM Trans. on Computational Biology and Bioinformatics, Special Sec-

  tion 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, 2012.

Co-editor, BMC Systems Biology, Special Issue-1 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)

Co-Chair, International Symposium of Optimization and Systems Biology (OSB 2007,2008,2009),

http://www.aporc.org/OSB/2009/Committees.php

Co-Chair, International Conference on Intelligent Computing (ICIC),

Co-Chair of International Committee, International Conference on Life System Modeling

and Simulation (LSMS),

General Co-Chair, International Conference on Bio-Science and Bio-Technology (BSBT 2008),

Chair of Workshop, International Symposium on Bioinformatics Research and Applications

(ISBRA),

Vice Chair, The IEEE International Conference on Bioinformatics and Biomedicine 2008,

2009 (BIBM2008, BIBM2009),

Symposium Chair, International Congress on Cell Biology (ICCB’08).

Program Committee, ISMB 2008, 2009.

Co-organizer and International coordinators, KITPC programs: Emergent behaviour of

biomolecular ensembles and networks, 2010.7.5 - 2010.8.31.

Co-Chair, Genome Informatics Workshop (GIW2010), 2010.

Co-Chair, 2010 International Conference on Computational Systems Biology, 2010.

Chairman, LSMS 2010 and ICSEE 2010 INTERNATIONAL PROGRAM COMMITTEE,

http://lsms-icsee-2010.org/

Co-Chair, Program Committee of the 2010 IEEE International Conference on Bioinformatics

& Biomedicine (IEEE BIBM 2010).

Co-Chair of Organizing Committee, Genome Informatics Workshop (GIW2011), 2011.

http://www.snubi.org/TBC2011/

Co-Chair, 2011 IEEE International Conference on Systems Biology, 2011.

http://www.aporc.org/ISB/2011/index.php

Co-Chair, 2011 Translational Bioinformatics Conference, 2011.

http://www.snubi.org/TBC2011/

Co-Chair, 2012 IEEE International Conference on Systems Biology, 2012.

http://www.aporc.org/ISB/2012/index.php

Co-Chair, 2012 The 1st International Conference on Translational Biomedical Informatics,

2012.

http://ictbi.imed-cn.org/english/index.html

Co-Chair, 2012 Translational Bioinformatics Conference, 2012.

http://www.snubi.org/TBC2012/

Co-Chair, 2013 InCoB2013 - 12th International Conference on Bioinformatics, 2013.

http://ictbi.imed-cn.org/incob2013/

Co-Chair, 2013 IEEE International Conference on Systems Biology, 2013.

http://www.aporc.org/ISB/2013/index.php

Co-Chair, 2013 The 2nd International Conference on Translational Biomedical Informatics,

2013.

http://ictbi.imed-cn.org/ictbi2013/

Co-Chair, 2013 COLD SPRING HARBOR ASIA CONFERENCES: Frontiers in Bioinfor-

matics and Computational Biology.

https://www.csh-asia.org/13bioinfo.html

C0-Chair, 2014 Asia Pacific Bioinformatics Conference: APBC2014.

http://admis.fudan.edu.cn/apbc2014/

C0-Chair, 2014 International Conference on Computational Systems Biology, Translational

Bioinformatics Conference.

http://www.aporc.org/ISB/2014/index.php

Research and professional experience

1991-1994 : Senior Engineer at the Scientific Systems Department, JPBS (Tokyo, Japan).

1994-1997 : Project manager at JPBS.

1995-1997 : Concurrent Associate professor at the Department of Electrical Engineering and

Electronics, Tsinghua University, Beijing, China.

1997-2000 : Associate professor at the Department of Electrical Engineering and Electronics,

Osaka Sangyo University.

2000-2002 : Visiting Professor at the Department of Computer Science, University of Cali-

fornia, Los Angeles (UCLA), USA.

2002- 2010 : Professor at the Department of Electrical Engineering and Electronics, Osaka

Sangyo University.

2006-2009: Concurrent Professor, Director, Institute of Systems Biology, Shanghai Univer-

sity, China.

2009-present: Research Professor, Institute of Industrial Science, The University of Tokyo,

Japan.

