Updated on 2024/05/14

写真a

 
KURATA Hiroyuki
 
Scopus Paper Info  
Total Paper Count: 0  Total Citation Count: 0  h-index: 21

Citation count denotes the number of citations in papers published for a particular year.

Affiliation
Faculty of Computer Science and Systems Engineering Department of Bioscience and Bioinformatics
Job
Professor
E-mail
メールアドレス
Laboratory
680-4 Kawazu, Iizuka-shi, Fukuoka
External link

Research Interests

  • Bioinformatics

  • Biochemical Engineering

  • Design

  • Simulation

  • AI

  • Systems Biology

Research Areas

  • Manufacturing Technology (Mechanical Engineering, Electrical and Electronic Engineering, Chemical Engineering) / Biofunction and bioprocess engineering

  • Life Science / Medical systems

  • Informatics / Life, health and medical informatics

Undergraduate Education

  • 1988.03   The University of Tokyo   Faculty of Engineering   Chemical Engineering   Graduated   Japan

Post Graduate Education

  • 1993.03   The University of Tokyo   Graduate School, Division of Engineering   Chemical Engineering   Doctoral Program   Completed   Japan

Degree

  • The University of Tokyo  -  Doctor of Engineering   1993.04

Biography in Kyutech

  • 2019.04
     

    Kyushu Institute of Technology   Faculty of Computer Science and Systems Engineering   Department of Bioscience and Bioinformatics   Professor  

  • 2012.04
     

    Kyushu Institute of Technology   Abolition organization   Biomedical Informatics R&D Center  

  • 2011.04
    -
    2012.03
     

    Kyushu Institute of Technology   School of Computer Science and Systems Engineering  

  • 2008.04
    -
    2019.03
     

    Kyushu Institute of Technology   Faculty of Computer Science and Systems Engineering   Department of Bioscience and Bioinformatics   Professor  

  • 2006.04
    -
    2008.03
     

    Kyushu Institute of Technology   School of Computer Science and Systems Engineering   Professor  

  • 2000.10
    -
    2006.03
     

    Kyushu Institute of Technology   School of Computer Science and Systems Engineering   Associate Professor (as old post name)  

▼display all

Biography before Kyutech

  • 1994.04 - 1996.03   University of California, Davis   Plant pathology   Special researcher of the Japan Society for the Promotion of Science   United States

  • 1993.04 - 2000.09   The University of Tokyo   Research Assistant   Japan

Academic Society Memberships

  • 2009.04   情報処理学会   Japan

  • 2002.04   The Society for Biotechnology, Japan   Japan

  • 2002.04   Japanese Society of Bioinformatics   Japan

  • 2002.04 - 2009.03   The Molecular Biology Society of Japan   Japan

  • 1990.04   The Society of Chemical Engineers   Japan

Research Career

  • Computer-Aided rational Design of a Biological System for Medicine and Environmental Science

    研究期間: 2008.04  - 

  • 生命システムがロバストネスを生み出すメカニズムの解明

    未設定

    研究期間: 2008.04  - 

  • バイオメディカルインフォマティクスに関する研究

    バイオメディカルインフォマティクス

    研究期間: 2012.04  - 

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    情報工学を基軸にした研究開発を活発化させて、アジアにおけるバイオメディカルインフォマティクスのトップレベルの教育研究拠点・産学官連携拠点を構築します。日本発の医療イノベーションを実現し、それを担うグローバル・エンジニアを持続的に養成して、人類の健康と福祉に貢献します。
    究極の目標として、分子、細胞、臓器、全身の各階層を統合するヒトのコンピュータモデル(Virtual Physiological Human、疾病予測シミュレータ)を開発します。一方、そこで培った情報工学技術(シーズ)を用いて、医学部、病院、企業のニーズに応え、コンピュータ支援による診断、予防、治療、介護、医薬品開発システムを提供します。

Papers

  • CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction Reviewed International journal

    Tsukiyama S., Hasan M.M., Kurata H.

    Computational and Structural Biotechnology Journal   21   644 - 654   2023.01

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.csbj.2022.12.043

    Scopus

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  • MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling Reviewed International journal

    Maeda K., Hatae A., Sakai Y., Boogerd F.C., Kurata H.

    BMC Bioinformatics   23 ( 1 )   2022.12

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    Authorship:Last author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1186/s12859-022-05009-x

    Scopus

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  • Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy Reviewed International journal

    Hasan M.M., Tsukiyama S., Cho J.Y., Kurata H., Alam M.A., Liu X., Manavalan B., Deng H.W.

    Molecular Therapy   30 ( 8 )   2856 - 2867   2022.08

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.ymthe.2022.05.001

    Scopus

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  • IACVP: Markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model Reviewed International journal

    Kurata H., Tsukiyama S., Manavalan B.

    Briefings in Bioinformatics   23 ( 4 )   2022.07

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1093/bib/bbac265

    Scopus

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  • BERT6mA: Prediction of DNA N6-methyladenine site using deep learning-based approaches Reviewed International journal

    Tsukiyama S., Hasan M.M., Deng H.W., Kurata H.

    Briefings in Bioinformatics   23 ( 2 )   2022.03

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1093/bib/bbac053

    Scopus

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  • Identification of a reliable sacral-sparing examination to assess the ASIA impairment scale in patients with traumatic spinal cord injury Reviewed International journal

    Ariji Y., Hayashi T., Ideta R., Koga R., Murai S., Naka T., Ifuku R., Towatari F., Sakai H., Kurata H., Maeda T.

    Journal of Spinal Cord Medicine   2022.01

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1080/10790268.2022.2047548

    Scopus

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  • Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT Reviewed International journal

    Maeda K., Kurata H.

    International Journal of Molecular Sciences   24 ( 8 )   2023.04

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    Authorship:Last author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.3390/ijms24087296

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  • ICAN: Interpretable cross-attention network for identifying drug and target protein interactions Reviewed International journal

    Kurata H., Tsukiyama S.

    PLoS ONE   17 ( 10 October )   2022.10

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1371/journal.pone.0276609

    Scopus

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  • Recent Development of Bioinformatics Tools for microRNA Target Prediction Invited Reviewed International journal

    Khatun M.S., Alam M.A., Shoombuatong W., Mollah M.N.H., Kurata H., Hasan M.M.

    Current Medicinal Chemistry   29 ( 5 )   865 - 880   2022.02

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)

    DOI: 10.2174/0929867328666210804090224

    Scopus

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  • Cross-attention PHV: Prediction of human and virus protein-protein interactions using cross-attention–based neural networks Reviewed International journal

    Tsukiyama S., Kurata H.

    Computational and Structural Biotechnology Journal   20   5564 - 5573   2022.01

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.csbj.2022.10.012

    Scopus

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  • NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning Reviewed

    Hasan M.M., Alam M.A., Shoombuatong W., Deng H.W., Manavalan B., Kurata H.

    Briefings in bioinformatics   22 ( 6 )   2021.11

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    Neuropeptides (NPs) are the most versatile neurotransmitters in the immune systems that regulate various central anxious hormones. An efficient and effective bioinformatics tool for rapid and accurate large-scale identification of NPs is critical in immunoinformatics, which is indispensable for basic research and drug development. Although a few NP prediction tools have been developed, it is mandatory to improve their NPs' prediction performances. In this study, we have developed a machine learning-based meta-predictor called NeuroPred-FRL by employing the feature representation learning approach. First, we generated 66 optimal baseline models by employing 11 different encodings, six different classifiers and a two-step feature selection approach. The predicted probability scores of NPs based on the 66 baseline models were combined to be deemed as the input feature vector. Second, in order to enhance the feature representation ability, we applied the two-step feature selection approach to optimize the 66-D probability feature vector and then inputted the optimal one into a random forest classifier for the final meta-model (NeuroPred-FRL) construction. Benchmarking experiments based on both cross-validation and independent tests indicate that the NeuroPred-FRL achieves a superior prediction performance of NPs compared with the other state-of-the-art predictors. We believe that the proposed NeuroPred-FRL can serve as a powerful tool for large-scale identification of NPs, facilitating the characterization of their functional mechanisms and expediting their applications in clinical therapy. Moreover, we interpreted some model mechanisms of NeuroPred-FRL by leveraging the robust SHapley Additive exPlanation algorithm.

    DOI: 10.1093/bib/bbab167

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  • LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec Reviewed International journal

    Tsukiyama S., Hasan M.M., Fujii S., Kurata H.

    Briefings in bioinformatics   22 ( 6 )   2021.11

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    Authorship:Lead author, Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1093/bib/bbab228

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  • Critical evaluation of web-based DNA N6-methyladenine site prediction tools Invited Reviewed

    Hasan M.M., Shoombuatong W., Kurata H., Manavalan B.

    Briefings in Functional Genomics   20 ( 4 )   258 - 272   2021.07

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1093/bfgp/elaa028

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  • Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework Reviewed

    Hasan M.M., Basith S., Khatun M.S., Lee G., Manavalan B., Kurata H.

    Briefings in bioinformatics   22 ( 3 )   2021.05

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1093/bib/bbaa202

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  • Prednts: Improved and robust prediction of nitrotyrosine sites by integrating multiple sequence features Reviewed

    Nilamyani A.N., Auliah F.N., Moni M.A., Shoombuatong W., Hasan M.M., Kurata H.

    International Journal of Molecular Sciences   22 ( 5 )   1 - 11   2021.03

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.3390/ijms22052704

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  • IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations Reviewed

    Hasan M.M., Alam M.A., Shoombuatong W., Kurata H.

    Journal of Computer-Aided Molecular Design   35 ( 3 )   315 - 323   2021.03

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1007/s10822-020-00368-0

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  • Virtual metabolic human dynamic model for pathological analysis and therapy design for diabetes Reviewed

    Kurata H.

    iScience   24 ( 2 )   2021.02

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.isci.2021.102101

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  • Pup-fuse: Prediction of protein pupylation sites by integrating multiple sequence representations Reviewed

    Auliah F.N., Nilamyani A.N., Shoombuatong W., Alam M.A., Hasan M.M., Kurata H.

    International Journal of Molecular Sciences   22 ( 4 )   1 - 12   2021.02

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.3390/ijms22042120

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  • iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features Reviewed

    Hasan M.M., Khatun M.S., Kurata H.

    Genomics, Proteomics and Bioinformatics   2021.01

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.gpb.2019.04.004

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  • RCGAToolbox: A Real-coded Genetic Algorithm Software for Parameter Estimation of Kinetic Models Reviewed

    Maeda K., Boogerd F.C., Kurata H.

    IPSJ Transactions on Bioinformatics   14   30 - 35   2021.01

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    Language:English   Publishing type:Research paper (scientific journal)

    Kinetic modeling is essential for understanding the dynamic behavior of biochemical networks, such as metabolic and signal transduction pathways. However, parameter estimation remains a major bottleneck in kinetic modeling. Although several software tools have been developed to address this issue, they are meant to be used by experts, and their lack of user-friendliness hampers their general usage by capable yet inexperienced scientists. One of the difficulties is the lack of graphical user interfaces (GUIs), which means that users must learn how to write scripts for parameter estimation. In this study, we present RCGAToolbox, a user-friendly parameter estimation software that provides real-coded genetic algorithms (RCGAs). The RCGAToolbox has two RCGAs: the unimodal normal distribution crossover with minimal generation gap (UNDX/MGG) and the real-coded ensemble crossover star with just generation gap (REXstar/JGG). To facilitate parameter estimation, RCGAToolbox offers straightforward access to powerful RCGAs, such as GUIs, an easy-to-use installer, and a comprehensive user guide. Moreover, the RCGAToolbox supports systems biology standards for better usability and interoperability. The RCGAToolbox is available at https://github.com/kmaeda16/RCGAToolbox under GNU GPLv3, along with the user guide and application examples. The RCGAToolbox runs on MATLAB (R2016a or later) in Windows, Linux, and Mac.

    DOI: 10.2197/IPSJTBIO.14.30

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  • Robust in-phase synchronization in repressor-based coupled gene oscillators Reviewed

    Shamim Ul Hasan A.B.M., Dey S., Kurata H., Singh A.

    IFAC-PapersOnLine   54 ( 15 )   574 - 579   2021.01

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.ifacol.2021.10.318

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  • RCGAToolbox: A Real-coded Genetic Algorithm Software for Parameter Estimation of Kinetic Models Reviewed

    Maeda Kazuhiro, Boogerd Fred C., Kurata Hiroyuki

    IPSJ Transactions on Bioinformatics   14 ( 0 )   30 - 35   2021.01

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.2197/ipsjtbio.14.30

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/130008120842

  • Coupling protocol of interlocked feedback oscillators in circadian clocks Reviewed

    Rashid M.M., Kurata H.

    Journal of the Royal Society, Interface   17 ( 167 )   2020.06

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1098/rsif.2020.0287

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  • Computer-Aided Rational Design of Efficient NADPH Production System by Escherichia coli pgi Mutant Using a Mixture of Glucose and Xylose Reviewed

    Matsuoka Y., Kurata H.

    Frontiers in Bioengineering and Biotechnology   8   2020.04

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.3389/fbioe.2020.00277

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  • Recent development of machine learning methods in microbial phos-phorylation sites Reviewed

    Rashid M.M., Shatabda S., Hasan M.M., Kurata H.

    Current Genomics   21 ( 3 )   194 - 203   2020.01

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    Authorship:Corresponding author   Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)

    DOI: 10.2174/1389202921666200427210833

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  • A prediction model of functional outcome at 6 months using clinical findings of a person with traumatic spinal cord injury at 1 month after injury Reviewed

    Ariji Y., Hayashi T., Ideta R., Koga R., Murai S., Towatari F., Terashi Y., Sakai H., Kurata H., Maeda T.

    Spinal Cord   2020.01

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    Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1038/s41393-020-0488-5

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  • i4mC-Mouse: Improved identification of DNA N4-methylcytosine sites in the mouse genome using multiple encoding schemes Reviewed

    Hasan M.M., Manavalan B., Shoombuatong W., Khatun M.S., Kurata H.

    Computational and Structural Biotechnology Journal   18   906 - 912   2020.01

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1016/j.csbj.2020.04.001

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  • ヒト全身代謝システムの数理モデル Invited Reviewed

    倉田 博之

    細胞   52   376 - 379   2020.01

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    Authorship:Lead author, Last author, Corresponding author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)

    CiNii Research

  • i6mA-Fuse: improved and robust prediction of DNA 6 mA sites in the Rosaceae genome by fusing multiple feature representation Reviewed

    Hasan M.M., Manavalan B., Shoombuatong W., Khatun M.S., Kurata H.

    Plant Molecular Biology   2020.01

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1007/s11103-020-00988-y

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  • ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations Reviewed

    Khatun M.S., Hasan M.M., Shoombuatong W., Kurata H.

    Journal of Computer-Aided Molecular Design   2020.01

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    DOI: 10.1007/s10822-020-00343-9

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  • Evolution of sequence-based bioinformatics tools for protein-protein interaction prediction Reviewed

    Khatun M.S., Shoombuatong W., Hasan M.M., Kurata H.

    Current Genomics   21 ( 6 )   454 - 463   2020.01

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    Authorship:Corresponding author   Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)

    © 2020 Bentham Science Publishers. Protein-protein interactions (PPIs) are the physical connections between two or more proteins via electrostatic forces or hydrophobic effects. Identification of the PPIs is pivotal, which contributes to many biological processes including protein function, disease incidence, and therapy design. The experimental identification of PPIs via high-throughput technology is time-consuming and expensive. Bioinformatics approaches are expected to solve such restrictions. In this review, our main goal is to provide an inclusive view of the existing sequence-based computational prediction of PPIs. Initially, we briefly introduce the currently available PPI databases and then review the state-of-the-art bioinformatics approaches, working principles, and their performances. Finally, we discuss the caveats and future perspective of the next generation algorithms for the prediction of PPIs.

    DOI: 10.2174/1389202921999200625103936

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  • Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation Reviewed International journal

    Hasan A., Kurata H., Pechmann S.

    BMC Bioinformatics   20 ( 1 )   2019.12

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)

    © 2019 The Author(s). Background: Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete. Stochastic fluctuations that are inherent to most biological systems have been shown to hamper memory function. Yet, how stochasticity changes the behavior of genetic circuits is generally not clear from a deterministic analysis of the network alone. Here, we apply deterministic rate equations, stochastic simulations, and theoretical analyses of Fokker-Planck equations to investigate how intrinsic noise affects the memory function in a mutual repression network. Results: We find that the addition of negative autoregulation improves the persistence of memory in a small gene regulatory network by reducing stochastic fluctuations. Our theoretical analyses reveal that this improved memory function stems from an increased stability of the steady states of the system. Moreover, we show how the tuning of critical network parameters can further enhance memory. Conclusions: Our work illuminates the power of stochastic and theoretical approaches to understanding biological circuits, and the importance of considering stochasticity when designing synthetic circuits with memory function.

    DOI: 10.1186/s12859-019-3315-2

    Kyutacar

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  • Computational identification of microbial phosphorylation sites by the enhanced characteristics of sequence information Reviewed International journal

    Hasan M., Rashid M., Khatun M., Kurata H.

    Scientific Reports   9 ( 1 )   2019.12

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    © 2019, The Author(s). Protein phosphorylation on serine (S) and threonine (T) has emerged as a key device in the control of many biological processes. Recently phosphorylation in microbial organisms has attracted much attention for its critical roles in various cellular processes such as cell growth and cell division. Here a novel machine learning predictor, MPSite (Microbial Phosphorylation Site predictor), was developed to identify microbial phosphorylation sites using the enhanced characteristics of sequence features. The final feature vectors optimized via a Wilcoxon rank sum test. A random forest classifier was then trained using the optimum features to build the predictor. Benchmarking investigation using the 5-fold cross-validation and independent datasets test showed that the MPSite is able to achieve robust performance on the S- and T-phosphorylation site prediction. It also outperformed other existing methods on the comprehensive independent datasets. We anticipate that the MPSite is a powerful tool for proteome-wide prediction of microbial phosphorylation sites and facilitates hypothesis-driven functional interrogation of phosphorylation proteins. A web application with the curated datasets is freely available at http://kurata14.bio.kyutech.ac.jp/MPSite/.

