Luonan Chen

Summary

Affiliation: Osaka Sangyo University
Country: Japan

Publications

  1. ncbi Biomolecular network querying: a promising approach in systems biology
    Shihua Zhang
    BMC Syst Biol 2:5. 2008
  2. ncbi Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli
    Rui Sheng Wang
    School of Information, Renmin University of China, Beijing 100872, PR China
    BMC Bioinformatics 10:S6. 2009
  3. ncbi Detecting disease associated modules and prioritizing active genes based on high throughput data
    Yu Qing Qiu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, PR China
    BMC Bioinformatics 11:26. 2010
  4. ncbi Analysis on multi-domain cooperation for predicting protein-protein interactions
    Rui Sheng Wang
    School of Information, Renmin University of China, Beijing 100872, China
    BMC Bioinformatics 8:391. 2007
  5. ncbi Gene function prediction using labeled and unlabeled data
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, 4 6 1 Komaba, Meguro, Tokyo, Japan
    BMC Bioinformatics 9:57. 2008
  6. ncbi Predicting gene ontology functions from protein's regional surface structures
    Zhi Ping Liu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China
    BMC Bioinformatics 8:475. 2007
  7. ncbi Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison
    Luonan Chen
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    BMC Struct Biol 6:18. 2006
  8. ncbi FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures
    Chenglei Sun
    Institute of Systems Biology, Shanghai University, Shanghai, China
    BMC Syst Biol 4:S12. 2010
  9. ncbi A discriminative approach for identifying domain-domain interactions from protein-protein interactions
    Xing Ming Zhao
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Proteins 78:1243-53. 2010
  10. ncbi Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
    Xiujun Zhang
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Bioinformatics 28:98-104. 2012

Collaborators

Detail Information

Publications57

  1. ncbi Biomolecular network querying: a promising approach in systems biology
    Shihua Zhang
    BMC Syst Biol 2:5. 2008
    ..In particular, we argue that user-friendly tools for network querying will greatly enhance our ability to study the fundamental properties of biomolecular networks at a system-wide level...
  2. ncbi Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli
    Rui Sheng Wang
    School of Information, Renmin University of China, Beijing 100872, PR China
    BMC Bioinformatics 10:S6. 2009
    ..On the other hand, with more and more high-throughput biological data becoming available, it is possible and imperative to quantitatively study gene regulation in a systematic and detailed manner...
  3. ncbi Detecting disease associated modules and prioritizing active genes based on high throughput data
    Yu Qing Qiu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, PR China
    BMC Bioinformatics 11:26. 2010
    ..In the study of human diseases, rather than to discover disease related genes, identifying disease associated pathways and modules becomes an essential problem in the field of systems biology...
  4. ncbi Analysis on multi-domain cooperation for predicting protein-protein interactions
    Rui Sheng Wang
    School of Information, Renmin University of China, Beijing 100872, China
    BMC Bioinformatics 8:391. 2007
    ..Revealing multi-domain cooperation can provide deep insights into the essential mechanism of protein-protein interactions at the domain level and be further exploited to improve the accuracy of protein interaction prediction...
  5. ncbi Gene function prediction using labeled and unlabeled data
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, 4 6 1 Komaba, Meguro, Tokyo, Japan
    BMC Bioinformatics 9:57. 2008
    ..Furthermore, the classifier may be degraded by the false negatives in the heuristically generated negative samples...
  6. ncbi Predicting gene ontology functions from protein's regional surface structures
    Zhi Ping Liu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China
    BMC Bioinformatics 8:475. 2007
    ..For example, CASTp provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities...
  7. ncbi Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison
    Luonan Chen
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    BMC Struct Biol 6:18. 2006
    ....
  8. ncbi FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures
    Chenglei Sun
    Institute of Systems Biology, Shanghai University, Shanghai, China
    BMC Syst Biol 4:S12. 2010
    ..graminearum proteins available now. Computational approaches provide an alternative way to predicting F. graminearum protein subcellular localizations due to the expensive and time-consuming biological experiments in lab...