2009-present: Professor, Executive Director, Key Laboratory of Systems Biology, Shang-

hai Institutes for Biological Sciences, Chinese Academy of Sciences, China

Languages

Chinese, English, Japanese in written and spoken

Areas of Research

Systems Biology, Systems Science, Computational Biology

SELECTED PUBLICATIONS

Books (Monographs)

Luonan Chen, Ruisheng Wang, Xiang-Sun Zhang, Biomolecular Networks: Methods and

Applications in Systems Biology, John Wiley & Sons, 2009.

Luonan Chen, Ruiqi Wang, Chunguang Li, Kazuyuki Aihara, Modelling Biomolecular Net-

works in Cells: Structures and Dynamics, Springer-Verlag, London, 2010.

Luonan Chen, Rui Liu, Xiangdong Wang, Kazuyuki Aihara, Dynamical Network Biomarkers,

Springer-Verlag, to be published in 2015.

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 Applica-

tions, 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: Appli-

cations 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).

Patents

System and method for operating power systems utilizing optimal power flow, US Patent,

US 6625520 B1. September 23, 2003.

Decomposition method for nodal prices in power systems, Japan, JP 2000-72531. March 15,

2008.

Computational method of transfer capability for transmission systems, Japan Patent, JP

3862970, 2007.

Dynamical network biomarkers for complex diseases, Japan, 110000947, 2012-233886, (in

submission).

Software and Computational Tools

1 GRNInfer: (Gene Regulatory Network Inference Tool:)

2 GNTInfer: (Gene Regulatory Network Reconstruction Tool with compound Targets:)

3 TRNInfer: (Inferring transcriptional regulatory networks from high-throughput data: )

4 InferPPI: (Inferring protein-protein interactions by parsimony principle: )

5 MDCinfer: (Inferring protein-protein interactions based on multi-domain Cooperation: )

6 MNAligner: (Molecular Network Aligner: )

7 MetaILP: (Detecting drug targets in metabolic networks by integer linear programming: )

8 Samo: (Protein Structure Alignment tool based on Multiple Objective optimization: )

9 AGPS: (Annotating Genes with Positive Samples: )

10 PTG: (Parsimonious Tree-Grow method for haplotype inference:)

11 MILPs : (Identifying differentially expressed pathways via a mixed integer linear pro-

gramming model : )

12PRNA: (Protein-RNA Binding-Site Prediction RNA)

13. FPPI: (Fusarium graminearum PPI )

14. NOA: (Network Ontology Analysis )

15. ellipsoidFN: (Identifying a heterogeneous set of cancer biomarkers based on gene expres-

sions )

16. APG: (Quantifying Regulatory Signals in Complex Biological Systems )

17. NARROMI: (Gene regulatory network inference )

18. EdgeBiomarker: (Edge Biomarker )

19. CMIP: (Genome-scale gene regulatory network reconstruction algorithm )

20. DNB: (Dynamical network biomarker )

Journal Papers

References

[1] Wanwei Zhang, Tao Zeng, Xiaoping Liu, Luonan Chen. Diagnosing phenotypes of single-

sample individuals by edge biomarkers. Journal of Molecular Cell Biology, 2015.

[2] Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura, Luonan Chen, and

Kazuyuki Aihara. Clustered Model Reduction of Positive Directed Networks. Automatica,

2015.

[3] 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.

[4] 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.2014.2329731, 2015.

[5] Jiang Xie, Wang Ding, Luonan Chen, Qiang Guo and Wu Zhang. Advances in Protein Contact

Map Prediction Based on Machine Learning. Medicinal Chemistry, 2015.

[6] Xingming Zhao, Keqin Liu, Luonan Chen. Identifying cancer-related microRNAs based on

gene expression data. Bioinformatics, doi:10.1093/bioinformatics/btu811, 2014.

[7] 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/gku1315, 2014.

[8] Huanfei Ma, Kazuyuki Aihara, Luonan Chen. Detecting Causality from Nonlinear Dynamics

with Short-term Time Series. Scientific Reports, doi:10.1038/srep07464, 2014.

[9] Yixue Li, Luonan Chen. Big Biological Data: Challenges and Opportunities. Genomics, Pro-

teomics & Bioinformatics, 12, 187C189, 2014.

[10] 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.2014.08.002, 2014.

[11] Andrew E Teschendorff, Xiaoping Liu, Helena Caren, Steve Pollard, Stephan Beck,

Martin Widschwendter,Luonan Chen. The dynamics of DNA methylation covari-

ation patterns in carcinogenesis. PLoS Computational Biology,10(7):e1003709.

doi:10.1371/journal.pcbi.1003709, 2014.