    DOI: 10.1038/s41598-019-44548-x

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  • Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network Reviewed International journal

    Maeda K., Westerhoff H., Kurata H., Boogerd F.

    npj Systems Biology and Applications   5 ( 1 )   2019.12

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    © 2019, The Author(s). The complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a ‘rubber band method’ to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia.

    DOI: 10.1038/s41540-019-0091-6

    Kyutacar

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  • Self-replenishment cycles generate a threshold response Reviewed International journal

    Kurata H.

    Scientific Reports   9 ( 1 )   2019.12

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    © 2019, The Author(s). Many metabolic cycles, including the tricarboxylic acid cycle, glyoxylate cycle, Calvin cycle, urea cycle, coenzyme recycling, and substrate cycles, are well known to catabolize and anabolize different metabolites for efficient energy and mass conversion. In terms of stoichiometric structure, this study explicitly identifies two types of metabolic cycles. One is the well-known, elementary cycle that converts multiple substrates into different products and recycles one of the products as a substrate, where the recycled substrate is supplied from the outside to run the cycle. The other is the self-replenishment cycle that merges multiple substrates into two or multiple identical products and reuses one of the products as a substrate. The substrates are autonomously supplied within the cycle. This study first defines the self-replenishment cycles that many scientists have overlooked despite its functional importance. Theoretical analysis has revealed the design principle of the self-replenishment cycle that presents a threshold response without any bistability nor cooperativity. To verify the principle, three detailed kinetic models of self-replenishment cycles embedded in an E. coli metabolic system were simulated. They presented the threshold response or digital switch-like function that steeply shift metabolic status.

    DOI: 10.1038/s41598-019-53589-1

    Kyutacar

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  • Efficient computational model for identification of antitubercular peptides by integrating amino acid patterns and properties Reviewed International journal

    Khatun S., Hasan M., Kurata H.

    FEBS Letters   593 ( 21 )   3029 - 3039   2019.11

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    © 2019 Federation of European Biochemical Societies Tuberculosis (TB) is a leading killer caused by Mycobacterium tuberculosis. Recently, anti-TB peptides have provided an alternative approach to combat antibiotic tolerance. We have developed an effective computational predictor, identification of antitubercular peptides (iAntiTB), by the integration of multiple feature vectors deriving from the amino acid sequences via random forest (RF) and support vector machine (SVM) classifiers. The iAntiTB combines the RF and SVM scores via linear regression to enhance the prediction accuracy. To make a robust and accurate predictor, we prepared the two datasets with different types of negative samples. The iAntiTB achieved area under the ROC curve values of 0.896 and 0.946 on the training datasets of the first and second datasets, respectively. The iAntiTB outperformed the other existing predictors.

    DOI: 10.1002/1873-3468.13536

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  • Large-scale assessment of bioinformatics tools for lysine succinylation sites Invited Reviewed International journal

    Hasan M.M., Khatun M.S., Kurata H.

    Cells   8 ( 2 )   2019.01

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    DOI: 10.3390/cells8020095

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  • PreAIP: Computational prediction of anti-inflammatory peptides by integrating multiple complementary features Reviewed International journal

    Khatun M., Hasan M., Kurata H.

    Frontiers in Genetics   10 ( MAR )   2019.01

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    © 2019 Khatun, Hasan and Kurata. Numerous inflammatory diseases and autoimmune disorders by therapeutic peptides have received substantial consideration; however, the exploration of anti-inflammatory peptides via biological experiments is often a time-consuming and expensive task. The development of novel in silico predictors is desired to classify potential anti-inflammatory peptides prior to in vitro investigation. Herein, an accurate predictor, called PreAIP (Predictor of Anti-Inflammatory Peptides) was developed by integrating multiple complementary features. We systematically investigated different types of features including primary sequence, evolutionary and structural information through a random forest classifier. The final PreAIP model achieved an AUC value of 0.833 in the training dataset via 10-fold cross-validation test, which was better than that of existing models. Moreover, we assessed the performance of the PreAIP with an AUC value of 0.840 on a test dataset to demonstrate that the proposed method outperformed the two existing methods. These results indicated that the PreAIP is an accurate predictor for identifying AIPs and contributes to the development of AIPs therapeutics and biomedical research. The curated datasets and the PreAIP are freely available at http://kurata14.bio.kyutech.ac.jp/PreAIP/.

    DOI: 10.3389/fgene.2019.00129

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  • i4mC-ROSE, a bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome Reviewed International journal

    Hasan M., Manavalan B., Khatun M., Kurata H.

    International Journal of Biological Macromolecules   2019.01

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    © 2018 Elsevier B.V. One of the most important epigenetic modifications is N4-methylcytosine, which regulates many biological processes including DNA replication and chromosome stability. Identification of N4-methylcytosine sites is pivotal to understand specific biological functions. Herein, we developed the first bioinformatics tool called i4mC-ROSE for identifying N4-methylcytosine sites in the genomes of Fragaria vesca and Rosa chinensis in the Rosaceae, which utilizes a random forest classifier with six encoding methods that cover various aspects of DNA sequence information. The i4mC-ROSE predictor achieves area under the curve scores of 0.883 and 0.889 for the two genomes during cross-validation. Moreover, the i4mC-ROSE outperforms other classifiers tested in this study when objectively evaluated on the independent datasets. The proposed i4mC-ROSE tool can serve users' demand for the prediction of 4mC sites in the Rosaceae genome. The i4mC-ROSE predictor and utilized datasets are publicly accessible at http://kurata14.bio.kyutech.ac.jp/i4mC-ROSE/.

    DOI: 10.1016/j.ijbiomac.2019.12.009

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  • Prediction of: S -nitrosylation sites by integrating support vector machines and random forest Reviewed International journal

    Hasan M., Manavalan B., Khatun M., Kurata H.

    Molecular Omics   15 ( 6 )   451 - 458   2019.01

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    © 2019 The Royal Society of Chemistry. Cysteine S-nitrosylation is a type of reversible post-translational modification of proteins, which controls diverse biological processes. It is associated with redox-based cellular signaling to protect against oxidative stress. The identification of S-nitrosylation sites is an important step to reveal the function of proteins; however, experimental identification of S-nitrosylation is expensive and time-consuming work. Hence, sequence-based computational prediction of potential S-nitrosylation sites is highly sought before experimentation. Herein, a novel predictor PreSNO has been developed that integrates multiple encoding schemes by the support vector machine and random forest algorithms. The PreSNO achieved an accuracy and Matthews correlation coefficient value of 0.752 and 0.252 respectively in classifying between SNO and non-SNO sites when evaluated on the independent dataset, outperforming the existing methods. The web application of the PreSNO and its associated datasets are freely available at http://kurata14.bio.kyutech.ac.jp/PreSNO/.

    DOI: 10.1039/c9mo00098d

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  • SIPMA: A systematic identification of protein-protein interactions in Zea mays using autocorrelation features in a machine-learning framework Reviewed International journal

    Khatun M., Hasan M., Mollah M., Kurata H.

    Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018   122 - 125   2018.12

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    © 2018 IEEE. Zea mays (maize) is one of the most vital crops which are grown widely in the world. To understand the molecular structures and functions of maize, the identification of protein-protein interaction (PPI) is very important. PPI identification by wet lab experiments is time-consuming, expensive and laborious. These days in silico methods that accurately predict potential PPIs based on protein sequence information are highly demanded. Research on PPI prediction in maize is currently very limited, and no dedicated bioinformatics schemes are available. In this work, we proposed a novel approach, termed SIPMA (Systematic Identification of PPI in Maize using Autocorrelation). A machine learning random forest classifier was trained with autocorrelation features to build the prediction model. The SIPMA, which was tested by the experimentally verified PPI dataset of maize, yielded a prediction accuracy of 0.899 when the specificity was 0.969 on the training set. The SIPMA achieved promising performances on the test datasets. Compared with different sequence-based encoding and statistical learning methods, the SIPMA was a powerful computational resource for identifying PPIs in maize.

    DOI: 10.1109/BIBE.2018.00030

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  • iLMS, computational identification of lysine-malonylation sites by combining multiple sequence features Reviewed International journal

    Hasan M., Kurata H.

    Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018   356 - 359   2018.12

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    © 2018 IEEE. Lysine malonylation is a newly discovered post-translational modification of proteins, which plays an important role in regulating many cellular fonctions. Several approaches are available to identify malonylation proteins and its malonylation sites, however; experimental identification of malonylation sites is often laborious and costly. Therefore, computational schemes are needed to identify potential malonylation sites prior to in vitro experimentation. In this paper, a novel computational scheme iLMS (Identification of Lysine-Malonylation Sites) has been developed by combining primary sequences and evolutionary features via a support vector machine classifier. The final iLMS scheme achieved a robust performance in cross-validation test in both human and mouse datasets. For the mouse data, the iLMS predictor outperformed other existing implementations. The iLMS is a promising computational scheme for the prediction of malonylation sites.

    DOI: 10.1109/BIBE.2018.00077

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  • GPSuc: Global prediction of generic and species-specific succinylation sites by aggregating multiple sequence features Reviewed International journal

    Hasan M., Kurata H.

    PLoS ONE   13 ( 10 )   2018.10

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    © 2018 Hasan, Kurata. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Lysine succinylation is one of the dominant post-translational modification of the protein that contributes to many biological processes including cell cycle, growth and signal transduction pathways. Identification of succinylation sites is an important step for understanding the function of proteins. The complicated sequence patterns of protein succinylation revealed by proteomic studies highlight the necessity of developing effective species-specific in silico strategies for global prediction succinylation sites. Here we have developed the generic and nine speciesspecific succinylation site classifiers through aggregating multiple complementary features. We optimized the consecutive features using the Wilcoxon-rank feature selection scheme. The final feature vectors were trained by a random forest (RF) classifier. With an integration of RF scores via logistic regression, the resulting predictor termed GPSuc achieved better performance than other existing generic and species-specific succinylation site predictors. To reveal the mechanism of succinylation and assist hypothesis-driven experimental design, our predictor serves as a valuable resource. To provide a promising performance in large-scale datasets, a web application was developed at http://kurata14.bio.kyutech.ac.jp/GPSuc/.

    DOI: 10.1371/journal.pone.0200283

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  • Computational modeling of lysine post-translational modification: an overview. Invited Reviewed International journal

    Curr Synthetic Sys Biol   6   1   2018.04

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    DOI: 10.4172/2332-0737.1000137

  • A novel isolation method for cancer prognostic factors via the p53 pathway by a combination of in vitro and in silico analyses Reviewed International journal

    Oncoscience ( Impact Journals )   5   88 - 98   2018.04

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    DOI: 10.18632/oncoscience.411

  • Long negative feedback loop enhances period tunability of biological oscillators Reviewed

    Maeda K., Kurata H.

    Journal of Theoretical Biology   440   21 - 31   2018.03

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    © 2017 Elsevier Ltd Oscillatory phenomena play a major role in organisms. In some biological oscillations such as cell cycles and heartbeats, the period can be tuned without significant changes in the amplitude. This property is called (period) tunability, one of the prominent features of biological oscillations. However, how biological oscillators produce tunable oscillations remains largely unexplored. We tackle this question using computational experiments. It has been reported that positive-plus-negative feedback oscillators produce tunable oscillations through the hysteresis-based mechanism. First, in this study, we confirmed that positive-plus-negative feedback oscillators generate tunable oscillations. Second, we found that tunability is positively correlated with the dynamic range of oscillations. Third, we showed that long negative feedback oscillators without any additional positive feedback loops can produce tunable oscillations. Finally, we computationally demonstrated that by lengthening the negative feedback loop, the Repressilator, known as a non-tunable synthetic gene oscillator, can be converted into a tunable oscillator. This work provides synthetic biologists with clues to design tunable gene oscillators.

    DOI: 10.1016/j.jtbi.2017.12.014

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  • Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures Reviewed International journal

    Kurata H., Sugimoto Y.

    Journal of Bioscience and Bioengineering   125 ( 2 )   251 - 257   2018.02

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    © 2017 The Society for Biotechnology, Japan Many kinetic models of Escherichia coli central metabolism have been built, but few models accurately reproduced the dynamic behaviors of wild type and multiple genetic mutants. In 2016, our latest kinetic model improved problems of existing models to reproduce the cell growth and glucose uptake of wild type, ΔpykA:pykF and Δpgi in a batch culture, while it overestimated the glucose uptake and cell growth rates of Δppc and hardly captured the typical characteristics of the glyoxylate and TCA cycle fluxes for Δpgi and Δppc. Such discrepancies between the simulated and experimental data suggested biological complexity. In this study, we overcame these problems by assuming critical mechanisms regarding the OAA-regulated isocitrate dehydrogenase activity, aceBAK gene regulation and growth suppression. The present model accurately predicts the extracellular and intracellular dynamics of wild type and many gene knockout mutants in batch and continuous cultures. It is now the most accurate, detailed kinetic model of E. coli central carbon metabolism and will contribute to advances in mathematical modeling of cell factories.

    DOI: 10.1016/j.jbiosc.2017.09.005

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  • libRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models Reviewed International journal

    Maeda Kazuhiro, Boogerd Fred C., Kurata Hiroyuki

    IPSJ Transactions on Bioinformatics   11 ( 0 )   31 - 40   2018.01

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    DOI: 10.2197/ipsjtbio.11.31

    CiNii Article

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  • A comprehensive review of in silico analysis for protein s-sulfenylation sites Invited Reviewed International journal

    Hasan M., Khatun M., Kurata H.

    Protein and Peptide Letters   25 ( 9 )   815 - 821   2018.01

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    © 2018 Bentham Science Publishers. Background: Cysteine S-sulfenylation is a major type of dynamic post-translational modification of the protein that plays an important role in regulating many biological processes in both of prokaryotic and eukaryotic species. To understand the function of S-sulfenylated proteins, identification of S-sulfenylation sites is an essential step. Due to numerous restrictions of experimental methods, computational prediction of the potential S-sulfenylation sites becomes popular. In this review, we discuss the recent development and challenges in protein S-sulfenylation site prediction from the available datasets, algorithms and accessible services. We also demonstrate the encountered limitation and future perspective of the computational prediction tools. Conclusion: The development of S-sulfenylation site prediction and their application is an emerging field of protein bioinformatics research. Accurate predictors are expected to identify general and species-specific S-sulfenylation sites when more experimental annotation data are available. Combining experimental and computational technologies will definitely accelerate an understanding of protein S-sulfenylation, discovering regulatory networks in living organisms.

    DOI: 10.2174/0929866525666180905110619

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  • Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations Reviewed International journal

    Matsuoka Y., Kurata H.

    Biotechnology for Biofuels   10 ( 1 )   183   2017.08

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    DOI: 10.1186/s13068-017-0867-0

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  • Mathematical comparison of memory functions between mutual activation and repression networks in a stochastic environment Reviewed International journal

    Hasan A., Kurata H.

    Journal of Theoretical Biology   427   28 - 40   2017.08

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    © 2017 Elsevier LtdBiological memory is a ubiquitous function that can generate a sustained response to a transient inductive stimulus. To better understand this function, we must consider the mechanisms by which different structures of genetic networks achieve memory. Here, we investigated two competitive gene regulatory network models: the regulated mutual activation network (MAN) and the regulated mutual repression network (MRN). Stochasticity deteriorated the persistence of memory of both the MAN and the MRN. Mathematical comparison by simulation and theoretical analysis identified functional differences in the stochastic memory between the competitive models: specifically, the MAN provided much more robust, persistent memory than the MRN. The stochastic persistent memory pattern of the MAN can be adjusted by changing the binding strength of the activators, whereas the MRN required highly cooperative and strong binding repressors for robust memory.

    DOI: 10.1016/j.jtbi.2017.05.036

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  • Robustness analysis of the detailed kinetic model of an ErbB signaling network by using dynamic sensitivity Reviewed International journal

    Masunaga H., Sugimoto Y., Magi S., Itasaki R., Okada-Hatakeyama M., Kurata H.

    PLoS ONE   12 ( 5 )   2017.05

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    © 2017 Masunaga et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The ErbB receptor signaling pathway plays an important role in the regulation of cellular proliferation, survival and differentiation, and dysregulation of the pathway is linked to various types of human cancer. Mathematical models have been developed as a practical complementary approach to deciphering the complexity of ErbB receptor signaling and elucidating how the pathways discriminate between ligands to induce different cell fates. In this study, we developed a simulator to accurately calculate the dynamic sensitivity of extracellular-signal-regulated kinase (ERK) activity (ERK∗) and Akt activity (Akt∗), downstream of the ErbB receptors stimulated with epidermal growth factor (EGF) and heregulin (HRG). To demonstrate the feasibility of this simulator, we estimated how the reactions critically responsible for ERK∗ and Akt∗ change with time and in response to different doses of EGF and HRG, and predicted that only a small number of reactions determine ERK∗ and Akt∗. ERK∗ increased steeply with increasing HRG dose until saturation, while showing a gently rising response to EGF. Akt∗ had a gradual wide-range response to HRG and a blunt response to EGF. Akt∗ was sensitive to perturbations of intracellular kinetics, while ERK∗ was more robust due to multiple, negative feedback loops. Overall, the simulator predicted reactions that were critically responsible for ERK∗ and Akt∗ in response to the dose of EGF and HRG, illustrated the response characteristics of ERK∗ and Akt∗, and estimated mechanisms for generating robustness in the ErbB signaling network.

    DOI: 10.1371/journal.pone.0178250

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  • Computational identification of protein S-sulfenylation sites by incorporating the multiple sequence features information Reviewed International journal

    Hasan M., Guo D., Kurata H.

    Molecular BioSystems   13 ( 12 )   2545 - 2550   2017.01

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    © 2017 The Royal Society of Chemistry. Cysteine S-sulfenylation is a major type of posttranslational modification that contributes to protein structure and function regulation in many cellular processes. Experimental identification of S-sulfenylation sites is challenging, due to the low abundance of proteins and the inefficient experimental methods. Computational identification of S-sulfenylation sites is an alternative strategy to annotate the S-sulfenylated proteome. In this study, a novel computational predictor SulCysSite was developed for accurate prediction of S-sulfenylation sites based on multiple sequence features, including amino acid index properties, binary amino acid codes, position specific scoring matrix, and compositions of profile-based amino acids. To learn the prediction model of SulCysSite, a random forest classifier was applied. The final SulCysSite achieved an AUC value of 0.819 in a 10-fold cross-validation test. It also exhibited higher performance than other existing computational predictors. In addition, the hidden and complex mechanisms were extracted from the predictive model of SulCysSite to investigate the understandable rules (i.e. feature combination) of S-sulfenylation sites. The SulCysSite is a useful computational resource for prediction of S-sulfenylation sites. The online interface and datasets are publicly available at http://kurata14.bio.kyutech.ac.jp/SulCysSite/.

