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陈洛南

 

姓 名:陈洛南

性 别:男

出生日期:1962-12-8

Mail地址:lnchen@sibs.ac.cn

 

个人简介

 

陈洛南(TEL021-6436-5937),中国科学院上海生命科学研究院研究员,博士生导师,中国科学院系统生物学重点实验室执行主任。 目前,在计算系统生物学领域的主要国际学术期刊都担任重要工作,在日本和美国从事科研教学工作等25年以上,近六年来,在系统生物学研究领域发表了100篇以上原创性研究论文。

 

工作经历:

1991.41997.3:日本开发计算中心,主查研究员

1997.42000.3:日本大阪产业大学电气工程与电子系,副教授

2000.42002.3:美国加州大学洛山矶分校(UCLA),访问教授

2002.42010.3:日本大阪产业大学电气工程与电子系,终身教授

2009.4~现在:日本东京大学生产技术研究所,研究教授(兼)

2009.10~现在:中科院系统生物学重点实验室执行主任、研究员

 

学术组织兼职:

1 BMC Systems Biology》,Section Editor

2 IEEE/ACM Trans. on Computational Biology and Bioinformatics》,Associate Editor

3 Neural Processing Letters, Associate Editor

4 IET Systems Biology》,编委(Editorial Board Member

5 Mathematical Biosciences》,编委(Editorial Board Member

6 Int. J. of Systems and Synthetic Biology》,编委(Editorial Board Member

7 Int. J. of Data Mining and Bioinformatics》,编委(Editorial Board Member

8 Int. J. of Bioinformatics Research and Applications, 编委(Editorial Board Member

9.      J. of Systems Science and Complexity, 编委(Editorial Board Member

10.    J. of Theoretical Biology, 编委(Editorial Board Member

11.    《系统生物学百科全书》(Encyclopedia of Systems Biology Springer出版社),编辑(Editor

12.      IEEE-SMC《系统生物学委员会》,主席(Chair

13.      中国运筹学会《计算系统生物学分会》理事长

  

主页: http://www.sysbio.ac.cn/cb/chenlab/LuonanChen.htm

http://www.iis.u-tokyo.ac.jp/cgi/teacher.cgi?prof_id=l-chen

 

 

主要研究方向为

 

1)网络系统生物学(Network Systems Biology),

2)合成系统生物学(Synthetic Systems Biology),

3)计算系统生物学(Computational Systems Biology)方面的研究。

 

采用系统工程、动力学分析、优化和数学建模的方式,结合生物信息学和现代生命科学实验,以生物复杂网络和动态行为为主线来研究生命系统。

 

 

 

近期论文

  

专著:

1 L.Chen(陈洛南), R-S.Wang, X.Zhang. Biomolecular Networks: Methods and Applications in Systems Biology, John Wiley & Sons, 2009.

2 L.Chen(陈洛南), R-Q.Wang, G.Li, K.Aihara. Modeling Biomolecular Networks in Cells: Structures and Dynamics, Springer-Verlag, 2010.

 

书籍的执笔章节:

1. 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.

2. 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.

3. 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.

4. 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.

 

编辑书籍:

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. Combinatorial Optimization by Modern Heuristic Techniques, 1997, Nikan Publish, L.Chen (coauthor).

7. Operation and Planning in Deregulated Power Systems, 2002, Tokyo DenKiDai Publish,

L.Chen (coauthor).

8. An Introduction to Environmental Systems, 2007, Denkishoin, L.Chen (coauthor).

 

2006年以后的有关的系统生物学的期刊论文:

1. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer’s disease patients. Molecular BioSystems, DOI: 10.1039/C0MB00325E, 2011.

2. Yong Wang, Xiang-Sun Zhang, Luonan Chen. Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Systems Biology, accepted, 2011.

3. Zhenping Li, Ruisheng Wang, Xiang-Sun Zhang, Luonan Chen. Drug target identification based on flux balance analysis in metabolic network. BMC Systems Biology, accepted, 2011.

4. Vasilescu Gabriel, Luonan Chen. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, accepted, 2011.

5. Huarong Zhou, Zhiping Liu, Kazu Horimoto, Luonan Chen. Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Systems Biology, accepted, 2011.

6. Hongbo Lei, Jifeng Zhang, Luonan Chen. Property of Multiple Equilibria for SSI Metabolic Module. BMC Systems Biology, accepted, 2011.

7. Hongbo Lei, Jifeng Zhang, Luonan Chen. Multi-equilibrium property of metabolic networks: Exclusion of multi-stability for SSN metabolic modules. International Journal of Robust and Nonlinear Control, accepted, 2011.

8. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen: Network-based analysis of complex diseases. IET Systems Biology, accepted, 2011.

9. 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.

10. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.

11. 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.

12. 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.

13. Zikai Wu, Xingming Zhao, Luonan Chen. A Systems biology approach to identify effective cocktail drugs. BMC Systems Biology, in press, 2010.

14. Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen. FGsub: Fusarium graminearum protein subcellular localization prediction from primary structures. BMC Systems Biology, in press, 2010.

15. Zhi-Ping Liu, Yong Wang, Luonan Chen. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer。ッs disease brains. BMC Systems Biology, in press, 2010.