[12] Zhenshu Wen, Wanwei Zhang,Tao Zeng, Luonan Chen. MCentridFS: a tool for identifying

module biomarkers for multi-phenotypes from high-throughput data. Molecular BioSystems,

DOI: 10.1039/C4MB00325J, 2014.

[13] Huanfei Ma, Tianshou Zhou, Kazuyuki Aihara, Luonan Chen. Predicting Time-series from

Short-term High-dimensional Data. International Journal of Bifurcation and Chaos, Vol. 24,

No. 12 (2014) 1430033, DOI: 10.1142/S021812741430033X, 2014.

[14] 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 lympho-

cytes. Journal of Cellular and Molecular Medicine, 2014 May;18(5):801-10. doi: 10.1111/jcm-

m.12302.

[15] Xiaodan Wu, Luonan Chen and Xiangdong Wang. Network biomarkers, interaction net-

works and dynamical network biomarkers in respiratory diseases. Clinical and Translational

Medicine 2014, 3:16 doi:10.1186/2001-1326-3-16.

[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,

doi: 10.1007/s11427-014-4757-4, 2014.

[17] C. George Priya Doss, Chiranjib Chakraborty, Luonan Chen, and Hailong Zhu. Integrating

In Silico Prediction Methods, Molecular Docking, and Molecular Dynamics Simulation to

Predict the Impact of ALK Missense Mutations in Structural Perspective. BioMed Research

International, http://dx.doi.org/10.1155/2014/895831, 2014.

[18] Xiaodan Wu, Luonan Chen and Xiangdong Wang. Network biomarkers, interaction net-

works and dynamical network biomarkers in respiratory diseases. Clinical and Translational

Medicine, 3:16, 2014.

[19] WanweiZhang,TaoZeng,LuonanChen.EdgeMarker:identifyingdifferentiallycorrelatedmolecule

pairsasedge-biomarkers.JournalofTheoreticalBiology,DOI:10.1016/j.jtbi.2014.05.041, 2014.

[20] B.Liu, Z.Yuan, K.Aihara, L.Chen. Reinitiation enhances reliable transcriptional responses in

eukaryotes. J. R. Soc. Interface, 20140326, 2014.

[21] 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/srep04819, 2014.

[22] Rui Liu, Xiangtian Yu , Xiaoping Liu, Dong Xu, Kazuyuki Aihara and Luonan Chen. I-

dentifying critical transitions of complex diseases based on a single sample. Bioinformatics,

DOI:10.1093/bioinformatics/btu084, 2014.

[23] Tao Zeng, Chuan-chao Zhang, Wanwei Zhang, Rui Liu, Juan Liu, Luonan Chen. Deci-

phering early development of complex diseases by progressive module network. Methods,

http://dx.doi.org/10.1016/j.ymeth.2014.01.021, 2014.

[24] 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, 9(4): e91315. doi:10.1371/journal.pone.00913152014.

[25] Duojiao Wu, Xiaoping Liu, Chen Liu, Zhiping Liu, Ming Xu, Ruiming Rong, Mengjia

Qian, Luonan Chen, Tongyu Zhu. Network analysis reveals roles of inflammatory factors

in different phenotypes of kidney transplant patients. Journal of Theoretical Biology, DOI:

10.1016/j.jtbi.2014.03.006, 2014.

[26] 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, DOI: 10.1002/ijc.28584, Vol.134, pp.2646-2655, 2014.

[27] 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.7473, 2014.

[28] 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.

[29] Xiangtan Yu, Guozheng Li, Luonan Chen. Prediction and early diagnosis of complex diseases

by edge-network. Bioinformatics, doi: 10.1093/bioinformatics/btt620, 2013.

[30] Tao Zeng, Shao-yan Sun, Yong Wang, Hailong Zhu, Luonan Chen. Network biomark-

ers reveal dysfunctional gene regulations during disease progression. FEBS Journal,

doi:10.1111/febs.12536, 2013.

[31] 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, 2013.

[32] Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology in the big data

era. BMC Systems Biology, doi:10.1186/1752-0509-7-S2-S1, 2013.

[33] Shao-Yan Sun, Zhi-Ping Liu, Tao Zeng, Yong Wang, and Luonan Chen. Spatio-temporal anal-

ysis of type 2 diabetes mellitus based on differential expression networks. Scientific Reports,

DOI: 10.1038/srep02268, 2013.