  9. ncbi A discriminative approach for identifying domain-domain interactions from protein-protein interactions
    Xing Ming Zhao
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Proteins 78:1243-53. 2010
    ..The PPI data sets used for prediction of DDIs and prediction results can be found at http://csb.shu.edu.cn/dipd...
  10. ncbi Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
    Xiujun Zhang
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Bioinformatics 28:98-104. 2012
    ..In particular, many properties of GRNs, such as topology sparseness and non-linear dependence, are generally in regulation mechanism but seldom are taken into account simultaneously in one computational method...
  11. ncbi A parsimonious tree-grow method for haplotype inference
    Zhenping Li
    Beijing Materials Institute, Beijing 101149, China
    Bioinformatics 21:3475-81. 2005
    ..aporc.org/bioinfo/ptg/ CONTACT: SUPPLEMENTARY INFORMATION: Supporting materials is available from http://zhangroup.aporc.org/bioinfo/ptg/bti572supplementary.pdf..
  12. ncbi Protein structure alignment by deterministic annealing
    Luonan Chen
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka 574 8530, Japan
    Bioinformatics 21:51-62. 2005
    ..A number of benchmark examples are tested by the proposed method with comparisons to several existing approaches...
  13. ncbi Noise-induced cooperative behavior in a multicell system
    Luonan Chen
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka 574 8530, Japan
    Bioinformatics 21:2722-9. 2005
    ..These results establish not only a theoretical foundation but also a quantitative basis for understanding essential roles of noises on cooperative dynamics, such as synchronization and communication among cells...
  14. ncbi Comparison of protein structures by multi-objective optimization
    Luonan Chen
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, Daito, Osaka 574 8530, Japan
    Genome Inform 16:114-24. 2005
    ..The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. The software is available upon request, or from http://zhangroup.aporc.org/bioinfo/samo/...
  15. ncbi Inferring protein interactions from experimental data by association probabilistic method
    Luonan Chen
    Osaka Sangyo University, Osaka, Japan
    Proteins 62:833-7. 2006
    ..Software is available from the authors upon request...
  16. ncbi A systems biology approach to identify effective cocktail drugs
    Zikai Wu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    BMC Syst Biol 4:S7. 2010
    ..However, most of existing combination drugs are developed based on clinical experience or test-and-trial strategy, which are not only time consuming but also expensive...
  17. ncbi Periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbations
    Yi Wang
    Shanghai University College of Science, Shanghai University, Shanghai, China
    Math Biosci 220:34-44. 2009
    ....
  18. ncbi Protein function prediction with the shortest path in functional linkage graph and boosting
    Xing Ming Zhao
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Int J Bioinform Res Appl 4:375-84. 2008
    ..In addition, the boosting algorithm is employed to further improve the prediction accuracy. The experiments on yeast genes show promising results and prove the efficiency of the proposed methods...
  19. ncbi DIPOS: database of interacting proteins in Oryza sativa
    Achyut Sapkota
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Mol Biosyst 7:2615-21. 2011
    ..Biological explanations of pathways and interactions are also provided based on the database. Public access to the DIPOS is available at and ...
  20. ncbi Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling
    Ruiqi Wang
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Bioinformatics 27:3158-65. 2011
    ..The model presented here might be a good candidate for providing the first qualitative mechanism of neural fate decisions mediated by both trans-activation and cis-inhibition...
  21. ncbi Identifying responsive functional modules from protein-protein interaction network
    Zikai Wu
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Mol Cells 27:271-7. 2009
    ..Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology...
  22. ncbi Automatic modeling of signaling pathways by network flow model
    Xing Ming Zhao
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    J Bioinform Comput Biol 7:309-22. 2009
    ..The numerical results on two known yeast MAPK signaling pathways demonstrate the efficiency and effectiveness of the proposed method...