    DOI: 10.1039/c7mb00491e

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  • In vitro evaluation of a combination treatment involving anticancer agents and an aurora kinase B inhibitor Reviewed International journal

    Sakai S., Izumi H., Yoshiura Y., Nakayama Y., Yamaguchi T., Harada Y., Koi C., Kurata H., Morimoto Y.

    Oncology Letters   12 ( 5 )   4263 - 4269   2016.11

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    © 2016, Spandidos Publications. All rights reserved. Aurora kinase B (AURKB) inhibitors are regarded as potential molecular-targeting drugs for cancer therapy. The present study evaluated the cytotoxic effect of a combination of AZD1152-hQPA, an AURKB inhibitor, and various anticancer agents on the HeLa human cervical cancer cell line, as well as its cisplatin-resistant equivalent HCP4 cell line. It was demonstrated that AZD1152-hQPA had an antagonistic effect on the cytotoxicity of cisplatin, etoposide and doxorubicin, but had a synergistic effect on that of all-trans-retinoic acid (ATRA), Am80 and TAC-101, when tested on HeLa cells. Cisplatin, etoposide and doxorubicin were shown to increase the cellular expression of AURKB, while ATRA, Am80 and TAC-101 downregulated its expression. These results suggested that AURKB expression is regulated by these anticancer agents at the transcriptional level, and that the level of expression of AURKB may influence the cytotoxic effect of AZD1152-hQPA. Therefore, when using anticancer agents, decreasing the expression of AURKB using a molecular-targeting drug may be an optimal therapeutic strategy.

    DOI: 10.3892/ol.2016.5156

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  • Metabolic analysis of antibody producing Chinese hamster ovary cell culture under different stresses conditions Reviewed

    Badsha M., Kurata H., Onitsuka M., Oga T., Omasa T.

    Journal of Bioscience and Bioengineering   122 ( 1 )   117 - 124   2016.07

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    © 2015 The Society for Biotechnology, Japan. Chinese hamster ovary (CHO) cells are commonly used as the host cell lines concerning their ability to produce therapeutic proteins with complex post-translational modifications. In this study, we have investigated the time course extra- and intracellular metabolome data of the CHO-K1 cell line, under a control and stress conditions. The addition of NaCl and trehalose greatly suppressed cell growth, where the maximum viable cell density of NaCl and trehalose cultures were 2.2-fold and 2.8-fold less than that of a control culture. Contrariwise, the antibody production of both the NaCl and trehalose cultures was sustained for a longer time to surpass that of the control culture. The NaCl and trehalose cultures showed relatively similar dynamics of cell growth, antibody production, and substrate/product concentrations, while they indicated different dynamics from the control culture. The principal component analysis of extra- and intracellular metabolome dynamics indicated that their dynamic behaviors were consistent with biological functions. The qualitative pattern matching classification and hierarchical clustering analyses for the intracellular metabolome identified the metabolite clusters whose dynamic behaviors depend on NaCl and trehalose. The volcano plot revealed several reporter metabolites whose dynamics greatly change between in the NaCl and trehalose cultures. The elastic net identified some critical, intracellular metabolites that are distinct between the NaCl and trehalose. While a relatively small number of intracellular metabolites related to the cell growth, glucose, glutamine, lactate and ammonium ion concentrations, the mechanism of antibody production was suggested to be very complicated or not to be explained by elastic net regression analysis.

    DOI: 10.1016/j.jbiosc.2015.12.013

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  • Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli Reviewed International journal

    Jahan N., Maeda K., Matsuoka Y., Sugimoto Y., Kurata H.

    Microbial Cell Factories   15 ( 1 )   2016.06

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    © 2016 The Author(s).Background: A kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters. Results: In this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture. Conclusions: This model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes.

    DOI: 10.1186/s12934-016-0511-x

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  • S-system-based Analysis of the Robust Properties Common to Many Biochemical Network Models Reviewed

    Yu Matsuoka, Nusrat Jahan, Hiroyuki Kurata

    Bioprocess and Biosystems Engineering   2016.03

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    DOI: 10.1007/s00449-016-1554-4

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  • Metabolic analysis of antibody producing CHO cell culture under different stresses conditions Reviewed

    Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

    Journal of Bioscience and Bioengineering   2016.03

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  • Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants. Reviewed International journal

    Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kazuhiro Maeda, Hiroyuki Kurata

    Journal of Bioscience and Bioengineering   2016.03

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    DOI: 10.1016/j.jbiosc.2015.12.001

    Scopus

  • Developing a kinetic model of the E. coli ammonium assimilation network International journal

    Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata

    Proceedings of the 16th International Conference on Systems Biology   2015.11

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    Singapore   Singapore   2015.11.23  -  2015.11.26

  • A detailed kinetic model of E. coli central metabolism in a batch culture Reviewed International journal

    Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata,

    Proceedings of Asian Congress on Biotechnology 2015 (ACB2015)   2015.11

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    Malaysia   Kuala Lumpur   2015.11.15  -  2015.11.19

  • Effect of NaCl and Trehalose Condition on Antibody Producing CHO Cell Culture Reviewed International journal

    Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

    Proceedings of Asian Congress on Biotechnology 2015 (ACB2015)   2015.11

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    Malaysia   Kuala Lumpur   2015.11.15  -  2015.11.19

  • Synthesis and decomposition approach for rational design of a biochemical network International journal

    Hiroyuki Kurata

    Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human   2015.03

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    Japan   Iizuka   2015.03.05  -  2015.03.06

    Kyutacar

  • Toward a quantitative in silico model for the E. coli ammonium assimilation system

    Kazuhiro Maeda, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, Hiroyuki Kurata

    Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human   2015.03

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    Japan   Iizuka   2015.03.05  -  2015.03.06

    Kyutacar

  • Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity Reviewed International journal

    Kazuhiro Maeda, Hiroyuki Kurata

    BMC Syst. Biol.   8 ( Suppl 5 )   S1 - S12   2014.12

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    DOI: 10.1186/1752-0509-8-S5-S1

    Kyutacar

    Scopus

  • Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity Reviewed

    Kazuhiro Maeda, Hiroyuki Kurata

    GIW/ISCB-Asia 2014   2014.12

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    Japan   Tokyo   2014.12.15  -  2014.12.17

  • Complementary elementary modes for fast and efficient analysis of metabolic networks Reviewed

    Md. Bahadur Badsha, Hiroyuki Kurata

    Biochem Eng J.   90   121 - 130   2014.06

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    DOI: 10.1016/j.bej.2014.05.022

    Scopus

  • Integration of omics into metabolic flux distribution by complementary elementary mode analysis for large-scale metabolic networks Reviewed

    Md Bahadur Badsha, Hiroyuki Kurata

    3rd International Conference and Exhibition on Metabolomics & Systems Biology   2014.03

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    USA   San Antonio   2014.03.24  -  2014.03.26

  • CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis, Reviewed

    Bioproc. Biosys. Eng.   2014.03

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    DOI: 10.1007/s00449-014-1167-8

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  • S-systemを用いた代謝反応モデルの感度解析 Reviewed

    松岡結 , NusratJahan , 倉田博之

    IPSJ SIG technical reports ( Information Processing Society of Japan (IPSJ) )   2014 ( 1 )   1 - 2   2014.02

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110009675848

  • Aim and scope of the BMIRC at Kyutech

    Hiroyuki Kurata

    Proceedings of the Second BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering   2014.02

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    Japan   Iizuka   2014.02.19  -  2014.02.20

    Kyutacar

  • Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes Reviewed

    Journal of Chemical Engineering of Japan   47   1 - 9   2014.01

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    DOI: 10.1252/jcej.13we152

    Scopus

    CiNii Article

  • バイオテクノロジー Reviewed

    神谷 典穂, 田中 孝明, 宮坂 武寛, 倉田 博之, 近藤 昭彦, 市川 創作

    化学工学 = Chemical engineering   77 ( 10 )   719 - 724   2013.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10031199937

  • 大腸菌アンモニア同化制御機構のダイナミックモデルの構築 Reviewed

    前田和勲 , FredC.Boogerd , FrankJ.Bruggeman , HansV.Westerhoff , 倉田博之

    IPSJ SIG technical reports ( Information Processing Society of Japan (IPSJ) )   2013 ( 7 )   1 - 6   2013.09

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110009605329

  • Robust Complementary Hierarchical Clustering for Gene Expression Data Analysis by β-Divergence Reviewed

    J Biosci Bioeng.   116   397 - 407   2013.09

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    DOI: 10.1016/j.jbiosc.2013.03.010

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  • Robust complementary hierarchical clustering for gene expression data analysis by β-divergence Reviewed

    Badsha Md. Bahadur, Mollah Md. Nurul Haque, Jahan Nusrat, Kurata Hiroyuki

    Journal of bioscience and bioengineering   116 ( 3 )   397 - 407   2013.09

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110009657240

  • BioFNet: Biological functional network database for analysis and synthesis of biological systems Reviewed

    Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata

    Briefings in Bioinformatics   15   699 - 709   2013.07

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    DOI: 10.1093/bib/bbt048

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  • Effect of cra gene mutation on the metabolism of Escherichia coli for a mixture of multiple carbon sources Reviewed

    Ruilian Yao, Hiroyuki Kurata, Kazuyuki Shimizu

    Advances in Bioscience and Biotechnology   4   477 - 486   2013.03

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    DOI: 10.4236/abb.2013.43A063

    Kyutacar

  • Bioalgorithms for rational design of biological systems

    Hiroyuki Kurata

    The Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering   2013.02

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    Japan   Iizuka   2013.02.28  -  2013.03.01

    Kyutacar

  • Metabolic Engineering for Systematic Organization and Analysis of Complex Metabolic Networks Reviewed

    Md. Bahadur Badsha, Nusrat Jahan, Md. Nurul Haque Mollah, Hiroyuki Kurata

    Proceedings of the International Conference on Statistical Data Mining for Bioinformatics Health Agriculture and Environment   2012.12

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    Bangladesh   Rajshahi   2012.12.22  -  2012.12.24

    Kyutacar

  • Sequential Extraction of Several Gene-sets with Proper Groups of Individuals for Gene Expression Data Analysis

    Md. Bahadur Badsha, Nusrat Jahan, Md. Nurul Haque Mollah, Hiroyuki Kurata

    Proceedings of the International Conference on Statistical Data Mining for Bioinformatics Health Agriculture and Environment   2012.12

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    Bangladesh   Rajshahi   2012.12.22  -  2012.12.24

    Kyutacar

  • Dynamic modeling of E. coli ammonia assimilation system Reviewed

    Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Frank J. Bruggeman, Hiroyuki Kurata

    FOSBE 2012   2012.10

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    Japan   Tsuruoka   2012.10.21  -  2012.10.25

  • バイオテクノロジー Reviewed

    神谷 典穂, 田中 孝明, 水本 博, 倉田 博之, 中崎 清彦, 安部 道玄, 酒井 昇

    化学工学 = Chemical engineering   76 ( 10 )   608 - 613   2012.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10031117614

  • Computational framework for integration of metabolic flux analysis with its associated omics data Reviewed

    Hiroyuki Kurata, Soma Tabata, Quanyu Zhao

    Proceedings of the14th International Biotechnology Symposium and Exhibition (IBS2012)   2012.09

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    Korea   Deagu   2012.09.18  -  2012.09.18

  • CADLIVE Optimizer: Web-based Parameter Estimation for Dynamic Models Reviewed

    7   9   2012.08

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    DOI: 10.1186/1751-0473-7-9

    Kyutacar

    Scopus

  • Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks Reviewed

    Bioproc Biosys Eng   36   333 - 344   2012.07

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    DOI: 10.1007/s00449-012-0789-y

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  • Computational framework for integration of metabolic flux analysis with its associated omics data Reviewed

    Hiroyuki Kurata, Soma Tabata, Quanyu Zhao

    The 8th Asia-Pacific Conference on Algal Biotechnology (APCAB 2012)   55   2012.07

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    Australia   Adelaide   2012.07.09  -  2012.07.12

  • Application of Systems Biology for CO2 Fixation and Biofuel Production Using Microalgae Reviewed

    Quanyu Zhao, Jiping Shi, Hiroyuki Kurata

    The 8th Asia-Pacific Conference on Algal Biotechnology (APCAB 2012)   2012.07

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    Australia   Adelaide   2012.07.09  -  2012.07.12

  • Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps Reviewed

    Kentaro Inoue, Shinichi Shimozono, Hideaki Yoshida, Hiroyuki Kurata

    7 ( 6 )   e37739   2012.06

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    DOI: 10.1371/journal.pone.0037739

    Kyutacar

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  • Biomedical Informatics R&D Center : Application of Informatics and Systems Engineering to Metabolic Systems Reviewed

    KURATA Hiroyuki

    IEICE technical report. Information theory ( The Institute of Electronics, Information and Communication Engineers )   112 ( 58 )   19 - 21   2012.05

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    Next generation sequencers enable decoding human genome at a surprisingly high speed. Furthermore, biological and medical data have rapidly been produced due to the development of systemic high-throughput technologies. Bioinformatics and systems biology have emerged, facilitating the interdisciplinary research and development among medicine, informatics, and engineering. In such a world-wide stream, we extensively apply the information technology and systems engineering to the research and development of medicine and medical care systems. In this study, we demonstrate that information technology is effective in analysis of metabolic networks.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110009569247

  • A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator Reviewed

    Kazuhiro Maeda, Hiroyuki Kurata

    PLoS ONE   7 ( 2 )   e30489   2012.02

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    DOI: 10.1371/journal.pone.0030489

    Kyutacar

    Scopus

  • Biological design principles of complex feedback modules in the E. coli ammonia assimilation system Reviewed

    Koichi Masaki, Kazuhiro Maeda, Hiroyuki Kurata

    Artificial Life   18   53 - 90   2012.01

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    DOI: 10.1162/artl_a_00049

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  • Grid layout algorithm for biochemical networks using approximate pattern matching Reviewed

    Kentaro Inoue, Sinichi Shimozono, Hiroyuki Kurata

    International Conference on Bioinformatics (InCoB2011)   229   2011.11

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    Malaysia   Kuala Lumpur   2011.11.30  -  2011.12.02

  • CADLIVE Converter for constructing a biochemical network map Reviewed

    Kentaro Inoue, Sayaka Tomeda, Shinpei Tonami, Yuki Shimokawa, Masayo Ono, Hiroyuki Kurata

    Biochem Eng J   54   200 - 206   2011.08

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    DOI: 10.1016/j.bej.2011.02.022

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  • An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks Reviewed

    Kazuhiro Maeda, Yuya Fukano, Shunsuke Yamamichi, Daichi Nitta, Hiroyuki Kurata

    Bioproc Biosys Eng   34   433 - 446   2011.08

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    DOI: 10.1007/s00449-010-0486-7

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  • Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks Reviewed

    Kazuhiro Maeda, Hiroyuki Kurata

    J Theor Biol   272   174 - 186   2011.08

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    DOI: 10.1016/j.jtbi.2010.12.012

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  • Maximum entropy principle optimizes the large-scale elementary modes for a broad range of genetic mutants Reviewed

    Hiroyuki Kurata, Quanyu Zhao

    Proceedings of Asian Congress on Biotechnology   B0768   2011.05

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    China   Shanghai   2011.05.11  -  2011.05.15

  • 生体分子ネットワークレイアウトのための2次元近似照合によるハイブリッドレイアウトアルゴリズム

    井上健太郎、下園真一、吉田英聡、倉田博之

    情報処理学会研究報告   BIO-24 ( 6 )   1 - 6   2011.03

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    Kyutacar

  • 概日リズムのフィードバックシステムのロバストネス解析

    前田和勲、倉田博之

    情報処理学会研究報告   BIO-24 ( 7 )   1 - 6   2011.03

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    Kyutacar

  • Diffusion model based spectral clustering for protein-protein interaction networks. Reviewed

    Inoue K., Li W., Kurata H.

    PloS one   5 ( 9 )   2010.12

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    A goal of systems biology is to analyze large-scale molecular networks including gene expressions and protein-protein interactions, revealing the relationships between network structures and their biological functions. Dividing a protein-protein interaction (PPI) network into naturally grouped parts is an essential way to investigate the relationship between topology of networks and their functions. However, clear modular decomposition is often hard due to the heterogeneous or scale-free properties of PPI networks. To address this problem, we propose a diffusion model-based spectral clustering algorithm, which analytically solves the cluster structure of PPI networks as a problem of random walks in the diffusion process in them. To cope with the heterogeneity of the networks, the power factor is introduced to adjust the diffusion matrix by weighting the transition (adjacency) matrix according to a node degree matrix. This algorithm is named adjustable diffusion matrix-based spectral clustering (ADMSC). To demonstrate the feasibility of ADMSC, we apply it to decomposition of a yeast PPI network, identifying biologically significant clusters with approximately equal size. Compared with other established algorithms, ADMSC facilitates clear and fast decomposition of PPI networks. ADMSC is proposed by introducing the power factor that adjusts the diffusion matrix to the heterogeneity of the PPI networks. ADMSC effectively partitions PPI networks into biologically significant clusters with almost equal sizes, while being very fast, robust and appealing simple.

    Scopus

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  • バイオテクノロジー Reviewed

    池田 宰, 上田 宏, 大河内 美奈, 吉見 靖男, 倉田 博之, 木村 幸敬

    化学工学 = Chemical engineering   74 ( 10 )   570 - 576   2010.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10026689209

  • Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis Reviewed

    Zhao Quanyu, Kurata Hiroyuki

    Journal of bioscience and bioengineering   110 ( 2 )   254 - 261   2010.08

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110007700578

  • Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis Reviewed

    J Biosci Bioeng   110   254 - 261   2010.08

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    DOI: 10.1016/j.jbiosc.2010.01.015

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  • JABEE認定校のカリキュラムと教育内容の特色 : (3) 九州工業大学生命情報工学科のプログラム Reviewed

    倉田 博之, 清水 和幸

    生物工学会誌 : seibutsu-kogaku kaishi   88 ( 5 )   233 - 236   2010.05

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110007619778

  • Diffusion Model Based Spectral Clustering For Protein-Protein Interaction Networks Reviewed

    Kentaro Inoue, Weijiang Li and Hiroyuki Kurata

    PLOS ONE   5   e12623   2010.04

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    DOI: 10.1371/journal.pone.0012623

    Kyutacar

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  • Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks Reviewed

    Maeda K., Kurata H.

    IPSJ Transactions on Bioinformatics   2   2 - 14   2009.12

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    DOI: 10.2197/ipsjtbio.2.2

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    CiNii Article

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  • Module-based analysis of the robustness generated by complex feedback regulations in biological networks Reviewed

    Kurata H.

    ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings   192 - 195   2009.12

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    Bacterial cells evolve complex networks to survive nutrient starvation. The E. coli ammonia assimilation system consists of many positive and negative feedbacks for synthesizing glutamine and glutamate, the source of most nitrogen-containing compounds. Our objectives are to understand the molecular architecture of how those feedback loops act in concert for enhanced robustness with respect to ammonia depletion. The ammonia assimilation system is decomposed into the hierarchical modular structure in analogy to engineering control architecture. This modular architecture is elaborately designed to solve contradictory design issues. Comparison of biological modules with engineering systems identifies interesting biologically specific design features. © 2009 SICE.

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  • バイオテクノロジー Reviewed

    倉田 博之, 中野 秀雄, 大河内 美奈, 吉見 靖男, 池田 宰, 吉井 英文

    化学工学 = Chemical engineering   73 ( 10 )   506 - 512   2009.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10026201207

  • Module-based analysis of the robustness generated by complex feedback regulations in biological networks Reviewed

    Hiroyuki Kurata

    Proceedings of ICROS-SICE International Joint Conference 2009   1A11-101   2009.08

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    Japan   Fukuoka   2009.08.18  -  2009.08.21

  • Elementary model-based prediction of the flux distribution for a variety of genetic mutants Reviewed

    Quanyu Zhao, Hiroyuki Kurata

    J Biosci Bioeng: Proceedings of APBioCHEC'2009   108   S165   2009.08

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    Japan   Kobe   2009.11.24  -  2009.11.28

  • Genetic modification of flux for flux prediction of mutants Reviewed

    Bioinformatics   25   1702 - 1708   2009.07

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  • Genetic modification of flux for flux prediction of mutants Reviewed

    Zhao Q., Kurata H.

    Bioinformatics   25 ( 13 )   1702 - 1708   2009.06

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    Motivation: Gene deletion and overexpression are critical technologies for designing or improving the metabolic flux distribution of microbes. Some algorithms including flux balance analysis (FBA) and minimization of metabolic adjustment (MOMA) predict a flux distribution from a stoichiometric matrix in the mutants in which some metabolic genes are deleted or non-functional, but there are few algorithms that predict how a broad range of genetic modifications, such as over- and underexpression of metabolic genes, alters the phenotypes of the mutants at the metabolic flux level. Results: To overcome such existing limitations, we develop a novel algorithm that predicts the flux distribution of the mutants with a broad range of genetic modification, based on elementary mode analysis. It is denoted as genetic modification of flux (GMF), which couples two algorithms that we have developed: modified control effective flux (mCEF) and enzyme control flux (ECF). mCEF is proposed based on CEF to estimate the gene expression patterns in genetically modified mutants in terms of specific biological functions. GMF is demonstrated to predict the flux distribution of not only gene deletion mutants, but also the mutants with underexpressed and overexpressed genes in Escherichia coli and Corynebacterium glutamicum. This achieves breakthrough in the a priori flux prediction of a broad range of genetically modified mutants. © The Author 2009. Published by Oxford University Press. All rights reserved.

    DOI: 10.1093/bioinformatics/btp298

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  • スペクトル法によるタンパク質相互作用ネットワークのモジュール分解,

    井上健太郎 Weijiang Li, 倉田博之

    情報処理学会研究報告   BIO-17 ( 14 )   1 - 4   2009.05

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    Kyutacar

  • 概日リズムのインターロックフィードバックのロバストネス解析

    前田和勲 倉田博之

    情報処理学会研究報告   BIO-17 ( 15 )   1 - 5   2009.05

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    Kyutacar

  • Modular decomposition based spectrum for protein-protein interaction network Reviewed

    INOUE Kentaro, LI Weijiang, KURATA Hiroyuki

    情報処理学会研究報告. BIO, バイオ情報学 = IPSJ SIG technical reports   17   H1 - H4   2009.05

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110007990807

  • Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks Reviewed

    IPSJ Transaction on Bioinformatics   2   2 - 14   2009.04

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    Kyutacar

  • Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

    J Biosci Bioeng   107   84 - 89   2009.03

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  • A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits Reviewed

    32   283 - 288   2009.02

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  • Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

    Zhao Quanyu, Kurata Hiroyuki

    Journal of bioscience and bioengineering   107 ( 1 )   84 - 89   2009.01

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    CiNii Article

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  • Two-phase Search (TPS) Method: Nonbiased and High-speed Parameter Search for Dynamic Models of Biochemical Networks Reviewed

    Maeda Kazuhiro, Kurata Hiroyuki

    Information and Media Technologies   4 ( 2 )   377 - 389   2009.01

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    DOI: 10.11185/imt.4.377

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/130000120679

  • Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

    Zhao Q., Kurata H.

    Journal of Bioscience and Bioengineering   107 ( 1 )   84 - 89   2009.01

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    Enzyme Control Flux (ECF) is a method of correlating enzyme activity and flux distribution. The advantage of ECF is that the measurement integrates proteome data with metabolic flux analysis through Elementary Modes (EMs). But there are a few methods of effectively determining the Elementary Mode Coefficient (EMC) in cases where no objective biological function is available. Therefore, we proposed a new algorithm implementing the maximum entropy principle (MEP) as an objective function for estimating the EMC. To demonstrate the feasibility of using the MEP in this way, we compared it with Linear Programming and Quadratic Programming for modeling the metabolic networks of Chinese Hamster Ovary, Escherichia coli, and Saccharomyces cerevisiae cells. The use of the MEP presents the most plausible distribution of EMCs in the absence of any biological hypotheses describing the physiological state of cells, thereby enhancing the prediction accuracy of the flux distribution in various mutants. © 2008 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jbiosc.2008.09.011

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  • CADLIVE: Computer aided design of biochemical systems Reviewed

    Supplement of Journal of Biotechnology:13 th International Biotechnology Symposium and Exhibition (IBS2008)   I4-O-001   2008.10

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    China   Dailen   2008.10.12  -  2008.10.17

  • Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Reviewed

    Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata

    Supplement of Journal of Biotechnology:13 th International Biotechnology Symposium and Exhibition (IBS2008)   I1-O-071   2008.10

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    China   Dailen   2008.10.12  -  2008.10.17

  • バイオテクノロジー Reviewed

    酒井 康行, 中野 秀雄, 吉本 誠, 倉田 博之, 池田 宰, 橋本 篤

    化学工学 = CHEMICAL ENGINEERING OF JAPAN   72 ( 10 )   551 - 557   2008.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10021982559

  • Prediction of flux distribution of mutants by enzyme control fluxes with maximum entropy principal Reviewed

    Quanyu Zhao, Hiroyuki Kurata

    Supplement of Journal of Biotechnology: 13 th International Biotechnology Symposium and Exhibition (IBS2008)   2008.10

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    China   2008.10.12  -  2008.10.17

  • Two-phase search (TPS) 法 : 動的生化学ネットワークモデルの偏りのない効率的なパラメータ探索 Reviewed

    前田 和勲, 倉田 博之

    情報処理学会研究報告. BIO, バイオ情報学 = IPSJ SIG technical reports   14   9 - 12   2008.09

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    CiNii Article

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  • 動的生化学ネットワークモデルの偏りのない効率的なパラメータ探索

    前田和勲,倉田博之

    情報処理学会研究報告   BIO-14   9 - 12   2008.08

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  • Visualizing global properties of large complex networks Reviewed

    Li W., Kurata H.

    PLoS ONE   3 ( 7 )   2008.07

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    For complex biological networks, graphical representations are highly desired for understanding some design principles, but few drawing methods are available that capture topological features of a large and highly heterogenous network, such as a protein interaction network. Here we propose the circular perspective drawing (CPD) method to visualize global structures of large complex networks. The presented CPD combines the quasi-continuous search (QCS) analogous to the steepest descent method with a random node swapping strategy for an enhanced calculation speed. The CPD depicts a network in an aesthetic manner by showing connection patterns between different parts of the network instead of detailed links between nodes. Global structural features of networks exhibited by CPD provide clues toward a comprehensive understanding of the network organizations. © 2008 Li, Kurata.

    DOI: 10.1371/journal.pone.0002541

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  • Estimation of Intracellular Flux Distribution under Underdetermined and Uncertain Conditions by Maximum Entropy Principle Reviewed

    Quanyu Zhao,Hiroyuki Kurata

    Chin J Biotech   Chin 24: 24   21352136 - 21352136   2008.04

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  • Maximum entropy decomposition of flux distribution at steadystate to elementary modes Reviewed

    Quanyu Zhao,Hiroyuki Kurata

    J Biosci Bioeng   107   8489 - 8489   2008.04

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  • A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits Reviewed

    Emi Shiraishi Kazuhiro Maeda Hiroyuki Kurata

    Bioprocess Biosyst. Eng   32   283288 - 283288   2008.04

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  • Visualizing Global Properties of Large Complex Networks Reviewed

    Li W.,Kurata H.

    PLoS ONE   3   e2541 - e2541   2008.04

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  • Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli Reviewed

    Yousuke Nishio,Yoshihiro Usuda,Kazuhiko Matsui,Hiroyuki Kurata

    Molecular Systems Biology   4   160 - 160   2008.04

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    Kyutacar

  • Two-phase search (TPS) method: Nonbiased and efficient parameter search for dynamic models of biochemical networks.

    Maeda,K.,Kurata,H.

    IPSJ SIG Technical Report   BIO-14   9 - 12   2008.04

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  • CADLIVE for Construction and Dynamic Simulation of Biochemical Networks Reviewed

    Kazuhiro Maeda,Hiroyuki Kurata

    Proceedings of Asia Pacific Biochemical Engineering Conference   ( J0013 )   2007.11

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    中華民国   台北   2007.11.04  -  2007.11.07

  • Systems Biology of the Nitrogen Assimilation System in E.coli Reviewed

    Koichi Masaki,Hiroyuki Kurata

    Proceedings of Asia Pacific Biochemical Engineering Conference   J0108 - J0108   2007.11

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    中華民国   台北   2007.11.04  -  2007.11.07

  • Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis Reviewed

    Kurata H., Inoue K., Maeda K., Masaki K., Shimokawa Y., Zhao Q.

    Nucleic Acids Research   35 ( 20 )   2007.11

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    Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents 'Domain expansion' for proteins and RNAs, 'Virtual reaction and nodes' that are responsible for illustrating domain-based interaction and 'InnerLink' that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis. © 2007 The Author(s).

    DOI: 10.1093/nar/gkm769

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  • Mathematical identification of critical reactions in the interlocked feedback model Reviewed

    Kurata H., Tanaka T., Ohnishi F.

    PLoS ONE   2 ( 10 )   2007.10

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    Dynamic simulations are necessary for understanding the mechanism of how biochemical network generate robust properties to environmental stresses or genetic changes. Sensitivity analysis allows the linking of robustness to network structure. However, it yields only local properties regarding a particular choice of plausible parameter values, because it is hard to know the exact parameter values in vivo. Global and firm results are needed that do not depend on particular parameter values. We propose mathematical analysis for robustness (MAR) that consists of the novel evolutionary search that explores all possible solution vectors of kinetic parameters satisfying the target dynamics and robustness analysis. New criteria, parameter spectrum width and the variability of solution vectors for parameters, are introduced to determine whether the search is exhaustive. In robustness analysis, in addition to single parameter sensitivity analysis, robustness to multiple parameter perturbation is defined. Combining the sensitivity analysis and the robustness analysis to multiple parameter perturbation enables identifying critical reactions. Use of MAR clearly identified the critical reactions responsible for determining the circadian cycle in the Drosophila interlocked circadian clock model. In highly robust models, while the parameter vectors are greatly varied, the critical reactions with a high sensitivity are uniquely determined. Interestingly, not only the per-timloop but also the dclk-cyc loop strongly affect the period of PER, although the dclk-cyc loop hardly changes its amplitude and it is not potentially influential. In conclusion, MAR is a powerful method to explore wide parameter space without human-biases and to link a robust property to network architectures without knowing the exact parameter values. MARS identifies the reactions critically responsible for determining the period and amplitude in the interlocked feedback model and suggests that the circadian clock intensively evolves or designs the kinetic parameters so that it creates a highly robust cycle. © 2007 Kurata et al.

    DOI: 10.1371/journal.pone.0001103

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  • 生物情報 Reviewed

    倉田 博之

    化学工学 = CHEMICAL ENGINEERING OF JAPAN   71 ( 10 )   682 - 683   2007.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10019952371

  • A Stochastic Simulation of Diffusion Reaction Model in Embryo Development Reviewed

    NAKANO Katsutoshi, IWASAKI Rei, KURATA Hiroyuki

    IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) )   66   95 - 98   2007.09

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    The deterministic simulation that uses ordinary differential equations to clarify dynamic behaviors of life-giving molecular networks is actively implemented now. However, gene expressions in cells happen stochastically and materials diffusion. In the deterministic simulation, time variations of molecular concentrations are decided when parameters are decided. Therefore, we propose the new method of spatiotemporal Monte Carlo simulation for achieving the simulation applied to gene expression and diffusion of materials in space and time.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110006403660

  • Global Optimization of Large-scale Dynamic Biomolecular Network Model Reviewed

    MAEDA KAZUHIRO, YOSHIDA KEISUKE, KURATA HIROYUKI

    IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) )   66   91 - 94   2007.09

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    Dynamic simulation is a way to analyze dynamics of biomolecular networks consisting of proteins, metabolites and genes. In order to simulate their intrinsic dynamics, it is necessary to optimize the values of many kinetic parameters by reverse-engineering. We developed a new optimization method, DIS (Decomposition and Integration with Statistical analysis) combining decomposition and integration method with statistical analysis. By using DIS and genetic algorithm (GA), we optimized the parameters of large-scale biomolecular network which conventional GA cannot optimize. In this article, we also show that this method can obtain global solutions.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110006403659

  • Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator Reviewed

    Tanaka S., Kurata H., Ohashi T.

    Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics   5   3596 - 3601   2007.08

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    In the field of systems biology, biochemical networks are being reconstructed in computer to understand their dynamic features. In this study, we focused on the estimation problem for a dynamic model of the Drosophila circadian oscillator, which is defined by two evaluation functions that represent oscillatory features. However, since the search space is multimodal and logarithmically large, it is quite difficult for ordinary GAs to optimize this evaluation problem. Therefore, we had used two-step optimizing, a random search with GA. It successfully optimized the circadian oscillator, but required a long calculation time, causing a local search. On the other hand, to optimize two evaluation functions simultaneously, we proposed the survival ratio GA, where genes have lifetimes and a population holds search histories. By alternating two evaluation functions every generation, the population holds previously evaluated genes and children inherit each and mixed properties. The survival ratio GA exhibited wider space search and higher success ratio, thus we applied the one-step optimizing with the survival ratio GA to the circadian estimation problem, which shortens the total calculation times and finds out more local optimums than the previous two-step optimizing method. © 2006 IEEE.

    DOI: 10.1109/ICSMC.2006.384687

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  • Integration of enzyme activities into metabolic flux distributions by elementary mode analysis Reviewed

    Kurata H., Zhao Q., Okuda R., Shimizu K.

    BMC Systems Biology   1   2007.07

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    Background: In systems biology, network-based pathway analysis facilitates understanding or designing metabolic systems and enables prediction of metabolic flux distributions. Network-based flux analysis requires considering not only pathway architectures but also the proteome or transcriptome to predict flux distributions, because recombinant microbes significantly change the distribution of gene expressions. The current problem is how to integrate such heterogeneous data to build a network-based model. Results: To link enzyme activity data to flux distributions of metabolic networks, we have proposed Enzyme Control Flux (ECF), a novel model that integrates enzyme activity into elementary mode analysis (EMA). ECF presents the power-law formula describing how changes in enzyme activities between wild-type and a mutant are related to changes in the elementary mode coefficients (EMCs). To validate the feasibility of ECF, we integrated enzyme activity data into the EMCs of Escherichia coli and Bacillus subtilis wild-type. The ECF model effectively uses an enzyme activity profile to estimate the flux distribution of the mutants and the increase in the number of incorporated enzyme activities decreases the model error of ECF. Conclusion: The ECF model is a non-mechanistic and static model to link an enzyme activity profile to a metabolic flux distribution by introducing the power-law formula into EMA, suggesting that the change in an enzyme profile rather reflects the change in the flux distribution. The ECF model is highly applicable to the central metabolism in knockout mutants of E. coli and B. subtilis. © 2007 Kurata et al; licensee BioMed Central Ltd.

    DOI: 10.1186/1752-0509-1-31

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  • Integration of enzyme activities into metabolic flux distributions by elementary mode analysis Reviewed

    Hiroyuki Kurata,Quanyu Zhao,Ryuichi Okuda,Kazuyuki Shimizu

    BMC Systems Biology   1   31 - 31   2007.04

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  • Mathematical identification of critical reactions in the interlocked feedback model Reviewed

    H. Kurata,T. Tanaka,F. Ohnishi

    PLoS One   2   e1103 - e1103   2007.04

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  • Extended CADLIVE: a novel graphical notation for designing a biochemical network map that enables computational pathway analysis Reviewed

    Hiroyuki Kurata,Kentaro Inoue,Kazuhiro Maeda,Koichi Masaki,Yuki Shimokawa,Quanyu Zhao

    Nucleic Acids Res   35   e134 - e134   2007.04

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  • 大腸菌窒素同化システムのポジティブフィードバック制御のシンプルモデル Reviewed

    真崎浩一,倉田博之

    情報処理学会論文誌数理モデル化と応用   48   104 - 109   2007.04

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  • 大規模な動的生命分子ネットワークモデルのグローバルな最適化

    前田和勲,吉田圭介,倉田博之

    情報処理学会研究報告   MPS-66   91 - 94   2007.04

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  • 胚発生における拡散反応モデルの確率的シミュレーション

    中野克俊,岩崎麗,倉田博之

    情報処理学会研究報告   MPS-66   95 - 98   2007.04

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  • A Simple Model of Positive Feedback of the Nitrogen Assimilation System in E. coli Reviewed

    MASAKI KOICHI, KURATA HIROYUKI

    情報処理学会論文誌数理モデル化と応用(TOM) ( Information Processing Society of Japan (IPSJ) )   48 ( 6 )   104 - 109   2007.03

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    Computer simulation predicted that the nitrogen assimilation system in the GlnK knockout mutant of E. coli shows hysteresis with respect to changes in the extracellular ammonia concentration. To theoretically elucidate the mechanism of how hysteresis is generated, we reduced the dynamic model to a simple model with third-order equations. Theoretical analysis of the simple model shows that a positive feedback control is responsible for hysteresis. The system has two steady-state solutions within a specific range of ammonia concentrations. The range that provides two solutions expands when the positive feedback becomes strong, while the system has only one solution when the positive feedback is weakened.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110006242974

  • Bioinformatics Reviewed

    倉田 博之

    化学工学 = CHEMICAL ENGINEERING OF JAPAN   70 ( 10 )   2006.10

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10020524742

  • Systems Biology and Design of Biological Systems Reviewed

    KURATA Hiroyuki

    Seibutsu Butsuri ( The Biophysical Society of Japan General Incorporated Association )   46 ( 5 )   244 - 250   2006.09

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    Advances in the postgenomic technology produce huge data regarding molecular interactions. Systems biology requires a model-based analysis to understand the molecular architecture of biological systems. Systems biology consists of four stages: network identification, system analysis, system control, and system design. First, a large-scale biochemical network model is reconstructed in computer by elucidating gene functions or by inferring gene regulation networks from postgenomic data. Second, we analyze the network architectures that generate robust properties to various types of perturbations and explore some design principles underlying molecular architectures. Third, dynamic behaviors are controlled at the molecular level. Finally, we develop new technologies to rationally design a biochemical system at the molecular levels.<br>

    DOI: 10.2142/biophys.46.244

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110004810269

  • CADLIVE : Computer-Aided Design of biological systems and its application Reviewed

    KURATA Hiroyuki

    Bioscience & industry   64 ( 9 )   508 - 511   2006.09

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/10018069281

  • Module-based analysis of robustness tradeoffs in the heat shock response system Reviewed

    Kurata H., El-Samad H., Iwasaki R., Ohtake H., Doyle J., Grigorova I., Gross C., Khammash M.

    PLoS Computational Biology   2 ( 7 )   0663 - 0675   2006.08

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    Biological systems have evolved complex regulatory mechanisms, even in situations where much simpler designs seem to be sufficient for generating nominal functionality. Using module-based analysis coupled with rigorous mathematical comparisons, we propose that in analogy to control engineering architectures, the complexity of cellular systems and the presence of hierarchical modular structures can be attributed to the necessity of achieving robustness. We employ the Escherichia coli heat shock response system, a strongly conserved cellular mechanism, as an example to explore the design principles of such modular architectures. In the heat shock response system, the sigma-factor σ32 is a central regulator that integrates multiple feedforward and feedback modules. Each of these modules provides a different type of robustness with its inherent tradeoffs in terms of transient response and efficiency. We demonstrate how the overall architecture of the system balances such tradeoffs. An extensive mathematical exploration nevertheless points to the existence of an array of alternative strategies for the existing heat shock response that could exhibit similar behavior. We therefore deduce that the evolutionary constraints facing the system might have steered its architecture toward one of many robustly functional solutions. © 2006 Kurata et al.

    DOI: 10.1371/journal.pcbi.0020059

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  • A Simple model of positive feedback of the nitrogen assimilation system in E. coli Reviewed

    MASAKI Koichi, KURATA Hiroyuki

    IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) )   59   61 - 64   2006.05

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    Computer simulation predicted that the nitrogen assimilation system shows hysteresis with respect to the change in ammonia concentration in environment. To theoretically elucidate the mechanism of how hysteresis is generated, we reduced the dynamic model to the simple model with the third-order equations. Theoretical analysis of the simple model shows that the positive feedback control is responsible for hysteresis. The system has two steady-state solutions for the ammonia concentration within specific ranges. The range of an ammonia concentration that provides two solutions expands when the positive feedback becomes strong, while the system has only one solution when the positive feedback is weakened.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110004849753

  • Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System Reviewed

    H. Kurata,H. El Samad,R. Iwasaki,H. Othake,J.C. Doyle,I. Grigorova,C. Gross,and M. Khammash

    PLoS Computational Biology   2   e59 - e73   2006.05

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  • システムバイオロジーの現状と未来 Reviewed

    倉田 博之

    生物物理   46   244 - 250   2006.04

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    主要雑誌

  • Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator Reviewed

    Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

    IEEE International Conference on Systems, Man, and Cybernetics   3596 - 3601   2006.04

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    中華民国   Taipei   2006.04  -  2006.04

  • CADLIVE: Integration for large-scale network data

    Yuki Shimokawa,Zazuhiro Maeda,Kentaro Inoue,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   S02-1-2   2006.04

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  • A steady-state approximation-based solver for stiff biochemical models

    Emi Shiraishi,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   P016-1-2   2006.04

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  • Comparison of the prediction abilities of FBA, MOMA, and ROOM for a pykF mutant of E. coli

    Quanyu Zhao,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   P107-1-2   2006.04

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  • Sensitivity analysis for the E. coli nitrogen assimilation system

    Koichi Masaki,Hiroyuki Kurata

    P010-1-2   2006.04

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  • A simple model of positive feedback of the nitrogen assimilation system in E. coli

    Masaki Kouichi,Kurata Hiroyuki

    ISPJ SIG Technical Reports   61 - 64   2006.04

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  • Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli Reviewed

    Tanaka S., Kurata H., Ohashi T.

    Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics   3   2078 - 2083   2005.12

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    In the field of bioinformatics, several studies have attempted to reconstruct biological reactions on a computer in order to understand their essence. In this study, we optimized the parameter tuning problem of the heat shock response in E. coli, one of the gene regulatory network simulations, which exhibits a transient peak by genetic algorithms (GAs). However, if the search area is too large, the optimization performance deteriorated significantly. To optimize this problem more efficiently, we defined two evaluation functions that represent two features of the simulation and used the survival ratio GA. This GA has a gene's lifetime as a new concept, that is, the population holds previous search histories. By alternating between two evaluation functions every generation, the population holds both previously evaluated genes and children inherit both properties. In the two-evaluation problem of the heat shock response, the survival ratio GA exhibited a considerably better optimization performance than traditional GA methods. © 2005 IEEE.

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  • Reverse engineering for a dynamic model of the Drosophila circadian oscillator Reviewed

    Tanaka S., Kurata H., Ohashi T.

    Proceedings - International Conference on Computational Intelligence for Modelling, Control and Automation, CIMCA 2005 and International Conference on Intelligent Agents, Web Technologies and Internet   1   625 - 632   2005.12

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    In the field of bioinformatics, biochemical networks have been reconstructed in computer to understand their dynamic features. A problem is how to estimate the values of many kinetic parameters that are hard to measure experimentally. In this study, we have proposed a novel parameter estimation method based on genetic algorithms (GAs) and applied it to the Drosophila circadian oscillator. We defined two evaluation functions that represent two features of the dynamic model. To optimize the two functions simultaneously, we proposed the survival ratio GA, which has a gene's lifetime as a new concept, that is, the population holds previous search histories. By alternating between two evaluation functions every generation, the population holds both previously evaluated genes and children inherit both properties. In the two-evaluation problem of the Drosophila circadian oscillation system, the survival ratio GA exhibited a considerably better optimizing performance than traditional GA methods. © 2005 IEEE.

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  • Reverse Engineering for a Dynamic Model of the Drosophila Circadian Oscillator Reviewed

    Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

    International Conference on Computational Intelligence for Modelling, Control and Automation   625 - 631   2005.11

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    Austria   2005.11.28  -  2005.11.30

  • Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli Reviewed

    Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

    Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics   2078 - 2083   2005.10

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    米国   Hawaii   2005.10.10  -  2005.10.12

  • A grid layout algorithm for automatic drawing of biochemical networks Reviewed

    Li W., Kurata H.

    Bioinformatics   21 ( 9 )   2036 - 2042   2005.05

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    Motivation: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. Results: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. © The Author 2005. Published by Oxford University Press. All rights reserved.

    DOI: 10.1093/bioinformatics/bti290

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  • 有用物質生産のための細胞設計工学 Reviewed

    倉田博之

    ケミカルエンジニヤリング   50   907 - 912   2005.04

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    主要雑誌

  • Surviving heat shock: Control strategy for robustness and performance Reviewed

    H. El-Samad,H. Kurata,J.C. Doyle,C. A. Gross,M. Khammash

    Proc Natl Acad Sci U S A.   102   2736 - 2741   2005.04

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  • CADLIVE Dynamic Simulator: Direct Link of Biochemical Networks to Dynamic Models Reviewed

    Hiroyuki Kurata,Kouichi Masaki,Yoshiyuki Sumida,Rei Iwasaki

    Genome Res.   15   590 - 600   2005.04

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  • A Grid Layout Algorithm for Automatic Drawing of Biochemical Networks Reviewed

    Weijiang Li,Hiroyuki Kurata

    Bioinformatics   21   2036 - 2042   2005.04

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  • A large-scale dynamic simulation of the cell cycle network Reviewed

    Yamamichi,S.,Kurata,H.

    Proceedings of 7th Asia-Pacific Biochemical Engineering Conference   SYS2 - 05   2005.04

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    Korea   Jezu Isaland   2005.04  -  2005.04

  • Module Decomposition and Integration Optimizes Gene Regulatory and Metabolic Networks

    Keisuke Yoshida,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   16   P123-1-2   2005.04

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  • Interlocked Feedback is not the Best Choice for PER Oscillators

    Fumitaka Ohnishi,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   16   P116-1-2   2005.04

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  • CADLIVE: Computer-Aided Design of Living Systems

    Hiroyuki Kurata,Marie Kajiwara,Yuki Shimokawa

    The 16th International Conference on Genome Informatics   16   P114-1-1   2005.04

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  • Optimization of a Large-Scale Dynamic Model of the Cell Cycle Network Using Multi Objective GA

    Shunsuke Yamamichi,Hiroyuki Kurata

    The 16th International Conference on Genome Informatics   16   P122-1-2   2005.04

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  • CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models Reviewed

    Kurata H., Masaki K., Sumida Y., Iwasaki R.

    Genome Research   15 ( 4 )   590 - 600   2005.04

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    We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The simulator supports the biochemical reaction maps that are generated by the previously developed GUI editor. Notice that the part of the GUI editor had been previously published, but, as yet, not the simulator. To directly link biochemical network maps to dynamic simulation, we have created the strategy of three layers and two stages with the efficient conversion rules in an XML representation. This strategy divides a molecular network into three layers, i.e., gene, protein, and metabolic layers, and partitions the conversion process into two stages. Once a biochemical map is provided, CADLIVE automatically builds a mathematical model, thereby facilitating one to simulate and analyze it. In order to demonstrate the feasibility of CADLIVE, we analyzed the Escherichia coli nitrogen-assimilation system (64 equations with 64 variables) that consists of multiple and complicated negative and positive feedback loops. CADLIVE predicted that the glnK gene is responsible for hysteresis or reversibility of nitrogen-related (Ntr) gene expression with respect to the ammonia concentration, supporting the experimental observation of the runaway expression of the Ntr genes. ©2005 by Cold Spring Harbor Laboratory Press.

    DOI: 10.1101/gr.3463705

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  • Surviving heat shock: Control strategies for robustness and performance Reviewed

    El-Samad H., Kurata H., Doyle J., Gross C., Khammash M.

    Proceedings of the National Academy of Sciences of the United States of America   102 ( 8 )   2736 - 2741   2005.02

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    Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures. © 2005 by The National Academy of Sciences of the USA.

    DOI: 10.1073/pnas.0403510102

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  • Optimization of E.Coli heat shock response parameter tuning using distributed and integrated genetic algorithms Reviewed

    Tanaka S., Kurata H., Ohashi T.

    Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics   2   1243 - 1248   2004.12

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    The progress of computer made the analysis that was difficult in traditional technology possible. In Gene Regulatory Network Simulation to recreate and understand actual biological reaction, we build a reaction model and find the several unknown parameters in order to show the same behavior as actual. However it is difficult to optimize them because the scopes of them are logarithm scale wide and the fitness space is multidimensional and multimodal. We optimized it using Distributed Genetic Algorithms (DGA) which has multiple populations. DGA showed better performance, if and only if the parameter of the emigrating operation is appropriate. Therefore we propose Distributed and Integrated Genetic Algorithms (DIGA) to reduce the cost to find the appropriate parameters of operation. We carried out some optimizing experiments on parameter tuning of Heat Shock Response simulation of E.Coli and several mathematical functions and inspected the characteristic of DIGA. © 2004 IEEE.

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  • モジュール分割統合法による大規模生命分子ネットワークの最適化

    吉田圭介,倉田博之

    数理モデル化と問題解決シンポジウム論文集   97 - 102   2004.10

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  • 生命における振動システムのモデリングとシステム解析

    山道俊介,大西史高,倉田博之

    数理モデル化と問題解決シンポジウム論文集   379 - 382   2004.10

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  • Computer-Aided Design of Metabolic and Gene Regulatory Networks Reviewed

    Proceedings of The 10th APCChE Congress   2L - 06   2004.10

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    Kitakyushu   2004.10.17  -  2004.10.21

  • Optimization of E.Coli Heat Shock Response Parameter Tuning Using Distributed and Integrated Genetic Algorithms Reviewed

    Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

    Proceedings of the IEEE International Conference on Systems, Man and Cybernetics   1243 - 1248   2004.10

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    Hague, Netherlands   2004.10.10  -  2004.10.13

  • Statistical And Integrative Approach For Constructing Biological Network Maps Reviewed

    Hiroyuki Kurata,Natsumi Shimizu,Kanako Misumi

    Genome Informatics   15   161 - 170   2004.04

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  • Optimization and System Analysis of the Heat Shock Response by CADLIVE

    Kouji Mitsukiyo,Marie Kajiwara,Hiroyuki Kurata

    Genome Informatics Series   15   P006   2004.04

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  • Simulation of Circadian Rhythms Using Grid Computing

    Takayuki Tanaka,Hiroyuki Kurata

    Genome Informatics Series   15   P011   2004.04

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  • A Large-Scale Dynamic Model of the Yeast Cell Cycle

    Shunsuke Yamamichi,Hiroyuki Kurata

    Genome Informatics Series   15   P007   2004.04

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  • CADLIVE: New Modules for Domain Expansions and Topological Analysis

    Hiroyuki Kurata,Yuki Shimokawa,Tomoko Noguchi,Natsumi Shimizu

    Genome Informatics Series   15   S05   2004.04

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  • Statistical and Integrative Approach for Constructing Biological Network Maps Reviewed

    Kurata Hiroyuki, Shimizu Natsumi, Misumi Kanako

    Genome Informatics   15 ( 2 )   161 - 170   2004.01

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    DOI: 10.11234/gi1990.15.2_161

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  • Statistical and integrative approach for constructing biological network maps. Reviewed

    Kurata H., Shimizu N., Misumi K.

    Genome informatics. International Conference on Genome Informatics   15 ( 2 )   161 - 170   2004.01

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    A goal of systems biology is to build a concrete biochemical network map, which provides an important instruction to trace the pathways of interest or to understand the mechanism of a biological system. In the postgenomic era, not only the concrete biochemical maps, but also postgenomic maps (mRNA coexpression and protein-protein interaction networks) have been extensively produced. In the biochemical map, the individual reactions are reliable, but the number of the reactions is limited, because molecular biology requires extensive experiments to verify them. By contrast, postgenomic data provide much information regarding interactions, but are coarse-grained. To expand the biochemical network, an intuitional approach, which superposes postgenomic data on the map one by one, has been carried out, but it is not effective when a large amount of the coarse-grained data is handled. In order to effectively integrate such postgenomic interactions into a biochemical map, a statistical approach would be suitable rather than intuition. In this article, we proposed a novel statistical approach that integrates postgenomic interaction networks into the biochemical network, predicting novel pathways. A statistical correlation for such different types of networks identifies functional modules; subsequently the superposition of the different networks on the functional modules predicts inter-modular relations, which are the key pathways to construct a large-scale biochemical network.

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  • Computer-Aided Design of Metabolic and Gene Regulatory Networks Reviewed

    Kurata Hiroyuki

    アジア・太平洋化学工学会議発表論文要旨集   2004 ( 0 )   419 - 419   2004.01

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    DOI: 10.11491/apcche.2004.0.419.0

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  • Integration of Postgenomic Data for GMA to Simulate a Metabolic Circuit

    Takayuki Tanaka,Hiroyuki Kurata

    Genome Informatics Series   ( 14 )   613 - 614   2003.12

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  • CADLIVE SYSTEM: Map-based dynamic simulation of biochemical networks. Genome Informatics Series

    Hiroyuki Kurata,Rei Iwasaki,Kouichi Masaki,Takayuki Tanaka,Kouji Mitsukiyo,Yoshiyuki Sumida

    Genome Informatics Series   ( 14 )   270 - 271   2003.12

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  • CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps

    Weijiang Li,Hiroyuki Kurata

    Genome Informatics Series   ( 14 )   388 - 389   2003.12

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  • CADLIVE-Based Analysis for the Budding Yeast Cell Cycle

    Natsumi Shimizu,Shunsuke Yamamichi,Hiroyuki Kurata

    Genome Informatics Series   ( 14 )   609 - 610   2003.12

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  • Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms

    Yoshiyuki Sumida,Fumitaka Ohnishi,Hiroyuki Kurata

    Genome Informatics Series   ( 14 )   611 - 612   2003.12

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  • Verification of the optimization performance of Real-Corded Genetic Algorithm with Dominant Direction Priority Searching Method Reviewed

    TANAKA Shin, KURATA Hiroyuki, OHASHI Takeshi

    IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) )   47   49 - 52   2003.12

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    Real-Corded GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore Hybrid Genetic Algorithm (gradient GA) to use a gradient shows high optimization performance. But we cannot apply gradient GA for the optimization problem that it is impossible to calculate a gradient value of fitness function. So Dominant Direction Priority search method (DDP Searching Method) is suggested in order to reduce these problems. In DDP Searching method, we suppose a vector facing a superior gene from an inferior gene in population to be an indirect gradient direction (a dominant direction) And we carry out prior local search of dominant direction and GA crossover simultaneously. In this paper, we inspected the optimization performance in some mathematical benchmark functions and gene regulatory network simulation using DDP Searching Method.

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  • Dominant direction priority searching method for real-corded genetic algorithm Reviewed

    Shin T., Hiroyuki K., Takeshi O.

    Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications   3   1113 - 1119   2003.12

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    GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore we propose DDP algorithm in order to reduce this problem. DDP calculates DDP vector from the inferior gene to superior of population and create multiple new genes on the DDP vector. We carried out computer simulation to optimize some functions. As a result, DDP adds a search of a global area at early stage of optimization and a search of local area at a late stage to GA. GA+DDP showed the effectiveness in optimization problems of mathematical function and gene regulatory network simulation.

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  • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Reviewed

    Kurata H., Matoba N., Shimizu N.

    Nucleic Acids Research   31 ( 14 )   4071 - 4084   2003.07

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    The further understanding of the mechanisms of gene regulatory networks requires comprehensive tools for both the representation of complicated signal transduction pathways and the in silico, identification of genomic signals that govern the regulation of gene expression. Consequently, sophisticated notation must be developed to represent the signal transduction pathways in a form that can be readily processed by both computers and humans. We propose the regulator-reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed graphical notation that is derived from modification of Kohn's method. We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways using a conventional XML-based representation. The regulator-reaction equations represent not only mechanistic reactions, but also semantic models containing ambiguous and incomplete processes. In order to demonstrate the feasibility of CADLIVE, we constructed a detailed map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, in a really compact space. CADLIVE enables one to look at the whole view of a large-scale map, to integrate postgenomic data into the map, and to computationally simulate the signal transduction pathways, which greatly facilitates exploring novel or unexpected interactions.

    DOI: 10.1093/nar/gkg461

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  • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Reviewed

    H. Kurata,N. Matoba,N. Shimizu

    Nucleic Acids Res.   31   4071 - 4084   2003.07

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  • 代謝シュミレーションの新展開 Reviewed

    倉田 博之

    生物工学会誌 : seibutsu-kogaku kaishi   81 ( 6 )   2003.06

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    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110002913118

  • Dominant Direction Priority Searching Method for Real-Corded Genetic Algorithm Reviewed

    TANAKA Shin, KURATA Hiroyuki, OHASHI Takeshi

    IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) )   45   9 - 12   2003.06

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    GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore we propose DDP algorithm in order to reduce this problem. GA+DDP showed the effectiveness in optimization problems of mathematical function and gene regulatory network simulation.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110002914201

  • Dominant direction priority searching method for real-coded genetic algorithm Reviewed

    Shin Tanaka,Hiroyuki Kurata,Ken Ohashi

    Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications PDPTA'03   1113 - 1119   2003.06

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    Las Vegas, Nevada, USA   2003.06.23  -  2003.06.23

  • Feedback Regulation of the Heat Shock Response in E. coli Reviewed

    Hana El-Samad,Mustafa Khammash,Hiroyuki Kurata,John C. Doyle

    Lecture Notes in Control and Information Sciences   289   115 - 128   2003.04

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  • Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms Reviewed

    Sumida Yoshiyuki, Ohnishi Fumitaka, Kurata Hiroyuki

    Genome Informatics   14   611 - 612   2003.01

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    DOI: 10.11234/gi1990.14.611

    CiNii Article

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  • CADLIVE-Based Analysis for the Budding Yeast Cell Cycle Reviewed

    Shimizu Natsumi, Yamamichi Shunsuke, Kurata Hiroyuki

    Genome Informatics   14   609 - 610   2003.01

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    DOI: 10.11234/gi1990.14.609

    CiNii Article

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  • CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps Reviewed

    Li Weijiang, Kurata Hiroyuki

    Genome Informatics   14   388 - 389   2003.01

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    DOI: 10.11234/gi1990.14.388

    CiNii Article

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  • Building common patterns of transcription factor binding sites of Escherichia coli

    W. Li,H. Kurata

    Genome Informatics Series   13   301 - 302   2002.12

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  • SANAC: Mathematical simulator for elucidating the architecture of biochemical networks

    H. Kurata,H. Kitano

    Genome Informatics Series   13   242 - 243   2002.12

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  • BIOCAD project for synthesis and analysis of gene regulatory networks

    Hiroyuki Kurata,Yoshiyuki Sumida,Shin Tanaka,Kouichi Masaki,Takayuki Tanaka,Yuki Urago,Ken Ohashi

    Genome Informatics Series   13   467 - 477   2002.12

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  • Screening for transgenic plant cells that highly express a target gene from genetically mixed cells Reviewed

    H. Akashi,H.Kurata,M. Seki,K. Taira,S. Furusaki

    Biochem. Eng. J.   10   175 - 182   2002.07

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  • Robustness Analysis of the heat shock response in E. coli Reviewed

    H. El-Samad,M. Khammash,H. Kurata,H. T.-M. Yi,J. C. Doyle

    Proceedings of the 2002 American Control Conference   1742 - 1747   2002.05

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    Anchorage   2002.05.15  -  2002.05.15

  • Screening for transgenic plant cells that highly express a target gene from genetically mixed cells Reviewed

    Akashi H., Kurata H., Seki M., Taira K., Furusaki S.

    Biochemical Engineering Journal   10 ( 3 )   175 - 182   2002.04

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    To establish a strategy for stably and highly expressing a target gene in transformed plant cell suspensions, we developed the co-selection method that linked the hygromycin phosphotransferase gene (hph) to the β-glucuronidase (uidA, GUS) gene in the opposite direction under the same transcriptional regulation of the cauliflower mosaic virus (CaMV) 35S promoter. The linked genes were transferred into a tobacco BY-2 cell suspension, which was cultivated under various levels of the antibiotic pressure. Under the high pressure of hygromycin, GUS expression was increased and maintained over 1.5 years. We presented a successful example for selecting the plant cell suspension that highly expressed the target gene out of genetically heterogeneous cells. © 2002 Elsevier Science B.V. All rights reserved.

    DOI: 10.1016/S1369-703X(01)00182-6

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  • BIOCAD Project for Synthesis and Analysis of Gene Regulatory Networks Reviewed

    Kurata Hiroyuki, Sumida Yoshiyuki, Tanaka Shin, Masaki Kouichi, Tanaka Takayuki, Urago Yuki, Ohashi Ken

    Genome Informatics   13   467 - 468   2002.01

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    DOI: 10.11234/gi1990.13.467

    CiNii Article

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  • Building Common Patterns for Transcription Factor Binding Sites of <I>Escherichia coli</I> Reviewed

    Li Weijiang, Kurata Hiroyuki

    Genome Informatics   13   301 - 302   2002.01

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    DOI: 10.11234/gi1990.13.301

    CiNii Article

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  • Robustness analysis of the heat shock response in E. coli Reviewed

    El-Samad H., Khammash M., Kurata H., Doyle J.

    Proceedings of the American Control Conference   3   1742 - 1747   2002.01

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    The bacterial heat shock response refers to the mechanism by which bacteria react to a sudden increase in the ambient temperature of growth. The consequences of such an unmediated temperature increase at the cellular level is the unfolding, misfolding, or aggregation of cell proteins, which threatens the life of the cell. Cells respond to the heat stress by initiating the production of heat-shock proteins whose function is to refold denatured proteins into their native states. The heat shock response, through the elevated synthesis of molecular chaperones and proteases, enables the repair of protein damage and the degradation of aggregated proteins. In a previous work [1], we have devised a dynamic model for the heat shock response in E. coli. In the present paper, we provide a thorough discussion of the dynamical nature of this model. We use sensitivity analysis and simulation tools to illustrate the remarkable efficiency, robustness, and stability of the heat shock response system.

    DOI: 10.1109/ACC.2002.1023817

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  • BIOCAD project for constructing a biological system in silico

    T.Adachi,N. Matoba,H. Kurata

    Genome Informatics Series   12   284 - 285   2001.12

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  • Simulation and system analysis of gene regulatory networks using the two-phase partition method

    H. Kurata,T. Inoue,Y. Sumida,S. Tanaka,T. Ohashi

    Genome Informatics Series   286 - 287   2001.12

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  • Feedback regulation of the heat shock response in E. coli Reviewed

    H. Kurata,H. El-Samad,T.-M. Yi,M. Khammash,J. C. Doyle

    Proceedings of the 40th IEEE Conference on Decision and Control   837 - 842   2001.12

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  • A simple and rapid system for the quantitation of RNA interference in plant cultured cells Reviewed

    Akashi H,Miyagishi M,Kurata H,Nagata T,Taira K.

    Nucleic Acids Res. Suppl.   ( 1 )   235 - 236   2001.01

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  • BIOCAD Project for Constructing a Biological System <I>in Silico</I> Reviewed

    Adachi Tadashi, Matoba Nana, Kurata Hiroyuki

    Genome Informatics   12   284 - 285   2001.01

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    DOI: 10.11234/gi1990.12.284

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/130003997024

  • A simple and rapid system for the quantitation of RNA interference in plant cultured cells. Reviewed

    Akashi H., Miyagishi M., Kurata H., Nagata T., Taira K.

    Nucleic acids research. Supplement (2001)   ( 1 )   235 - 236   2001.01

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    The phenomenon known as RNA interference (RNAi) by double-stranded RNA (dsRNA) that was reported recently in the nematode Caenorhabditis elegans has been shown to operate by a mechanism that is widely conserved among species including plant cells. No quantitative analysis of the effects of RNAi on the expression of specific genes in plant cultured cells has been reported. An RNAi effect was observed 24 h after the introduction of dsRNA expression plasmids into tobacco BY-2 cells by electroporation. The simple system for suppression of specific genes in plant cells should be useful in attempts to elucidate the roles of individual genes in plant cells.

    DOI: 10.1093/nass/1.1.235

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  • Glucocorticoid-induced expression of a foreign gene by the GVG system in transformed tobacco BY-2 cells Reviewed

    Nara Y., Kurata H., Seki M., Taira K.

    Biochemical Engineering Journal   6 ( 3 )   185 - 191   2000.12

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    A glucocorticoid-induced target gene expression system was used to control the expression of the uidA gene, whose product was β-glucuronidase (GUS), in tobacco BY-2 cell suspension culture. This targeting system showed quick, sensitive, and reversible response to dexamethazone (DEX), an artificial glucocorticoid hormone. Addition of DEX greatly and quickly enhanced uidA gene expression, whose level was as high as that under the control of the CaMV 35S promoter whereas in the absence of DEX, the GUS specific activity was suppressed to be as low as that of nontransformed BY-2 cells. The dilution of DEX decreased GUS specific activity showing that the concentration of DEX plays a major role in controlling the expression level of the target. The use of the glucocorticoid-induced system in plant cell suspension culture was demonstrated to precisely control target gene expression. (C) 2000 Elsevier Science S.A.

    DOI: 10.1016/S1369-703X(00)00087-5

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  • MAXIZYMEs: Allosterically controllable ribozymes with biosensor functions Reviewed

    Kurata H., Miyagishi M., Kuwabara T., Warashina M., Taira K.

    Journal of Biochemistry and Molecular Biology   33 ( 5 )   359 - 365   2000.09

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    Ribozymes are catalytic RNAs that can cleave RNAs at specific sites, thus they have been employed to degrade a target mRNA in vivo. Development of allosterically controllable ribozymes is of great current interest, but it remained difficult to furnish such functions to ribozymes in cultured cells or in animals. Recently, we designed allosterically controllable ribozymes termed maxizymes, which have sensor arms that recognize target mRNA sequences and, in the presence of such target sequences only, they form a cavity that can capture catalytically indispensable Mg2+ ions, cleaving the target The maxizyme was applied to therapy for chronic myelogenous leukemia (CML). It cleaved specifically the chimeric BCR-ABL mRNA, which caused CML, without damaging the normal ABL or BCR mRNA in mammalian cells and also in mice, providing the first successful example for allosteric control of the activity of artificial ribozymes in vivo.

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  • Intermittent light irradiation with second- or hour-scale periods controls anthocyanin production by strawberry cells Reviewed

    Kurata H., Mochizuki A., Okuda N., Seki M., Furusaki S.

    Enzyme and Microbial Technology   26 ( 8 )   621 - 629   2000.05

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    Anthocyanin production by strawberry cells depends not only on light intensity but also on the light/dark cycle operation with hour- or second- scale periods. These findings are useful for designing and operating photobioreactors for enhanced anthocyanin production. Intermittent illumination with a second-scale period produces the same amount of anthocyanin as continuous light, suggesting that the light intensity distribution within a photobioreactor does not cause suppressed production. In the hour-scale cycle, continuous light operation enhanced anthocyanin production more than the light/dark cycle process. (C) 2000 Elsevier Science Inc.

    DOI: 10.1016/S0141-0229(00)00143-5

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  • Intermittent light irradiation with second- or hour- scale periods controls anthocyanin production by strawberry cells Reviewed

    Kurata H.,Mochizuki A.,Okuda N.,Seki M.,Furusaki S.

    Enzyme Microb. Technol.   26 ( # )   621 - 629   2000.04

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  • Grucocorticoid-induced expression of a foreign gene by the GVG system in transformed tobacco BY-2 Reviewed

    Nara Y.,Kurata H.,Seki M,Taira K.

    Biochem. Eng. J.   6 ( # )   185 - 191   2000.04

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  • Two-phase partition method for simulating a biological system at an extremely high speed Reviewed

    Kurata H.,Taira K.

    Genome Informatics   11 ( # )   185195 - 185195   2000.04

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  • Complexity in Regulation Generates Robustness in Bacterial Molecular Networks

    Kurata H.,Taira K.

    Proceedings of the First International Conference on Systems Biology   1 ( # )   167 - 172   2000.04

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  • Evolution of Ammonia Assimilation System in E. coli. ,17-24.

    Kurata H.,Taira K.

    Technical Report of IEICE   AI2000-12 ( # )   17 - 24   2000.04

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  • Two-Phase Partition Method for Simulating a Biological System at an Extremely High Speed Reviewed

    Kurata Hiroyuki, Taira Kazunari

    Genome Informatics   11   185 - 195   2000.01

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    DOI: 10.11234/gi1990.11.185

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/130003996847

  • Two-phase partition method for simulating a biological system at an extremely high speed. Reviewed

    Kurata H., Taira K.

    Genome informatics. Workshop on Genome Informatics   11   185 - 195   2000.01

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    To accelerate the calculation speed for simulating a biological system, we proposed a novel simulation method, the two-phase partition method, which calculated molecular processes at a higher speed than any other proposed method. This method divides a biological system, which can be described by chemical reaction equations, into two-phases: the binding and reaction phases. We demonstrated the capability of the two-phase partition method to simulate a complex biological system at an extremely high speed and clarified the accuracy of the simulation. The two-phase partition method is very useful for simulating complex interactions among proteins and DNAs.

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  • Mathematical model analyzes light-controlled expression of the CHS promoter in BY-2 cells Reviewed

    Kurata H., Kaizuka Y., Seki M., Furusaki S.

    Biochemical Engineering Journal   4 ( 1 )   65 - 72   1999.09

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    The β-glucuronidase (GUS) reporter gene was fused to the 2.0-kb upstream region of Arabidopsis thaliana chalcone synthase (CHS) gene and transferred into BY-2 cells. CHS promoter expression showed a quick response to light/darkness and its expression level was more than that by the Cauliflower Mosaic Virus (CaMV) 35S promoter [1]. In this study, a kinetic model was developed for describing light-enhanced expression of the CHS promoter by tobacco BY-2 cells. This model simulates the behavior of CHS promoter expression by two factors: the specific light absorption rate (light intensity) and the illumination time. The dependency of GUS synthesis on light intensity is well characterized by using the Monod equation. The dependency on the illumination time is calculated by using a saturation time constant of illumination. The mathematical model demonstrated that the conditioned medium or past illumination changed the kinetics of CHS promoter expression.

    DOI: 10.1016/S1369-703X(99)00034-0

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  • Software of living systems Reviewed

    Ohtake H., Tsuji T., Kurata H.

    Kagaku Kogaku Ronbunshu   25 ( 2 )   174 - 176   1999.03

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    To understand the elaborate system of a living organism, it is essential to know its "software", as well as its "hardware". The software of a living organism may be defined as the package of algorithms (methods and procedures) for its survival. The hardware of a living organism is encoded by genes on the chromosome. Its behaviors should be explainable on the basis of algorithms. The algorithms of a living system can be viewed as biological information that has been envolved over its long history of evolution. Among living organisms are bacteria that are probably the simplest systems for analyzing the software of living organisms. In the present paper, we describe our method for constructing a virtual bacterial system as a tool for analyzing the software of a living organism. We also describe bacterial algorithms for surviving during phosphate starvation and exhibiting an intelligent behavior called chemotaxis. In addition, we demonstrate a mobile robot whose behavior is controlled by a computer program designed on the basis of the bacterial chemotaxis algorithm.

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  • Intermittent light irradiation with a second-scale interval enhances caffeine production by Coffea arabica cells Reviewed

    Kurata H., Achioku T., Okuda N., Furusaki S.

    Biotechnology Progress   14 ( 5 )   797 - 799   1998.09

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    We developed novel equipment that intermittently illuminates Coffea arabica cell suspensions at a second-scale interval and investigated how intermittent irradiation enhances caffeine biosynthesis by C. arabica cells. The light/dark cycles consisting of 2 s of illumination and 18 s of darkness enhanced caffeine production, reaching the same level as for continuous light. The intermittent illumination increased the production efficiency regarding light consumption by a factor of 10. Caffeine production was determined by light intensity regardless of intermittent or continuous light irradiation. We propose a new concept for designing a photobioreactor that is applicable to secondary metabolite production by plant cell culture.

    DOI: 10.1021/bp980065u

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  • Light enhanced target gene expression in tobacco BY-2 by the combination of overexpressed phytochrome and rbcS3A promoter Reviewed

    Kurata H., Furusaki S., Kado C.

    Biotechnology Letters   20 ( 5 )   463 - 468   1998.07

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    Enhanced expression of the rbcS3A promoter was achieved by overproducing phytochrome in BY-2 tobacco cells. The transformed cells contained the oat phytochrome A gene fused the 35S promoter of Cauliflower Mosaic Virus (CaMV) and the gus gene to the rbcS3A promoter. The transformed cells exhibited 1.5- to -2.8 fold enhanced the β-glucuronidase (GUS) activity when subjected to light.

    DOI: 10.1023/A:1005484011673

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  • The light/dark cycle operation with an hour-scale period enhances caffeine production by Coffea arabica cells Reviewed

    Kurata H., Achioku T., Furusaki S.

    Enzyme and Microbial Technology   23 ( 7-8 )   518 - 523   1998.01

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    The intermittent light irradiation with an hour-scale period is used for producing caffeine by Coffea arabica cells. Three factors concerning the light/dark cycle operation such as light intensity, the length of the cycle (period), and the ratio of the illumination time to the dark time (light/dark ratio) were investigated to optimize the caffeine production efficiency regarding light consumption. The light/dark ratio of 1/1 enhanced caffeine production, reaching the same level as continuous light; thus, the intermittent light irradiation improved the production efficiency twofold. The production was not influenced by the period, but was determined by light intensity regardless of intermittent or continuous light irradiation. Copyright (C) 1998 Elsevier Science Inc.

    DOI: 10.1016/S0141-0229(98)00081-7

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  • Light-controlled expression of a foreign gene using the chalcone synthase promoter in tobacco BY-2 cells Reviewed

    Kurata H., Takemura T., Furusaki S., Kado C.

    Journal of Fermentation and Bioengineering   86 ( 3 )   317 - 323   1998.01

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    The light-activated chalcone synthase (CHS) gene promoter was used to control the expression of a foreign gene - the uidA gene, whose product is β-glucuronidase (GUS) - in tobacco BY-2 cell suspensions. Light enhanced GUS specific activity rapidly and greatly in transgenic BY-2 containing a fusion of the CHS promoter and uidA gene. GUS production was turned on/off by using a light/dark cycle. The level of promoter activity was almost proportional to the intensity of light, surpassing the strength of the 35S promoter of Cauliflower Mosaic Virus (CaMV). Intermittent illumination induced the same level of GUS production as continuous light. The CHS promoter is thus useful for producing a foreign protein in plant cell bioreactors.

    DOI: 10.1016/S0922-338X(98)80137-2

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  • Light irradiation causes physiological and metabolic changes for purine alkaloid production by a Coffea arabica cell suspension culture Reviewed

    Kurata H., Matsumura S., Furusaki S.

    Plant Science   123 ( 1-2 )   197 - 203   1997.03

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    Light irradiation not only enhanced purine alkaloid (caffeine and theobromine) production by a Coffea arabica cell suspension culture, but also caused physiological changes in cell growth, and sugar and oxygen uptake rates. Both sugar and oxygen uptake rates showed maxima between 7 and 10 W/m 2 of light intensity, where the specific production rate reached the highest, although the specific cell growth rate was reduced by more than 50%. Light acts as a stress for enhanced production. The activities of enzymes related to purine alkaloid production were induced by light after a lag-time of 1 day. Light is an inducer for these enzymes. However, the de novo synthesis of purine alkaloids required at least 6 days of light irradiation. This discrepancy was caused by the insufficient supply of purine rings, the precursors for biosynthesis of purine alkaloids.

    DOI: 10.1016/S0168-9452(96)04588-8

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  • Increased alkaloid production in a suspension culture of Coffea arabica cells using an adsorption column for product removal Reviewed

    Kurata H., Kawai A., Seki M., Furusaki S.

    Journal of Fermentation and Bioengineering   78 ( 1 )   117 - 119   1994.01

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    Since caffeine suppresses purine alkaloid (caffeine and theobromine) production by Coffea arabica cells, the effect of removing caffeine from the medium was investigated using the hydrophobic resin Amberlite XAD-4. An in situ removal method did not result in increased production because the adsorbent removed not only the products, but also essential components (hormones). Therefore, the use of an adsorption column employing the hydrophobic resin was investigated with a 35-d semicontinuous culture under light irradiation. Caffeine was removed within 30 min by the adsorption column on day 23 of the cultivation. In this system, the negative effects of hormone removal by the adsorbent were canceled out by the addition of fresh medium. This method increased alkaloid production 1.4-fold compared to the culture with no removal treatment. © 1994.

    DOI: 10.1016/0922-338X(94)90192-9

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  • Immobilized Coffea arabica cell culture using a bubble‐column reactor with controlled light intensity Reviewed

    Kurata H., Furusaki S.

    Biotechnology and Bioengineering   42 ( 4 )   494 - 502   1993.08

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    Coffea arabica cells immobilized by calcium alginate gel were photocultured using a bubble‐column reactor under controlled light intensity. This process was carried out after their alkaloid productivity was improved by increasing the cell density in the initial gel matrix and preculturing the immobilized cells in the dark prior to light irradiation. The cells were grown in the form of a biofilm on gel beads, producing 100 mg/L of purine alkaloids in a 24‐day batch culture. Alkaloid production was relatively constant with respect to light intensity changes, and also cell growth was not suppressed much at high light intensity, with these behaviors being different from those obtained using suspended cells. These phenomena are explained by estimating the light intensity gradient within the cell‐immobilizing particles and by measuring the viable cell distribution within them. It subsequently suggests that the subsurface cells affect both the production and growth behaviors. © 1993 John Wiley & Sons, Inc. Copyright © 1993 John Wiley & Sons, Inc.

    DOI: 10.1002/bit.260420413

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  • Nonisotropic Scattering Model for Estimation of Light Absorption Rates in a Suspension Culture of Coffea arabica Cells Reviewed

    Kurata H., Furusaki S.

    Biotechnology Progress   9 ( 1 )   86 - 92   1993.01

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    A nonisotropic scattering model is proposed to estimate the light absorption rates in a heterogeneous photoreactor containing plant cells of Coffea arabica and is compared with an isotropic scattering model. In order to determine the directions of noniso‐tropically scattered light, optical theorems (geometrical optics and wave optics) are applied to light scattering caused by a homogeneous and perfect sphere. Two parameters, relative refractive index and attenuation coefficient, are used to characterize the ideal sphere. The primary feature of this model is that various phenomena of light scattering and absorption can be simulated by the combination of the two parameters. A measuring system composed of parallel plates was developed for evaluating the model. The nonisotropic scattering model was successfully applied to the heterogeneous reactor with the cultured plant cells. Copyright © 1993 American Institute of Chemical Engineers (AIChE)

    DOI: 10.1021/bp00019a600

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  • Influence of light irradiation rates and irradiation modes on caffeine production and cell growth in suspension culture of coffea arabica cells Reviewed

    Kurata H., Seki M., Furusaki S., Furuya T.

    JOURNAL OF CHEMICAL ENGINEERING OF JAPAN   24 ( 6 )   783 - 788   1991.01

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    The effect of light on caffeine production by Coffea arabica cells was investigated using chemical actinometry for the purpose of industrial application of plant cell cultures. Caffeine production by the Coffea arabica cells was greatly increased by light. About a six-day irradiation period was required to increase the caffeine production in a batch culture. Caffeine production significantly increased at a low light irradiation rate of 0.11 J/L/s. Meanwhile, cell growth was suppressed by increasing the irradiation rate. Maximum production was achieved at a moderate irradiation rate of 0.70 J/L/s in a 20-day batch culture. It was shown there was a light irradiation rate that optimized production. Since long-term continuous light greatly suppressed cell growth, the culture was divided into two stages: the production period in the light and the growth period in the dark. The high production and good growth were maintained for 65 days. © 1991, The Society of Chemical Engineers, Japan. All rights reserved.

    DOI: 10.1252/jcej.24.783

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  • Effect of Light on Caffeine Production by Plant Cells of Coffea arabica<sup>a</sup> Reviewed

    KURATA H., SEKI M., FURUSAKI S., FURUYA T.

    Annals of the New York Academy of Sciences   613 ( 1 )   538 - 541   1990.12

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    DOI: 10.1111/j.1749-6632.1990.tb18216.x

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Publications (Books)

  • BIODESIGN

    Hiroyuki Kurata, Many(Joint author)

    2015.10 

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  • システム工学的アプローチを用いた細胞モデリング,In 抗体医薬における細胞構築・培養・ダウンストリームのすべて(ファインケミカルシリーズ)

    倉田博之(Joint editor)

    シーエムシー出版  2015.04 

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    Language:Japanese

  • Modularity of biochemical networks, Technological Advancements in Biomedicine for Healthcare Applicationsm. In: Biomedical Engineering and Cognitive Neuroscience for Healthcare: Interdisciplinary Applications

    (Joint author)

    2012.04 

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    Language:English

  • システム工学的アプローチを用いた細胞設計,In 抗体医薬のための細胞構築と培養技術(ファインケミカルシリーズ),監修:大政健史

    倉田博之(Joint author)

    シーエムシー出版  2010.04 

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  • コンピュータエイデッドなバイオシステムの構築, In: バイオプロセスシステム

    倉田博之(Joint author)

    シーエムシー出版  2009.04 

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  • システム生物学入門 生物回路の設計原理

    倉田博之,宮野悟(Joint author)

    共立出版  2008.10 

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  • 九工大世界トップ技術2

    倉田博之(Joint author ,  1章)

    西日本新聞社  2008.04 

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  • バイオプロダクション-ものつくりのためのバイオテクノロジー

    倉田博之(Joint author ,  生命現象のシミュレーション)

    コロナ社  2006.05 

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  • バイオインフォマティクス事典

    倉田博之,多数(Joint author)

    共立出版  2006.04 

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  • ゲノム研究実験ハンドブック

    宮野悟,松野浩嗣,倉田博之(Joint author)

    羊土社  2004.10 

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Conference Prsentations (Oral, Poster)

  • 嫌気好気条件下での回分培養大腸菌の代謝動力学モデル

    松岡結, 倉田博之

    化学工学会第83回年会 

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    Event date: 2018.03.13   Language:Japanese  

  • スマートセルインダストリーを指向した中心代謝系の定量的モデル

    松岡結, 倉田博之

    第6回生命医薬情報学連合大会 

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    Event date: 2017.09.27 - 2017.09.29   Language:Japanese  

  • A critical evaluation of bioinformatics tools for the prediction of protein succinylation sites

    Md. Mehedi Hasan, Hiroyuki Kurata

    Conference of Informatics In Biology, Medicine and Pharmacology (IIBMP2017) 

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    Event date: 2017.09.27 - 2017.09.29   Language:Japanese  

  • 中心代謝反応系のコンピュータモデル:酸素制限下での発酵性能

    松岡結, 倉田博之

    情報処理学会バイオ情報学研究会研究報告 

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    Event date: 2017.09.26   Language:Japanese  

  • ネガティブフィードバック構造に基づく生物振動子の周期調節可能性の解析

    前田和勲, 倉田博之

    情報処理学会バイオ情報学研究会研究報告 

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    Event date: 2017.09.26   Language:Japanese  

  • 細胞工場のコンピュータ支援設計

    倉田博之

    化学工学会第49回秋季大会 

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    Event date: 2017.09.20 - 2017.09.22   Language:Japanese  

  • ノイズ下でロバストなメモリー機能を生み出す遺伝子ネットワーク機構の解明

    Shamim Ul Hasan, 倉田博之

    化学工学会第82回年会 

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    Event date: 2017.03.08   Language:Japanese  

  • 動的感度を用いたErbBシグナル伝達ネットワークのロバストネス解析

    増永拓之、倉田博之

    化学工学会第81回年会 

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    Event date: 2016.03.15   Language:Japanese  

  • 抗体産生を向上させるためのCHO 細胞代謝の数学モデリング

    バッチャモハメド,杉本 友里恵,倉田 博之

    第67回日本生物工学会大会 

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    Event date: 2015.10.26   Language:Japanese  

  • 抗体生産強化のためのCHO細胞メタボロームの統計解析

    倉田博之

    化学工学会第47回秋季大会 

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    Event date: 2015.09.19 - 2015.09.21   Language:Japanese  

  • アンモニア同化システムの詳細なダイナミックモデル

    倉田博之

    化学工学第80回年会 

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    Event date: 2015.03.19 - 2015.03.21   Language:Japanese  

  • マルチパラメータ感度を用いたネガティブフィードバック振動子のロバストネス解析

    前田和勲

    生命情報科学若手の会第6回研究会 

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    Event date: 2014.10.30   Language:Japanese  

  • 生物システムの合理的設計を支援するBioFNetデータベース

    倉田博之

    化学工学会第46回秋季大会 

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    Event date: 2014.09.17 - 2014.09.19   Language:Japanese  

  • 生物学的基本ネットワークの組み立てによるダイナミックモデルの合理的設計

    倉田博之

    化学工学会第79年会 

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    Event date: 2014.03.18 - 2014.03.20   Language:Japanese  

  • ゲノムスケールヒト代謝ネットワークの高速エレメンタリモード解析

    倉田博之

    化学工学会第45回秋季大会 

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    Event date: 2013.09.16 - 2013.09.18   Language:Japanese  

  • 合理的生物回路設計のためのバイオアルゴリズムデータベース

    倉田博之

    化学工学会第78年会 

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    Event date: 2013.03.17 - 2013.03.19   Language:Japanese  

  • アンモニア同化システムのダイナミックモデルの開発

    倉田博之

    化学工学会第77年会 

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    Event date: 2012.03.15 - 2012.03.17   Language:Japanese  

  • Grid layout algorithm for biochemical networks using approximate pattern matching

    The 10-th International Conference on Bioinformatics (InCoB2011) 

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    Event date: 2011.11.30 - 2011.12.02   Language:English  

  • Hybrid Grid Layout Algorithm For Biochemical. Network Maps

    The 2011 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2011.11.08 - 2011.11.10   Language:English  

  • ゲノムネットワークを構成する全基本回路の構造と機能のデータベース化

    倉田博之

    化学工学会第43回秋季大会 

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    Event date: 2011.09.14 - 2011.09.16   Language:Japanese  

  • Dual Feedback Loop Architecture is a Robust and Entrainable Oscillator for Circadian Rhythm

    The 12-th international Conference on Systems biology 

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    Event date: 2011.08.28 - 2011.09.01   Language:English  

  • Use of elementary mode analysis predicts the flux distributions of a broad range of genetic mutants

    The 12-th international Conference on Systems biology 

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    Event date: 2011.08.28 - 2011.09.01   Language:English  

  • 合成生物学のためのバイオアルゴリズムデータベース開発

    倉田博之

    化学工学会第76回年会 

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    Event date: 2011.03.05 - 2011.03.07   Language:Japanese  

  • Regulome database for systematic search of biological design principles

    The 2010 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2010.12.13 - 2010.12.15   Language:English  

  • CADLIVE: A platform for network modeling and simulation of biological pathway

    The 2010 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2010.12.13 - 2010.12.15   Language:English  

  • Flux Module-based Decomposition for Parameter Optimization in a Dynamic Model of Biochemical Networks

    The 2010 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2010.12.13 - 2010.12.15   Language:English  

  • Development of elementary mode-based algorithms for designing a metabolic system

    The 2010 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2010.12.13 - 2010.12.15   Language:English  

  • CADLIVE: Data Integrator with Network Layout Module

    The 11-th international Conference on Systems biology 

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    Event date: 2010.10.10 - 2010.10.16   Language:English  

  • Quasi-Multiparameter Sensitivity Analysis reveals Remarkable Robustness of Dual Feedback Circadian Oscillators

    The 11-th international Conference on Systems biology 

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    Event date: 2010.10.10 - 2010.10.16   Language:English  

  • Development of elementary mode-based algorithms for designing a metabolic system

    Souma Tabata, Quanyu Zhao, Hiroyuki Kurata

    The 9-th International Conference on Bioinformatics (InCoB2010) 

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    Event date: 2010.09.26 - 2010.09.28   Language:English  

  • An integrative and practical strategy for optimizing a large-scale dynamic model of biochemical systems

    The 9-th International Conference on Bioinformatics (InCoB2010) 

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    Event date: 2010.09.26 - 2010.09.28   Language:English  

  • A Novel Spectral Clustering of Protein Interaction Networks

    The 9-th International Conference on Bioinformatics (InCoB2010) 

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    Event date: 2010.09.26 - 2010.09.28   Language:English  

  • Exploring huge parameter space of a large-scale model of biochemical networks

    The 9-th International Conference on Bioinformatics (InCoB2010) 

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    Event date: 2010.09.26 - 2010.09.28   Language:English  

  • 多様な遺伝子組換え微生物における代謝流束分布の新規な予測法

    倉田博之

    化学工学会第42回秋季大会 

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    Event date: 2010.09.07 - 2010.09.09   Language:Japanese  

  • Genetic Modification of Flux: エレメンタリーモードを用いた組換え細胞の代謝流束予測

    倉田博之

    化学工学会第75年会 

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    Event date: 2010.03.18 - 2010.03.20   Language:Japanese  

  • Extended CADLIVE: Multi-User Framework and Data Integrator

    The 20th International Conference on Genome Informatics 

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    Event date: 2009.12.14 - 2009.12.16   Language:English  

  • Adjustable Diffusion Matrix-Based Spectral Clustering for Protein-Protein Interaction Network

    The 20th International Conference on Genome Informatics 

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    Event date: 2009.12.14 - 2009.12.16   Language:English  

  • Novel Robustness Analysis Reveals Remarkable Robustness of Dual Feedback Loops in a Circadian Clock

    The 20th International Conference on Genome Informatics 

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    Event date: 2009.12.14 - 2009.12.16   Language:English  

  • Module Decomposition and Integration Method Optimizes a Large-Scale Cell Cycle Model

    The 20th International Conference on Genome Informatics 

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    Event date: 2009.12.14 - 2009.12.16   Language:English  

  • Prediction of Transcriptional Patterns of Gene Deletion Mutants

    The 20th International Conference on Genome Informatics 

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    Event date: 2009.12.14 - 2009.12.16   Language:English  

  • 生物学と工学の統合にむけて

    倉田博之

    化学工学会第41回秋季大会 

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    Event date: 2009.09.15 - 2009.09.17   Language:Japanese  

  • Searching multiple sets of kinetic parameters values reproducing target experimental data in dynamic biochemical models

    The 2008 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2008.12.15 - 2008.12.17   Language:English  

  • Extended CADLIVE: Computer-aided rational design of living systems

    The 2008 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2008.12.15 - 2008.12.17   Language:English  

  • Computer aided rational design of biochemical systems

    The 21st Annual and International Meeting of the Japanese Association for Animal Cell Technology. 

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    Event date: 2008.11.24 - 2008.11.27   Language:English  

  • 創薬を指向した細胞周期モデルインテグレータ

    倉田博之

    化学工学会第40回秋季大会 

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    Event date: 2008.09.24 - 2008.09.26   Language:Japanese  

  • Computer-Aided Rational Design of Biochemical Networks in E. coli

    UK-Japan Systems Biology workshop 

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    Event date: 2008.07.07 - 2008.07.08   Language:English  

  • Parameter search of large-scale dynamic biochemical network models

    The 2007 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2007.12.17 - 2007.12.19   Language:English  

  • CADLIVE : An integrative system of life information

    The 2007 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2007.12.17 - 2007.12.19   Language:English  

  • Systems biology for analysis of nitrogen assimilation system in E. coli

    The 2007 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2007.12.17 - 2007.12.19   Language:English  

  • Optimization of a large-scale cell cycle model using multi-objective GAs

    The 2007 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2007.12.17 - 2007.12.19   Language:English  

  • Stochastic simulation of diffusion reaction model in embryo development

    The 2007 annual conference of Japanese Society for Bioinformatics 

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    Event date: 2007.12.17 - 2007.12.19   Language:English  

  • 遺伝子発現プロファイルを統合する代謝流束予測法

    倉田博之

    化学工学会第39回秋季大会 

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    Event date: 2007.09.13 - 2007.09.15   Language:Japanese  

  • CADLIVE:Computer-Aided Design of Living Systems

    The 15th annual international conference on intelligent systems for molecular biology 

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    Event date: 2007.07.21 - 2007.07.25   Language:English  

  • 細胞の代謝流束を予測・設計するためのゲノムスケール代謝経路解析法

    本人

    化学工学会第38回秋季大会 

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    Event date: 2006.09.16 - 2006.09.18   Language:Japanese  

  • Robustness analysis for the mechanism for a temperature-compensated circadian oscillator

    20th IUBMB International Congress of Biochemistry and Molecular Biology and 11 th FAOBMB Congress  

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    Event date: 2006.06.22   Language:English  

  • Dynamic simulation and robustness analysis for the E. coli nitrogen assimilation system

    The 20th IUBMB International Congress of Biochemistry and Molecular Biology and the 11 th FAOBMB Congress 

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    Event date: 2006.06.22   Language:English  

  • Automatically building and visualizing biochemical networks

    The third Asia-Pacific Bioinformatics Conference 

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    Event date: 2005.01   Language:English  

  • 大規模遺伝子制御・代謝ネットワークの動的モデルの最適化

    本人

    第5回システムバイオロジー研究会 

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    Event date: 2004.11.08   Language:Japanese  

  • 大腸菌窒素同化システムのシミュレーションとシステム解析

    第4回システムバイオロジー研究会 

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    Event date: 2004.08.27   Language:Japanese  

  • CADLIVE: A Direct Link of Biochemical Networks to Dynamic Simulations

    12th International Conference of Intelligent Systems for Molecular Biology 

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    Event date: 2004.07.31 - 2004.08.04   Language:English  

  • CADLIVE Simulatorを用いた窒素同化システムのマルチフィードバック解析

    第26回日本分子生物学会年会 

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    Event date: 2003.12.10 - 2003.12.13   Language:Japanese  

  • Gillespie のアルゴリズムを用いた哺乳類細胞における時空間代並ⅸするの確率的シミュレーション

    第26回日本分子生物学会年会 

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    Event date: 2003.12.10 - 2003.12.13   Language:Japanese  

  • CADLIVE:コンピュータ上での経路探索による突然変異体のシステム解析

    第26回日本分子生物学会年会 

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    Event date: 2003.12.10 - 2003.12.13   Language:Japanese  

  • 熱ショック応答システムのインターコネクトフィードバック制御

    第26回日本分子生物学会年会 

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    Event date: 2003.12.10 - 2003.12.13   Language:Japanese  

  • 生命分子間相互作用ネットワークをコンピュータ上で合成・解析するためのCADLIVEシステムの開発

    第26回日本分子生物学会年会 

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    Event date: 2003.12.10 - 2003.12.13   Language:Japanese  

  • CADLIVE for designing metabolic and gene regulatory networks

    The 9th Symposium of Young Asian Biochemical Engineers' Community 

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    Event date: 2003.11.14   Language:English  

  • Map-based dynamic simulator of gene regulatory networks

    4th International Conference on Systems Biology 

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    Event date: 2003.11.05 - 2003.11.09   Language:English  

  • CADLIVE for constructing a yeast cell cycle

    11th International Conference of Intelligent Systems for Molecular Biology 

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    Event date: 2003.06.30   Language:English  

  • CADLIVE for constructing and simulating biochemical networks

    11th International Conference of Intelligent Systems for Molecular Biology 

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    Event date: 2003.06.30   Language:English  

  • 実数値遺伝的アルゴリズムのための優性方向優先探索

    情報処理学会研究報告 

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    Event date: 2003.06.24   Language:Japanese  

  • 熱ショック応答システムにおけるフィードバック制御とフィードフォワード制御の戦略

    第25回日本分子生物学会年会 

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    Event date: 2002.12.11 - 2002.12.14   Language:Japanese  

  • BIOCAD:生命設計支援システム

    第25回日本分子生物学会年会 

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    Event date: 2002.12.11 - 2002.12.14   Language:Japanese  

  • BIOCAD for constructing gene regulatory networks

    10th International Conference of Intelligent Systems for Molecular Biology 

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    Event date: 2002.08.04 - 2002.08.09   Language:English  

  • BIOCAD for constructing gene regulatory networks

    ISMB Satellite Meeting on Computer Modeling of Cellular Processes 

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    Event date: 2002.08.03   Language:English  

  • 複雑な制御は生命システムのロバスト性を向上させる

    第24回日本分子生物学会年会 

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    Event date: 2001.12.09 - 2001.12.12   Language:Japanese  

  • A two-phase partition method that simulates the dynamic behavior of the gene regulatory networks with high accuracy at a remarkably high speed

    Proceedings of the Second International Conference on Systems Biology 

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    Event date: 2001.11.04 - 2001.11.07   Language:English  

  • 生命設計支援のための大規模シミュレータ開発

    化学工学会第34回秋季大会 

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    Event date: 2001.09.28 - 2001.09.30   Language:Japanese  

  • Complexity in regulation generates the robustness in bacterial heat shock response

    4th international Conference on Biological Physics 

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    Event date: 2001.07.30 - 2001.08.03   Language:English  

  • Complexity in regulation generates the robustness in bacterial molecular network

    Search for Logic of Life as Complex Systems 

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    Event date: 2001.07.27 - 2001.07.28   Language:English  

  • A two-phase partition method simulates the dynamics behavior of the heat shock response with high accuracy at a remarkably high speed

    9th International Conference on Intelligent Systems for Molecular Biology 

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    Event date: 2001.07.21 - 2001.07.25   Language:Japanese  

  • System analysis of complex molecular networks by mathematical simulation and control theory

    9th International Conference on Intelligent Systems for Molecular Biology 

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    Event date: 2001.07.21 - 2001.07.25   Language:Japanese  

  • The two-phase partition method simulates a gene regulatory network at an extremely high speed

    Pacific. Symp. Biocomputing 

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    Event date: 2001.01.03   Language:Japanese  

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Industrial Property

  • Simulator, Method and Recording Medium For Simulating a Biological System

    Kurata Hiroyuki

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    Application no:"09/727 699  Date applied:2000.12.18

  • 生命システムシミュレータ及び生命システムシミュレーション方法並びに記録媒体

    倉田博之

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    Application no:'2000-106295  Date applied:2000.04.25

Lectures

  • Linguistic approaches in deep learning for predicting protein-protein interactions between human and virus

    6TH INTERNATIONAL CONFERENCE ON COMPUTER, COMMUNICATION, CHEMICAL, MATERIALS AND ELECTRONIC ENGINEERING  2021.12  University of Rajshahi

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    Event date: 2021.12.26 - 2021.12.27   Language:English   Presentation type:Invited lecture   Venue:online  

  • Computational prediction of anti-coronavirus peptides using a word2vec model

    Sungkyun Biotech International Conference 2022   2022.12  Korea

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    Event date: 2022.12.22 - 2022.12.23   Language:English   Presentation type:Invited lecture   Venue:online   Country:Japan  

Press

  • 九工大・MKI, パスウエイ情報の数式変換ソフトを共同開発

    倉田博之

    日経バイオテク  2003.10.13

Honors and Awards

  • 論文編集貢献賞

    情報処理学会   論文編集貢献賞   2023.05.01

    倉田博之

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    Country:Japan

  • 研究会活動功労賞

    情報処理学会   2023.03.27

    倉田博之

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    Country:Japan

Grants-in-Aid for Scientific Research

  • ゲノムスケールヒト代謝のdFBAモデル開発と多剤併用療法への応用

    Grant number:16H02898  2016.04 - 2019.03   基盤研究(B)

  • ノイズが引き起こす確率的挙動を考慮した生体分子ネットワークの実用的設計

    Grant number:26119716  2014.04 - 2017.03   新学術領域研究

  • バーチャルメタボリズム:代謝システムの標準ダイナミックモデル開発

    Grant number:25280107  2013.04 - 2016.03   基盤研究(B)

  • メタボロームを代謝ネットワークへ統合する数理モデルの開発

    Grant number:23134506  2011.04 - 2013.03   新学術領域研究

  • 生物回路の設計原理に基づく合成生物学

    Grant number:22300101  2010.04 - 2013.03   基盤研究(B)

  • 分子ネットワークのコンピュータ支援設計法の開発とグルコース同化システムへの応用

    Grant number:20016021  2008.04 - 2010.03   特定領域研究

  • 大規模代謝・遺伝子ネットワークのダイナミックシミュレーションとシステム解析

    Grant number:18300098  2006.04 - 2009.03   基盤研究(B)

  • ネットワークマップに基づく大規模生命分子ネットワークのロバスト解析

    Grant number:16014220  2004.04 - 2005.03   特定領域研究

  • ファイブロブラスト運動制御の画像解析とシミュレーション

    Grant number:15500198  2003.04 - 2006.03   基盤研究(C)

  • 植物遺伝子機能解析のためのハイブリッド型リボザイムの開発

    Grant number:13750742  2001.04 - 2003.03   奨励研究(A)→若手研究(B)

  • 2相分離計算法を用いた生命分子ネットワーク解析により生命の設計原理の解明

    Grant number:13208027  2001.04 - 2002.03   特定領域研究

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Other External Funds

  • 翻訳後・分泌プロセスを含む生化学ネットワークに基づく抗体生産モデルの開発

    2013.04

    次世代バイオ医薬品製造技術開発研究組合「個別化医療に向けた次世代医薬品創出基盤技術開発  

  • 癌細胞統合シミュレータの開発

    2007.04 - 2008.03

    シーズ発掘試験  

Other Research Activities

  • BioFNet Biological functional network database

    2013.04

Charge of off-campus class subject

  • 2004.08   Institution:北九州市立大学

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    Level:undergraduate_special_subjects  Country:Japan

Activities of Academic societies and Committees

  • 情報処理学会   バイオ情報学研究会主査(会長)  

    2019.04 - 2023.03

  • 情報処理学会   バイオ情報学研究会論文誌編集委員長  

    2020.04 - 2023.03

  • 北九州SDGsイノベーション&アントレプレナーシッププラットフォーム   プログラム代表補佐  

    2021.04

  • 飯塚医療イノベーション推進会議   幹事  

    2011.04

  • Platform for All Regions of Kyushu & Okinawa for Startup-ecosystem(PARKS)  

    2022.04

  • 公益財団法人飯塚研究開発機構筑豊地域医療・福祉関連支援委員会   委員長  

    2020.04

  • Japanese Society of Bioinformatics  

    2017.04 - 2019.03

  • The Society of Chemical Engineers  

    2005.04 - 2021.03

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Social activity outside the university

  • 中高生がヘルスケア課題解決プランを競うプログラム

    Role(s):Lecturer, Demonstrator

    inochi WAKAZO Project と inochi未来プロジェクト  inochi Gakusei Innovators’ Program 2023 Kyushu  九州大学医学部百年講堂  2023.07.16

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    Audience: High school students

    Type:Seminar, workshop

  • 九工大起業家コンテスト2023主催

    Role(s):Presenter, Planner, Organizing member

    九州工業大学  九工大起業家コンテスト2023主催  戸畑キャンパス GYMLABO  2023.03.03

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    Audience: College students, Graduate students, General

    Type:Seminar, workshop

    企画と司会を務めた

  • 第1回九工大起業家コンテスト主催

    Role(s):Presenter, Planner, Organizing member

    九州工業大学情報工学部将来構想検討委員会  第1回九工大起業家コンテスト  飯塚キャンパス、オンライン  2021.03.06

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    Audience: College students, Graduate students, General

    Type:Seminar, workshop

    実行委員長を務めた。

  • 第63回 BMIRC研究会

    2018.07.30

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    Type:Seminar, workshop

    第63回BMIRC研究会
    イノベーションの聖地シリコンバレーから学び、世界を変える起業家になろう 日時:2018年7月30日 16:20-17:50
    場所:九州工業大学飯塚キャンパスグローバルコミュニケーションラウンジ
    講師:CEO, Silicon Valley Ventures株式会社
    CEO, Startup Fire株式会社
    森若幸次郎, John Kojiro Moriwaka

  • 第62回 BMIRC研究会

    2018.07.24

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    Type:Seminar, workshop

    デザイン思考と医療ビジネス入門講義(第62回BMIRC研究会)
    「病院のしくみを知る」 日時:2018年7月24日 13:00-14:30:14:40-16:10
    場所:九州工業大学飯塚キャンパス 1204講義室
    飯塚病院イノベーション推進本部
    稗島 武 :日本の医療制度について
    井桁 洋貴:飯塚病院における改善活動とイノベーションの取り組み

  • 第61回 BMIRC研究会

    2018.07.02

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    Audience: College students

    Type:Seminar, workshop

    第61回BMIRC研究会
    非AUG開始コドンの翻訳制御―広がる生物学的役割
    日時:2017年7月2日 16:20-17:50
    場所:九州工業大学飯塚キャンパス 1202講義室
    カンザス州立大学生物学科 教授
    浅野 桂, Asano, Katsura

  • 第59回 BMIRC研究会

    2018.03.08

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    Type:Seminar, workshop

    第59回BMIRC研究会(2017年度BMIRC教育研究報告会)
    九工大のバイオメディカルインフォマティクスの成果と発展 日時:2018年3月8日 15:30-17:30
    場所:九州工業大学飯塚キャンパス
    大学院セミナー室N712

  • 第58回 BMIRC研究会

    2018.03.02

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    Type:Seminar, workshop

    第58回BMIRC研究会
    バイオメディカルデザイン演習最終発表会 日時:2018年3月2日 14:40-15:40
    場所:九州工業大学飯塚キャンパス
    大学院セミナー室N712

  • 第57回 BMIRC研究会

    2018.02.28

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    Type:Seminar, workshop

    第57回BMIRC研究会
    バイオメディカルデザイン演習最終発表会 日時:2018年2月28日 13:00-14:30
    場所:九州工業大学飯塚キャンパス
    大学院セミナー室N712

  • 第56回 BMIRC研究会

    2018.01.15

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    Type:Seminar, workshop

    第56回BMIRC研究会
    2017年度シリコンバレー研修旅行発表会 日時:2018年1月15日 16:20-17:20
    場所:九州工業大学飯塚キャンパス
    グローバルコミュニケーションラウンジ
    九州工業大学
    平安克也 (情報工学部)
    岩崎美夏 (生命体工学研究科)
    井原康  (工学部)
    村竹菜々瀬(工学部)

  • 第55回 BMIRC研究会

    2017.10.03

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    Type:Seminar, workshop

    第55回BMIRC研究会
    バイオメディカルデザイン演習中間発表会
    日時:2017年10月3日(火)10:30-12:00
    場所:九州工業大学飯塚キャンパス 大学院セミナー室N712

  • 第52回 BMIRC研究会

    2017.07.14

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    Type:Seminar, workshop

    デザイン思考と医療ビジネス入門講義(第52回BMIRC研究会)
    「病院のしくみを知る」 日時:2017年7月14日 13:00-14:30:14:40-16:10
    場所:九州工業大学飯塚キャンパス 1201講義室
    飯塚病院イノベーション推進本部
    稗島 武 :日本の医療制度について
    井桁 洋貴:飯塚病院における改善活動とイノベーションの取り組み

  • 第53回 BMIRC研究会

    2017.07.13

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    Type:Seminar, workshop

    第53回BMIRC研究会
    資金調達するためのピッチ道場!
    シリコンバレー流ビジネスプランの作り方10のポイントとピッチのやり方 日時:2017年7月13日 16:20-17:50
    場所:九州工業大学飯塚キャンパスグローバルコミュニケーションラウンジ
    CEO, Silicon Valley Ventures Co., Ltd
    山口大学客員教授
    森若幸次郎, John Kojiro Moriwaka

  • 第54回 BMIRC研究会

    2017.07.07

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    Type:Seminar, workshop

    The 54th BMIRC Seminar(第54回BMIRCセミナー)
    Protein-DNA interaction patterns revealed from large scale data analysis of sequence, gene expression and conformational dynamics 日時:16:20–17:50, on July 7, 2017
    場所:N712 at the Kyutech Iizuka Campus
    Professor Shandar Ahmad
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi

  • 第50回 BMIRC研究会

    2017.07.06

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    Audience: College students

    Type:Seminar, workshop

    第50回BMIRC研究会
    非AUG開始コドンの翻訳制御
    日時:2017年7月6日 13:00-14:30
    場所:九州工業大学飯塚キャンパス N712
    カンザス州立大学生物学科 教授
    浅野 桂, