Kyushu University Academic Staff Educational and Research Activities Database
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Researcher Informations
Last modified date：2010.5.10
Masahiro Okamoto
Professor
Applied Biological Regulation Technology
Bioscience & Biotechnology
Faculty of Agriculture

Graduate School

Department of Systems Life Sciences
Graduate School of Systems Life Sciences

Other Organization

Mathematical Research Center for Industrial Technology
Bio-Architecture Center

E-Mail

Homepage

http://www.brs.kyushu-u.ac.jp/bioinfo/
homepage of laboratory.

Phone

092-642-2795

Fax

092-642-3030

Academic Degree

Ph.D. in Biochemistry

Field of Specialization

Bioinformatics

Outline Activities

: Analysis of bio-functional network and control by using information technology and practical implementation in biotechnological or engineering fields
:
(1) Development of web-based biosimulator for analyzing metabolic network
(http://www.best-kit.org/)
(2) Development of inferrence system of genetic interactions in genetic netrwork
(3) Development of recognition system of time-variant signals based on information processing
of physiological neural netowrk
(4) Design of adaptive routing system in telecommunication network with using biochmical
feedback control mechanism

Research

Research Interests

  • Bio-inspired adaptive control system for traffic jam by mimiking enzymatic feedback system in cell
    keyword : biomimics, trafic control, load balance, traffic jam control
    2008.04.
  • Theoretical Study on Entrainment Mechanism of Heart Beating Cells
    keyword : beating cell, entrainment, pacemaking, refractory period
    2008.05～2011.05.
  • System Analysis of Signal Transduction System in Cell
    keyword : cell cycle, computer simulation, systems biology, system analysis
    2006.04.
  • Development of biosimulator for analyzing metabolic control pathway with using high resolution of mass spectorometry
    keyword : omics study, simulator, interface, systems biology
    2006.04～2007.03.
  • Inference of genetic interactions of large scale genetic network
    keyword : genetic interaction, inverse problem, nonlinear numerical optimization, genetic algorithm
    1999.01.
  • Development of Windows-based biosimulator for analyzing metabolic control pathway;Win-BESTKIT
    keyword : metabolic simulator, parameter oprimization, computer simulation
    1995.01.
  • Bio-inspired adaptive routing system by mimiking enzymatic feedback system in cell
    keyword : biomimics, trafic control, load balance
    2002.01.
  • Recognition system of Time-series signal based on neuron information processing system
    keyword : timeseries of data, voice recognition, neural network, artificial neuron
    1998.01～2003.06.

Current and Past Project

  • Project for the development of inference system of genetic interactions
  • Project for the development of optimization system of large-scale numerical parameters by using grid computers

Academic Activities

Books

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1. 富永大介、岡本正宏,マイクロアレイデータ統計解析プロトコール,234-242,2008.05.
2. Masahiro Okamoto, Kouji Tanaka,Biophysical Neural Networks: Analytical Approaches to Neuronal Function,Mary Ann Libert, Inc. Publishers,"Hebbian Learning in a Network of Biochemical Neurons", pp.123-146,2001.07.
3. Bioprocess Engineering.