[34] 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.

[35] 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.21293, 2013.

[36] 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.

[37] 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:

10.2174/1381612819666140110114902, 2014.

[38] Jiang Xie, Zhonghua Zhou, Kai Lu, Luonan Chen, Wu Zhang. Visualization of Biomolecular

Networks Comparison on Cytoscape. Tsinghua Science and Technology, 2013.

[39] Zikai Wu, Yong Wang, Luonan Chen. A New Framework for Drug Repositioning by In-

corporating Functional Information. IET Systems Biology, 7(5):188-94, doi: 10.1049/iet-

syb.2012.0064, 2013.

[40] Meiyi Li, Tao Zeng, Rui Liu, 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.

[41] Rui Liu, Kazuyuki Aihara, Luonan Chen. Dynamical network biomarkers for identifying

critical transitions of biological processes. Quantitative Biology, DOI:10.1007/s40484-013-

0008-0, 2013.

[42] Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen. A Sequence-based Computational Ap-

proach to Predicting PDZ Domain-Peptide Interactions. BBA - Proteins and Proteomics,

2013.

[43] Zikai Wu, Yong Wang, Luonan Chen. Network-Based Drug Repositioning. Molecular BioSys-

tems, DOI:10.1039/C3MB25382A, 2013.

[44] Chenglei Sun, Zheng-Zheng Shi, Xiaobo Zhou, Luonan Chen, Xing-Ming Zhao. Predic-

tion of S-Glutathionylation Sites Based on Protein Sequences. PLoS ONE 8(2): e55512.

doi:10.1371/journal.pone.0055512, 2013.

[45] 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/srep01097, 2013.

[46] George Priya Doss C, Nagasundaram N, Chiranjib Chakraborty, Luonan Chen and Hailong

Zhu. Extrapolating the effect of deleterious nonsynonymous single nucleotide polymorphisms

in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics ap-

proach, Human Genomics, 7:10, http://www.humgenomics.com/content/7/1/10, 2013.

[47] Zhiyuan Yang, Yan Zhang, and Luonan Chen. Investigation of anti-cancer mechanisms by

comparative analysis of naked mole rat and rat. BMC Systems Biology, doi:10.1186/1752-

0509-7-S2-S5, 2013.

[48] 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, 7(5):143-52, doi: 10.1049/iet-syb.2012.0062, 2013.

[49] 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, 7242, 2013.

[50] 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: 10.1039/c2mb25292a, 2013.

[51] XiaopingLiu,JiguangWang,LuonanChen.Whole-exome sequencing reveals recurrent somatic mutation networks in cancer. Cancer Letters,http://dx.doi.org/10.1016/j.canlet.2012.11.002, 2013.

[52] 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, doi:10.1093/nar/gks1288, 2013.

[53] 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:10.1186/1755-8794-6-S2-S8, 2013.

[54] Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Batrice Duval, Jean-Michel Richer, Xing-Ming

Zhao, Jin-Kao Hao, and Luonan Chen. NARROMI: a noise and redundancy reduc-

tion technique improves accuracy of gene regulatory network inference. Bioinformatics,

DOI:10.1093/bioinformatics/bts619, 2012.

[55] 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, 2, 813;

DOI: 10.1038/srep00813, 2012.

[56] Bengong Zhang, Luonan Chen, Kazuyuki Aihara. Incremental stability analysis of stochastic

hybrid systems. Nonlinear Analysis (Series B: Real World Applications), 14, 1225-1234, 2012.

[57] 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.

[58] Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen. An integrated ap-

proach 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-

001168, 2012.

[59] 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), e41854, 2012.

[60] Luonan Chen, Rui Liu, Zhiping Liu, Meiyi Li, Kazuyuki Aihara. Detecting early-warning sig-

nals for sudden deterioration of complex diseases by dynamical network biomarkers. Scientific

Reports. 2, 342; DOI:10.1038/srep00342 (2012).

[61] Zhiping Liu, Luonan Chen. Proteome-wide prediction of protein-protein interactions from

high-throughput data. Protein & Cell, 3(7):508-20. doi: 10.1007/s13238-012-2945-1, 2012.

[62] 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, 6:80, 2012.

[63] Ke-Qin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao. Identifying dysreg-

ulated pathways in cancers from pathway interaction networks. BMC Bioinformatics, 13:126

doi:10.1186/1471-2105-13-126, 2012.