  23. ncbi Protein classification with imbalanced data
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, Tokyo 151 0064, Japan
    Proteins 70:1125-32. 2008
    ..The Matlab code and supplementary materials are available at http://eserver2.sat.iis.u-tokyo.ac.jp/ approximately xmzhao/proteins.html...
  24. ncbi Inferring transcriptional interactions and regulator activities from experimental data
    Rui Sheng Wang
    Department of Electronics, Information and Communication Engineering, Osaka Sangyo University, Osaka 574 8530, Japan
    Mol Cells 24:307-15. 2007
    ....
  25. ncbi Bridging protein local structures and protein functions
    Zhi Ping Liu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100080, Beijing, China
    Amino Acids 35:627-50. 2008
    ..We also discuss remaining problems and possible directions for this exciting and challenging area...
  26. ncbi Analysis of protein surface patterns by pocket similarity network
    Zhi Ping Liu
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China
    Protein Pept Lett 15:448-55. 2008
    ....
  27. ncbi Intercellular communications induced by random fluctuations
    Tianshou Zhou
    Tsinghua University, Beijing 100084, China
    Genome Inform 15:223-33. 2004
    ..A multi-cell system with a synthetic gene network with both noises and delays is adopted to demonstrate the effect of noises on cellular communication...
  28. ncbi Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks
    Chunguang Li
    Centre for Nonlinear and Complex Systems, School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu 610054, People s Republic of China
    Chaos 18:023132. 2008
    ..Several numerical examples are also presented to verify the theoretical results...
  29. ncbi Controlling the onset of Hopf bifurcation in the Hodgkin-Huxley model
    Yong Xie
    MOE Key Laboratory for Strength and Vibration, School of Aerospace, Xi an Jiaotong University, Xi an 710049, People s Republic of China
    Phys Rev E Stat Nonlin Soft Matter Phys 77:061921. 2008
    ....
  30. ncbi Synchronization of coupled nonidentical genetic oscillators
    Chunguang Li
    ERATO Aihara Complexity Modelling Project, JST, Room M204, Komaba Open Laboratory, University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo 153 8505, Japan
    Phys Biol 3:37-44. 2006
    ..To demonstrate the effectiveness of our theoretical results, a population of genetic oscillators based on the Goodwin model are adopted as numerical examples...
  31. ncbi Aligning multiple protein structures by deterministic annealing
    Tianshou Zhou
    School of Mathematics and Computational Sciences, Zhongshan University, Guangzhou 510275, China
    J Bioinform Comput Biol 3:837-60. 2005
    ..The proposed method is robust with respect to choice of iteration parameters for a wide range of proteins, and performs well in both multiple and pairwise structure alignment cases, compared with existing alignment methods...
  32. ncbi Supervised classification of protein structures based on convex hull representation
    Yong Wang
    Academy of Mathematics and Systems Science, CAS, Beijing 100080, China
    Int J Bioinform Res Appl 3:123-44. 2007
    ..The CATH scheme is highlighted in the classification experiments. The results indicate that the proposed supervised classification scheme is effective and efficient...
  33. ncbi Design and implementation of probability-based scoring function for peptide mass fingerprinting protein identification
    Zhao Song
    Comput. Sci. Dept, Missouri Univ, Columbia, MO 65211-2060, USA
    Conf Proc IEEE Eng Med Biol Soc 1:4556-9. 2006
    ..Our new scoring function is assessed better than existing ones by comparing the computational results using experimental PMF data. A standalone version of "ProteinDecision" is freely available upon request...
  34. ncbi Unique optimal foldings of proteins on a triangular lattice
    Zhenping Li
    Beijing Materials Institute, Beijing, China
    Appl Bioinformatics 4:105-16. 2005
    ....
  35. ncbi Molecular communication through stochastic synchronization induced by extracellular fluctuations
    Tianshou Zhou
    School of Mathematics and Computational Sciences, Zhongshan University, Guangzhou 510275, China
    Phys Rev Lett 95:178103. 2005
    ..On the other hand, extracellular noises that are common to all cells can induce collective dynamics and stochastically synchronize the multicellular system by actively enhancing the integrated interchange of signaling molecules...
  36. ncbi Inferring gene regulatory networks from multiple microarray datasets
    Yong Wang
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka 574-8530, Japan
    Bioinformatics 22:2413-20. 2006
    ..AVAILABILITY: The software is available from http://zhangorup.aporc.org/bioinfo/grninfer/, http://digbio.missouri.edu/grninfer/ and http://intelligent.eic.osaka-sandai.ac.jp or upon request from the authors...
  37. ncbi Exploring protein's optimal HP configurations by self-organizing mapping
    Xiang Sun Zhang
    Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China
    J Bioinform Comput Biol 3:385-400. 2005
    ..Several HP benchmark examples with up to 36 amino acids are tested to verify the effectiveness of the proposed approach in this paper...
  38. ncbi Discrimination of outer membrane proteins by a new measure of information discrepancy
    Zikai Wu
    Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China
    Protein Pept Lett 14:37-44. 2007
    ..Furthermore, this method is able to correctly exclude alpha-helical membrane proteins at an accuracy of 100%...
  39. ncbi Stochastic synchronization of genetic oscillator networks
    Chunguang Li
    Centre for Nonlinear and Complex Systems, School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu 610054, PR China
    BMC Syst Biol 1:6. 2007
    ..From the synthetic biology viewpoint, it is also important to implement biological systems that minimizing the negative influence of the perturbations...
  40. ncbi Alignment of molecular networks by integer quadratic programming
    Li Zhenping
    Beijing Wuzi University, Beijing 101149, China
    Bioinformatics 23:1631-9. 2007
    ..However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden...
  41. ncbi A Markov chain model for haplotype assembly from SNP fragments
    Rui Sheng Wang
    Faculty of Engineering, Osaka Sangyo University, Osaka 574 8530, Japan
    Genome Inform 17:162-71. 2006
    ..Experiment results on several data sets illustrate the effectiveness of the new method...
  42. ncbi Alignment of protein interaction networks by integer quadratic programming
    Zhenping Li
    Beijing Wuzi University, Beijing, China
    Conf Proc IEEE Eng Med Biol Soc 1:5527-30. 2006
    ..From the viewpoint of graph theory, the proposed method can identify similar subsets between two graphs, which allow gaps for nodes and edges...
  43. ncbi Inferring transcriptional regulatory networks from high-throughput data
    Rui Sheng Wang
    School of Information, Renmin University of China, Beijing 100872, China
    Bioinformatics 23:3056-64. 2007
    ..The extensive results illustrate the effectiveness of the proposed method for predicting transcription regulatory relationships between TFs with co-regulators and target genes...
  44. ncbi Design of genetic switches with only positive feedback loops
    Tetsuya Kobayashi
    The University of Tokyo, Tokyo, Japan
    Proc IEEE Comput Soc Bioinform Conf 1:151-62. 2002
    ..Finally, we demonstrate our theoretical results by designing a biologically plausible synthesized genetic switch with experimentally well investigated lacI, tetR, and cI genes...
  45. ncbi Discovering functions and revealing mechanisms at molecular level from biological networks
    Shihua Zhang
    Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
    Proteomics 7:2856-69. 2007
    ....
  46. ncbi Modeling genetic switches with positive feedback loops
    Tetsuya Kobayashi
    Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Hongo 7 3 1, Bunkyo ku, Tokyo 113 8656, Japan
    J Theor Biol 221:379-99. 2003
    ..Finally, to demonstrate our theoretical results, we show biologically plausible examples by designing a synthetic genetic switch with experimentally well investigated lacI, tetR, and cI genes for numerical simulation...