Reports

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Papers

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1. Masahiko Nakatsui, Katsuhisa Horimoto, Masahiro Okamoto, Yasuhito Tokumoto, Jun Miyake,Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions,BMC Systems Biology,in press (2010),2010.05.
2. Mugihito Oshiro, Hideaki Shinto, Yukihiro Tashiro, Noriko Miwa, Tatsuya Sekiguchi, Masahiro Okamoto, Ayaaki Ishizaki, Kenji Sonomoto,Kinetic Modeling and Sensitivity Analysis of Xylose Metabolism in Lactococcus lactis IO-1,Journal of Bioscience and Binengineering,108(5), 376-384 (2009),2009.05.
3. Nahoko Shikata, Yukihiro Maki, Masahiko Nakatsui, Masato Mori, Yasushi Noguchi, Shintaro Yoshida, Michio Takahashi, Nobuo Kondo, Masahiro Okamoto,Determining Important Regulatory Relations of Amino Acids from Dynamic Network Analysis of Plasma Amino Acids,Amino Acids,38, 179-187 (2010),2010.01.
4. Hiroyuki Hamada, Yoshihiko Tashima, Yu Kisaka, Kazunari Iwamoto, Taizo Hanai, Yukihiro Eguchi, Masahiro Okamoto
,Sophisticated Framework Between Cell Cycle Arrest and Apoptosis Induction Based on p53 Dynamics,PLoS one,4(3), e4795 (2009),2009.03.
5. Kazunari Iwamoto, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto,Blind Spot of G1/S Checkpoint: G1/S Checkpoint is Invaded by DNA-Damage After R-Point,Proc. of the IASTED Intl. Symp. on Computational Biology and Bioinformatics (CBB2008),pp 241-246 (2008),2008.11.
6. Akiyuki Iwasaki, Tadasuke Nozoe, Takashi Kawauchi, Masahiro Okamoto,Fault Tolerant Mechanism of Bio-inspired Adaptive Routing System,3rd. International Conference on Bio-Inspired Models of Network, Information, and
Computing Systems (BIONETICS 2008),CD-ROM (session2-1) 6 pages,2008.11.
7. Hideaki Shinto, Yukihiro Tashiro, Genta Kobayashi,Tatsuya Sekiguchi, Taizo Hanai, Yuki Kuriya, Masahiro Okamoto, Kenji Sonomoto,Kinetic Study of Substrate Dependency for Higher Butanol Production in Acetone-Butanol-Ethanol Fermentation,Process Biochemistry ,43(12), 1452-1461 (2008),2008.12.
8. Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto,Mathematical Modeling and Sensitivity Analysis of G1/S Phase in the Cell Cycle Including the DNA Damage Signal Transduction Pathway,BioSystems,94(1), 109-117 (2008),2008.10.
9. Yoshihiko Tashima, Hiroyuki Hamada, Masahiro Okamoto, Taizo Hanai,Prediction of Key Factor for Control of G1/S Phase in Mammalian Cell Cycle by using System Analysis,J. Bioscience and Boengineering,106(4), 368-374 (2008),2008.10.
10. Abdullah Al. Mamun, Hiroyuki Hamada, Tomokazu Karino, Shinji Namoto, Akihiro C. Yamashita, Makoto Ishizaki, Masahiro Okamoto,Clinical Application of Computer-Aided Diagnostic System for Harmonious Introduction of Complementary Dialysis Theraphy,The Open Biomedical Rngineering J.,vol.2, pp10-16,2008.05.
11. Masahiko Nakatsui, Takanori Ueda, Yukihiro Maki, Isao Ono, Masahiro Okamoto,Method for Inferring and Extracting Reliable Genetic Interactions from Time-series Profile of Gene Expression,Mathematical Biosciences,Vol.215, pp105-114 ,2008.06.
12. Chinatsu Arima, Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai,Modified Fuzzy Gap Statistic for Estimating Preferable Number of Clusters in Fuzzy k-Means Clustering,Journal of Bioscience and Bioengineering,105, 273-281(2008),2008.01.
13. Masahiko Nakatsui, Takanori Ueda, Yukihiro Maki, Isao Ono, Masahiro Okamoto,Efficient Inferring Method of Genetic Interactions based on Time-Series of Gene Expression Profile,Proc. of 13th. International Symposium on Artificial Life and Robotics (AROB 13th ’08),71-76 (2008),2008.01.
14. Akiyuki Iwasaki, Tadasuke Nozoe, Takashi Kawauchi, Masahiro Okamoto,Design of Bio-inspired Fault-tolerant Adaptive Routing Based on Enzymatic Feedback Control in the Cell: Towads Averaging Load Balance in the Network,Proc. of Frontiers in the Convergence of Bioscience and Information Technologies (FBIT2007),2007.10.
15. Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto,Mathematical Modeling and Sensitivity Analysis of G1/S Phase in the Cell Cycle Including the DNA Damage Signal Transduction Pathway,Proc. of Seventh International Workshop on Information Processing in Cells and Tissues (IPCAT2007),281 - 292 (2007),2007.08.
16. Hiroyuki Hamada, Shinji Namoto, Ryo Yamada, Abdula A. Mamun, Akihiro C. Yamashita, Makoto Ishizaki, Masahiro Okamoto,Development of a Computer-aided Diagnosis System for Continuous Peritoneal Dialysis: An Availavilty of the Simultaneous Numerical Optimizaton Technique for Kinetic Parameters in the Peritoneal Dialysis Model,Computers in Biology and Medicine,37, 1700-1708 (2007),2007.08.