16. Y-Q.Qiu, S.Zhang, X-S.Zhang, L.Chen. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics, 11:26, 2010.

17. X.Zhao, K.Aihara, L.Chen. A discriminative approach to identifying domain-domain interactions from protein-protein interactions. PROTEINS: Structure, Function, and Bioinformatics, 78(5), 1243-1253, 2009.

18. X Zhao, X.W. Zhang, W. Tang, L. Chen. FPPI: Fusarium graminearum protein-protein interaction database. Journal of Proteome Research, DOI: 10.1021/pr900415b, 2009.

19. J. Wang, S. Zhang, Y. Wang, L. Chen, X.S. Zhang. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology, PLoS Comput Biol 5(9): e1000521. doi:10.1371/journal.pcbi.1000521, 2009.

20. Z. Song, L. Chen, D. Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.

21. 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.

22. 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.

23. 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.

24. 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.

25. 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.

26. Y.Qiu, S.Zhang, X-S.Zhang, L.Chen. Identifying differentially expressed pathways via a mixed integer linear programming model. IET Systems Biology, 3(6):475-486, 2009.

27. J. Shen, Z. Liu, W. Zheng, F. Xu, L. Chen. Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs. Physica A: Statistical Mechanics and its Applications. 388(14), 2995-3000. 2009.

28. 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.

29. H. Fan, Z. Wang, L. Chen, K. Aihara. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:026107, 2009.

30. X.M. Zhao, R.S. Wang, L. Chen, K. Aihara. Automatic modeling of signaling pathways by network flow model. Journal of Bioinformatics and Computational Biology, 7(2):309-22, 2009.

31. Z.Wu, X.Zhao, L.Chen. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.

32. 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.

33. 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.

34. X. Zhao, R.Wang, L. Chen, K.Aihara. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Research, doi:10.1093/nar/gkn145, 2008.

35. 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.

36. X.Zhao, K.Aihara, L.Chen. Protein function prediction with high-throughput data. Amino Acids, DOI 10.1007/s00726-008-0077-y, 2008.

37. B. Wang, K. Aihara and L. Chen. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 28006, 2008.

38. 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.

39. T.Zhou, J. Zhang, Z. Yuan, L. Chen. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 037126, 2008.

40. Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen. Novel quantitative function for community detection. Physical Review E, 77, 036109, 2008.

41. 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.

42. 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.

43. Z.P. Liu, L.Y. Wu, Y. Wang, L. Chen and X.S. Zhang. Predicting Gene Ontology Functions from Protein's Regional Surface Structures. BMC Bioinformatics, 8:475, doi:10.1186/1471-2105-8-475, 2007.

44. G. Jin, S. Zhang, X.S. Zhang, L. 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.

45. R.S. Wang, X.S Zhang, L. Chen. Inferring transcriptional interactions and regulator activities from experimental data. Molecules and Cells, vol.24, 307-315, 2007.

46. 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.

47. R. Wang, Y.Wang, X-S. Zhang, L.Chen. Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics, 23(22):3056-3064, 2007.

48. X.Zhao, L.Chen, K.Aihara. Protein classification with imbalanced data. Proteins: Structure, Function, and Bioinformatics, Vol.70, 1125 - 1132, 2007.

49. 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.

50. R.Wang, C.Li, L.Chen, K.Aihara. Modeling and Analyzing Biological Oscillations in Molecular Networks. Proceedings of The IEEE, Vol.96, 1361-1385, 2008.

51. 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.

52. 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.

53. 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.

54. 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.

55. C. Li, L. Chen, K. Aihara. Stochastic Stability of Genetic Networks with Disturbance Attenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.

56. 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.

57. Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639, 2007.

58. 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.

59. R.Wang, L.Chen, K.Aihara. Detection of Cellular Rhythms and Global Stability within Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.

60. C.Li, L.Chen, K.Aihara. Stochastic Synchronization of Genetic Oscillator Networks. BMC Systems Biology, doi:10.1186/1752-0509-1-6, 2007.

61. 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.

62. 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.

63. Z. Song, L. Chen, A. Ganapathy, X.F. Wan, L. Brechenmacher, N. Tao, D. Emerich, G. Stacey, D. Xu. Development and Assessment of Scoring Functions for Protein Identification Using Peptide Mass Fingerprinting Data. ELECTROPHORESIS,28, 864-870, 2007.

64. 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.

65. Y.Wang, T.Joshi, D.Xu, X.S.Zhang, L.Chen, Inferring Gene Regulatory Networks from Multiple Microarray Datasets, Bioinformatics, 22, 2413 - 2420, 2006.

66. 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.

67. R.Wang, L.Chen,K.Aihara, Synchronizing a Multicellular System by External Input: An Artificial Control Strategy, Bioinformatics, 22, 1775 - 1781, 2006.

68. R.Wang, L.Chen, K.Aihara,"Construction of Genetic Oscillators with Interlocked Feedback Networks", Journal of Theoretical Biology,Vol.242, 454-463, 2006.

69. C.Li, L.Chen, K.Aihara, "Synchronization of Coupled Nonidentical Genetic Oscillators",Physical Biology, 3, 37-44, 2006.

70. 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.

71. 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.

72. 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.

 

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