  47. ncbi Construction of genetic oscillators with interlocked feedback networks
    Ruiqi Wang
    Aihara Complexity Modelling Project, ERATO, JST, Komaba Open Laboratory, The University of Tokyo, 4 6 1 Komaba, Meguro, Tokyo 153 8505, Japan
    J Theor Biol 242:454-63. 2006
    ..The method can be directly applied to design, construct genetic oscillators, and further control their dynamics, even for large-scale networks...
  48. ncbi Development and assessment of scoring functions for protein identification using PMF data
    Zhao Song
    Computer Science Department and Christopher S Bond Life Sciences Center, University of Missouri Columbia, Columbia, MO 65211 2060, USA
    Electrophoresis 28:864-70. 2007
    ..Our software is freely available upon request. The scoring functions can be easily incorporated into other proteomics software packages...
  49. ncbi Dynamics of gene regulatory networks with cell division cycle
    Luonan Chen
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, 3-1-1 Nakagaito, Daito, Osaka 574-8530, Japan
    Phys Rev E Stat Nonlin Soft Matter Phys 70:011909. 2004
    ..We show that the cell cycle may play a significant role in gene regulation due to the nonlinear dynamics of a gene regulatory network although gene expressions are usually tightly controlled by transcriptional factors...
  50. ncbi Synchronizing genetic oscillators by signaling molecules
    Ruiqi Wang
    Department of Electrical Engineering and Electronics, Osaka Sangyo University, Osaka, Japan
    J Biol Rhythms 20:257-69. 2005
    ..These results establish not only a theoretical foundation but also a quantitative basis for understanding the essential cooperative dynamics, such as collective rhythms or synchronization, in a population of cells...
  51. ncbi Transient resetting: a novel mechanism for synchrony and its biological examples
    Chunguang Li
    ERATO Aihara Complexity Modelling Project, Komaba Open Laboratory, University of Tokyo, Tokyo, Japan
    PLoS Comput Biol 2:e103. 2006
    ..Examples of the synchronization of neural and circadian oscillators as well as a chaotic neuron model are presented to verify our hypothesis...
  52. ncbi Synchronizing a multicellular system by external input: an artificial control strategy
    Ruiqi Wang
    Aihara Complexity Modelling Project, ERATO, JST, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
    Bioinformatics 22:1775-81. 2006
    ..availability: contact: ...
  53. ncbi Protein domain annotation with integration of heterogeneous information sources
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, Tokyo 151 0064, Japan
    Proteins 72:461-73. 2008
    ..We show that the integration of heterogeneous information sources improves not only prediction accuracy but also annotation reliability when compared with the methods using only individual information sources...
  54. ncbi Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems
    Ruiqi Wang
    Osaka Sangyo University, Nakagaito 3-1-1, Daito, Osaka 574-8530, Japan
    Bull Math Biol 67:339-67. 2005
    ..Since there is less restriction on the network structure, the results of this paper can be expected to apply to a wide variety of areas on modelling, analyzing and designing of biological systems...
  55. ncbi Uncovering signal transduction networks from high-throughput data by integer linear programming
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, Tokyo 151 0064, Japan
    Nucleic Acids Res 36:e48. 2008
    ..In addition, the proposed model is simple to be interpreted and easy to be implemented even for a large-scale system...
  56. ncbi Protein function prediction with high-throughput data
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, Tokyo, 151 0064, Japan
    Amino Acids 35:517-30. 2008
    ..In addition to describing recently developed theoretical methodologies, we also cover representative databases and software tools that are widely utilized in the prediction of protein function...
  57. ncbi Protein domain annotation with predicted domain-domain interaction networks
    Xing Ming Zhao
    ERATO Aihara Complexity Modelling Project, JST, Tokyo 151 0064, Japan
    Protein Pept Lett 15:456-62. 2008
    ..Specially, domain annotation is formalized as a multi-class classification problem in this work. The numerical experiments on InterPro domains show promising results, which proves the efficiency of our proposed methods...