17. Masahiko Nakatsui, Yukihiro Maki, Tatsuya Sekiguchi, Masahiro Okamoto,Integrated Comprehensive Workbench for Systems Biology: Inference of Genetic Interaction and Systems Analysis of Metabolic Pathways,Proc. of 11th. World Multi Conference on Systemics, Cybernetics and Informatics (WMSCI2007),7-12 (2007),2007.07.
18. Hideaki Shinto, Yukihiro Tashiro, Mayu Yamashita, Genta Kobayashi, Tatsuya Sekiguchi, Taizo Hanai, Yuki Kuriya, Masahiro Okamoto, Kenji Sonomoto,Kinetic Modeling and Sensitivity Analysis of Acetone-Butanol-Ethanol Production,Journal of Biotechnology,131(1), 45-56 (2007),2007.04.
19. Tadasuke Nozoe, Takashi Kawauchi, Masahiro Okamoto,A Bio-inspired Adaptive Routing Based on Enzymatic Feedback Control Mechanism in Metabolic Networks,Proc. of International MultiConference of Engineers and Computer Scientists 2007 (IMECS2007),1361-1365 (2007),2007.03.
20. Nahoko Shikata, Yukihiro Maki, Yasushi Noguchi, Masato Mori, Taizo Hanai, Michio Takahashi, Masahiro Okamoto,Multi-layered Network Structure of Amino Acid (AA) Metabolism Characterized by Each Essential AA-deficient Condition,Amino Acids,33(1), 113-121 (2007),2007.02.
21. Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto,Application of Bioinformatics for DNA Microarray Data to Bioscience, Bioengineering and Medical Field,Journal of Bioscience and Bioengineering,101(5), pp377-384,2006.08.
22. Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai,Novel Technique for Preprocessing High Dimensional Tome-cours Data from DNA Microarray: Mathematical Model-based Clustering,Bioinformatics,22(7), pp843-848,2006.06.
23. Tatsuya Sekiguchi, Masahiro Okamoto,WinBEST-KIT: Windows-based Biochemical Reaction Simulator for Metabolic Pathways,Journal of Bioinformatics and Computational Biology,4(3), pp621-638,2006.05.
24. Takashi Kawauchi, Tadasuke Nozoe, Masahiro Okamoto,Biologically Inspired Adaptive Routing by Mimicking Enzymic Feedback Control Mechanism in the Cell,Lecture Notes in Computer Science,Vol.3853, pp.371-378,2006.05.
25. Yoshihiko Tashima, Yu Kisaka, Taizo Hanai, Hiruyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto,Mathematical Modeling of G2/M Phase in Cell Cycle with Involving the p53/Mdm2 Oscillation System,Med. Biol. Comut. Proc. of IFMBE,14, 195-198 (2006)
,2006.05.
26. Application of Real-coded Genetic Algorithm to Biological Research Fields: Inference of Genetic Interactions in Large Scale Gene Networks.
27. Jun Yoshimura, Tadahiro Shimonobou, Tatsuya Sekiguchi, Masahiro Okamoto,Development of the Parameter-fitting Module for Web-based Biochemical Reaction Simulator BEST-KIT,Chem-Bio Informatics J.,3(3), pp.114-129,2003.02.
28. Masahiro Okamoto, Kenji Sakuraba, Jun Yoshimura, Kouji Tanaka, Jun-ichi Ueno, Masakazu Mori, Tadahiro Simonobou, Tatsuya Sekiguchi,Web-based BEST-KIT: Development of Web-based Biochemical Engineering System Analyzing Tool-KIT,Chem-Bio Informatics J.,2(1), pp.1-17,2002.01.
29. Yukihiro Maki, Daisuke Tominaga, Masahiro Okamoto, Shoji Watanabe, Yukihiro Eguchi,Development of a System for the Inference of Large Scale Genetic Networks,Pacific Symposium on Biocomputing 2001 (PSB2001),pp.446-458,2001.01.
30. Daisuke Tominaga, Nobuto Koga, Masahiro Okamoto,Efficient Numerical Optimization Algorithm Based on Genetic Algorithm for Inverse Problem,Proc. of Genetic and Evolutionary Computation Conference (GECCO 2000),pp.252-258,2000.07.
31. Masahiro Okamoto, Tatsuya Sekiguchi, Kouji Tanaka, Yukihiro Maki, Satoshi Yoshida,Biochemical Neuron: Hardware Implementation of Functional Devices by Mimicking the Natural Intelligence Such As Metabolic Control Systems,Computers and Electric. Engng.,25(5), pp.421-438,1999.09.
32. Daisuke Tominaga, Masahiro Okamoto, Yukihiro Maki, Shoji Watanabe, Yukihiro Eguchi,Nonlinear Numerical Optimization Technique Based on a Genetic Algorithm for Inverse Problems: Towards the Inference of Genetic Networks,Proceeding of German Conference on Bioinformatics '99,pp.127-140,1999.06.

Works, Software and Database

1. Web-based Biosimulator for Analyzing Nonlinear Reaction Network
(http://www.best-kit.org/).

Presentations

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Educational

Educational Activities

Graduate School:
.Foundamental Course for Systems　Biology
.Advanced Course for Mathematical Molecular Biology
.Advanced Course for Sytems Biotechnology
.Advanced Course for Systems Analysis
Undergraduate School:
.Overview of Applied Biological Regulation Technology
.Cellular Biology

Social

Professional and Outreach Activities

.2000-2005: Group leader of Grant-in-Aid for Scientific Research on Priority Areas, "Genome Information Sciences" from the Ministry of Education, Culture, Sports, Science and Technology, Japan
.2002-2004: Boardman of Japanese Society for Bioinformatics
.2002- : Administrator of Chem-Bio Information Society, Japan
Copyright © 2006, Kyushu University. All right reserved.