[64] 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 tumori-

genesis. Journal of Molecular Cell Biology, 4(4):197-206, doi:10.1093/jmcb/mjs029, 2012.

[65] Jiajun Zhang,Luonan Chen,and Tianshou Zhou. Analytical Distribution and Tunability of

Noise in a Model of Promoter Progress. Biophysical Journal, Vol.102, 1247C1257, 2012.

[66] Luonan Chen, Jiarui Wu. Systems biology for complex diseases. Journal of Molecular Cell

Biology, doi:10.1093/jmcb/mjs022, 2012.

[67] H.J. Li, J.H. Zhang, Z.P. Liu, L. Chen, X.S. Zhang. Identifying overlapping communities in

social networks using multi-scale local information expansion. The European Physical Journal

B, 85: 190, DOI: 10.1140/epjb/e2012-30015-5, 2012.

[68] Danning He, Zhiping Liu, Masao Honda, Shuichi Kaneko, Luonan Chen. Coexpression net-

work 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):140-52, 2012.

[69] Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Modelling biological systems from

molecules to dynamical networks. BMC Systems Biology, doi:10.1186/1752-0509-6-S1-S1,

2012.

[70] 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.

[71] 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:10.1186/1471-2105-13-S7-S6, BMC Bioinformatics,

2012.

[72] 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.

[73] 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:10.1209/0295-5075/97/48005, 2012.

[74] Tao Zeng and Luonan Chen. Tracing dynamic biological processes during phase transition.

BMC Systems Biology, doi:10.1186/1752-0509-6-S1-S12, 2012.

[75] Guanyin Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu, 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:10.1186/1752-0509-6-S1-S2, 2012.

[76] 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.

[77] 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.

[78] 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/bioin-

formatics/btr626, 2011.

[79] Ruiqi Wang, Kaihui Liu, Luonan Chen and Kazuyuki Aihara. Neural fate decision-

s mediated by trans-activation and cis-inhibition in Notch signaling. Bioinformatics,

doi:10.1093/bioinformatics/btr551, 2011.

[80] Achyut Sapkota, Xiaoping Liu, Xingming Zhao, Yongwei Cao, Jingding Liu, Zhiping Liu, Lu-

onan Chen. DIPOS: Database of Interacting Proteins in Oryza Sativa. Molecular BioSystems,

DOI: 10.1039/C1MB05120B, 2011.

[81] 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.

[82] 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.

[83] 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.

[84] Graziano Chesi, Luonan Chen. Systems Biology. Int. J. Robust. Nonlinear Control, 21:1729,

2011.

[85] D. Liu, X. Chang, Z.Liu, L.Chen, R.Wang. Bistability and oscillations in gene regulation medi-

ated by small noncoding RNAs. PLoS ONE 6(3): e17029. doi:10.1371/journal.pone.0017029,

2011.

[86] 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

[87] 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.

[88] 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.

[89] 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.

[90] 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.

[91] Hong-Bo Lei, Xin Wang, Ruiqi Wang, Xin-Guang Zhu, Luonan Chen, Ji-Feng Zhang. A pa-

rameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism.

Asian Journal of Control, Volume 13, Issue 5, pages 611C624, September 2011.

[92] Luonan Chen, James Lam, Zidong Wang. ANALYSIS AND CONTROL OF BIOLOGICAL

NETWORKS. Asian Journal of Control, DOI: 10.1002/asjc.424, 2011.

[93] 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.

[94] Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion.

Asian Journal of Control, Volume 13, Issue 5, pages 738C748, September 2011

[95] 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.

[96] 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.

[97] 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.

[98] Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology.

BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.

[99] 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.

[100] 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.

[101] 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.

[102] Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen. FGsub: Fusarium gramin-

earum protein subcellular localization prediction from primary structures. BMC Systems

Biology, doi:10.1186/1752-0509-4-S2-S12, 2010.

[103] 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.

[104] 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.

[105] 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.

[106] 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.

[107] Xingming Zhao, Kazuyuki Aihara, Luonan Chen. A discriminative approach to identifying

domain-domain interactions from protein-protein interactions. PROTEINS: Structure, Func-

tion, and Bioinformatics, 78(5), 1243-1253, 2009.

[108] 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.

[109] 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 Compu-

tational Biology, PLoS Comput Biol 5(9): e1000521. doi:10.1371journal.pcbi.1000521, 2009.

[110] Zhao Song, Luonan Chen, Dong Xu. Confidence Assessment for Protein Identification by

Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.

[111] 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.

[112] 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.

[113] R.Wang, G.Jin, X-S. Zhang, L.Chen. Modelling post-transcriptional regulation of microR-

NAs in E.coli. BMC Bioinformatics, 10(Suppl 4):S6, 2009.

[114] 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.

[115] 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.

[116] 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.

[117] 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.

[118] Jianwei Shen, Zengrong Liu, Weixing Zheng, Fengdan Xu, Luonan Chen. Oscillatory dy-

namics in a simple gene regulatory network mediated by small RNAs. Physica A: Statistical

Mechanics and its Applications. 388(14), 2995-3000, 2009.

[119] 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 can-

cer. IET Systems Biology, 3(6), 505-512, 2009.

[120] B.Wang, L.Chen, K.Aihara. Limited ability driven phase transitions in the coevolution pro-

cess in Axelrod’s model. Physics Letters A, 373(17), 1519-1523, 2009.

[121] L-Y.Wu, Z.Li, R.Wang, X-S.Zhang, L.Chen. Self-organizing map approaches for the haplo-

type assembly problem Mathematics and Computers in Simulation. Mathematics and Com-

puters in Simulation,79(10), 3026-3037, 2009.

[122] 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.

[123] H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with

preferential flow. Physical Review E, 79:026107, 2009.

[124] 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.

[125] Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data.

Mol. Cells, 27, 271-277, 2009.

[126] 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.

[127] 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.

[128] 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.

[129] 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.

[130] X. Zhao, R.Wang, L. Chen, K.Aihara. Uncovering signal transduction networks from high-

throughput data by integer linear programming. Nucleic Acids Research, Vol.36, No.9, e48,

doi:10.1093/nar/gkn145, 2008.

[131] 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.

[132] 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.

[133] 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.

[134] B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Euro-

physics Letters. 83, 28006, 2008.

[135] 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.

[136] T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18,

No.3, 037126, 2008.

[137] Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community

detection. Physical Review E, 77, 036109, 2008.

[138] 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.

[139] X.Zhao, Y.Wang, L.Chen, K.Aihara. Protein domain annotation with integration of hetero-

geneous information sources. Proteins: Structure, Function, and Bioinformatics, Vol.72, no.1,

461 - 473, 2008.

[140] G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network.

Neurocomputing, 71, 2794-2805, 2008.

[141] 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.

[142] R.Wang, C.Li, L.Chen, K.Aihara. Modeling and Analyzing Biological Oscillations in Molec-

ular Networks. Proceedings of The IEEE, Vol.96, 1361-1385, 2008.

[143] 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.

[144] 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.

[145] 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.

[146] 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.

[147] 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.

[148] 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

[149] 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.

[150] 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.

[151] 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.

[152] 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.

[153] R. Wang, Y.Wang, X-S. Zhang, L.Chen. Inferring Transcriptional Regulatory Networks from

High-throughput Data. Bioinformatics, 23(22):3056-3064, 2007.

[154] X.Zhao, L.Chen, K.Aihara. Protein classification with imbalanced data. Proteins: Structure,

Function, and Bioinformatics, Vol.70, 1125 - 1132, 2007.

[155] L.Chen, Y.Wang, M.Fei, Z.Liu. Systems Biology from Theoretical and Engineering Perspec-

tive. SCIENCE & TECHNOLOGY REVIEW, Vol.25, No.10, 5-10, 2007.

[156] C. Li, L. Chen, K. Aihara. Stochastic Stability of Genetic Networks with Disturbance At-

tenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.

[157] Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer

quadratic programming. Bioinformatics, 23, 1631-1639, 2007.

[158] 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.

[159] R.Wang, L.Chen, K.Aihara. Detection of Cellular Rhythms and Global Stability within

Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.

[160] C.Li, L.Chen, K.Aihara. Stochastic Synchronization of Genetic Oscillator Networks. BMC

Systems Biology, doi:10.1186/1752-0509-1-6, 2007.

[161] 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.

[162] 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.

[163] C.Li, L.Chen, K.Aihara. A systems biology perspective on signal processing in genetic net-

work motifs. IEEE Signal Processing Magazine, Vol.24, No.2, 136-147, 2007.

[164] Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-Feng Wan, Laurent Brechenmacher,

Nengbing Tao, David Emerich, Gary Stacey, Dong Xu. Development and Assessment of

Scoring Functions for Protein Identification Using Peptide Mass Fingerprinting Data. ELEC-

TROPHORESIS, 28, 864-870, 2007.

[165] 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.

[166] 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.

[167] 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.

[168] 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.

[169] Y.Wang, X-S.Zhang, L.Chen. Supervised Classification of Protein Structures, International

Journal of Bioinformatics Research and Applications, Vol.3, No.2, 2006.

[170] 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.

[171] Y.Wang, T.Joshi, D.Xu, X-S.Zhang, L.Chen, Inferring Gene Regulatory Networks from

Multiple Microarray Datasets, Bioinformatics, 22, 2413 - 2420, 2006.

[172] 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.

[173] 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.

[174] 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.

[175] R.Wang, L.Chen,K.Aihara, Synchronizing a Multicellular System by External Input: An

Artificial Control Strategy,Bioinformatics, 22, 1775 - 1781, 2006.

[176] R.Wang, L.Chen, K.Aihara, ”Construction of Genetic Oscillators with Interlocked Feedback

Networks”, Journal of Theoretical Biology, Vol.242, 454-463, 2006.

[177] C.Li, L.Chen, K.Aihara, ”Synchronization of Coupled Nonidentical Genetic Oscillators”,

Physical Biology, 3, 37-44, 2006.

[178] 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.

[179] X-S.Zhang, R-S. Wang, L-Y. Wu, L. Chen, ”Models and Algorithms for Haplotyping Prob-

lem,” Current Bioinformatics, 1, 105-114, 2006.

[180] 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.

[181] T.Wachi, S.Fukutome, L.Chen, Y.Makino, ”Decomposition of Market Clearing Price in Elec-

tricity Markets,” Transactions IEE of Japan, Vol. 126-B, No.3, pp.297-307, 2006.

[182] 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.

[183] 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.

[184] Z. Jing, R. Wang, L.Chen, J.Deng, ”Attractive Regions in Power Systems by Singular Per-

turbation Analysis,” DOI 10.1007/3-7643-7429-28, Differential Equations with Symbolic Com-

putation, 2006.

[185] S.Fan, L.Chen, ”Short-Term Load Forecasting Based on an Adaptive Hybrid Method,” IEEE

Trans. on Power Systems, 21, 392- 401, 2006.

[186] 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.

[187] L.Chen, L-Y.Wu, R.Wang, Y.Wang, S.Zhang, X-S.Zhang, ”Comparison of Protein Struc-

tures by Multi-Objective Optimization,” Genome Informatics, Vol.16, No.2, pp.114-124, 2005.

[188] T. Zhou,L.Chen, K.Aihara, ”Molecular Communication through Stochastic Synchronization

Induced by Extracellular Fluctuations,” Physical Review Letter, 95, 178103, 2005.

[189] R.Li, R.Yokoyama, L.Chen, ”Pricing for Load and Wheeling Charge Considering Trans-

mission Paths in Deregulated Power Markets” International Journal of Electrical Power &

Energy Systems, Vol.27, pp.496-505, 2005.

[190] T.Zhou, L.Chen, R.Wang, ”A mechanism of synchronization in interacting multi-cell genetic

systems,” Physica D, 211, 107-127, 2005.

[191] Z.Li, W.Zhou, X.Zhang, L.Chen, ”A Parsimonious Tree-Grow Method for Haplotype Infer-

ence,” Bioinformatics, 21, 3475-3481, 2005.

[192] T.Zhou, L.Chen, R.Wang, ”Excitation functions of coupling,” Physical Review E, 71,

066211, 2005.

[193] R.Wang, L.Chen, ”Synchronizing genetic oscillators by signalling molecules,” Journal of

Biological Rhythms, 20, 257-269, 2005.

[194] L.Chen, R.Wang, T.Zhou, K.Aihara,”Noise-induced Cooperative Behavior in a Multi-Cell

System,” Bioinformatics, Vol.21, 2722-2729, 2005.

[195] T.Zhou, L.Chen, Y.Tang, X.Zhang,”Aligning Multiple Protein Structures by Determinis-

tic Annealing,” Journal of Bioinformatics and Computational Biology, Vol.3, No.4, 837-860,

2005.

[196] 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.

[197] 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.

[198] S.Fan, C.Mao, L.Chen, ”Peak load forecasting using the self-organizing map”, 640-647,

Advances in Neural Networks, Springer, 2005.

[199] Geerli, L.Chen, I.Kurihara, K.Takahasi, ”Cooperative Game Theory Applied to Transmis-

sion Expansion Cost Allocation for Congestion Relief,” International Journal of Electrical

Power & Energy Systems, Vol.27, 61-67, 2005.

[200] Z.Li, X.Zhang,L.Chen, ”Unique Optimal Foldings of Protein on a Triangular Lattice,” Jour-

nal of Applied Bioinformatics, Vol.4, 105-116, 2005.

[201] L.Chen, T.Zhou, Y.Tang, ”Protein Structure Alignment by Deterministic Annealing,” Bioin-

formatics, Vol.21, 51-62, 2005.

[202] 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.

[203] 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.

[204] T.Zhou, L.Chen, R.Wang, K.Aihara, Intercellular Communications Induced by Random

Fluctuations, Genome Informatics, Vol.15, No.2, 223-233, 2004.

[205] 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.

[206] 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.

[207] L. Chen, R. Wang, T. Kobayashi, K.Aihara, ”Dynamics of gene regulatory networks with

cell division cycle,” Physical Review E, Vol. 70, 011909, 2004.

[208] P.Charusanti, X.Hu, L.Chen, D.Neuhauser, J.Distefano, A mathematical model of BCR-

ABL 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.

[209] 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.

[210] 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.

[211] T.Kobayashi, L.Chen, K.Aihara, ”Modeling Genetic Switches with Positive Feedback Loop-

s,” Journal of Theoretical Biology, Vol.221, pp.379-399, 2003.

[212] 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.

[213] R. Yuan, Z.Jing, L.Chen, ”UNIFORM ASYMPTOTIC STABILITY OF HYBRID DYNAM-

ICAL SYSTEMS WITH DELAY,” IEEE Trans. on Automatic Control, Vol.48, No.2, pp.344-

348, 2003.

[214] 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.

[215] 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.

[216] 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.

[217] 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.

[218] 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.

[219] L.Chen, K.Aihara, ”Chaotic dynamics of neural networks and its application to combinato-

rial optimization,” Journal of Dynamical Systems and Differential Equations, invited review

paper, vol.9, no.3, pp.139-168, 2001.

[220] L.Chen, K.Aihara, ”Stability and Bifurcation Analysis of Differential-Difference-Algebraic

Equations,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Ap-

plications. Vol.48, No.3, pp.308-326,2001.

[221] 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.

[222] 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.

[223] 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.

[224] 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.

[225] 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.

[226] L.Chen, et al., ”Analysis of Nodal Prices for Power Systems,” Transactions IEE of Japan,

Vol.120-B, No.5, pp.686-693, 2000.

[227] Geerli, L.Chen, et al., ”Negotiation Models for Electric Pricing and Load Dispatch in Elec-

tricity Market,” Transactions IEE of Japan, Vol.120-B, No.2, pp.219-226, 2000.

[228] 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.

[229] L.Chen, K.Aihara, ”Global Searching Ability of Chaotic Neural Networks,” IEEE Transac-

tions on Circuits and Systems- I: Fundamental Theory and Applications, Vol.46, No.8,pp.974-

993, 1999.

[230] 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.

[231] 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.

[232] L.Chen, K.Aihara, ”Chaos and Asymptotical Stability in discrete-time neural networks”,

Physica D, Vol.104, pp.286-325, 1997.

[233] L.Chen, et al ”A Comparison of Reliability Evaluation Techniques for Power Systems,”

Transactions of IEE Japan, Vol.116-B,No.3, 1996.

[234] 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.

[235] 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.

[236] L.Chen, K.Aihara, ”Chaotic simulated annealing and combinatorial optimization,” Journal

of Computation Technology, Vol.25, No.2, pp.20-28, 1994.

[237] 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.

[238] 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.

[239] 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.

[240] L. Chen, J. Toyoda, ”Power Arrival Evaluation of Bulk System Including Network Con-

straints Based on Linear Programming Approach,” IEEE Transactions on Power Systems,

Vol.PWRS-6, No.1, pp.37-42, February 1991.

[241] 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.

[242] 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.

[243] 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.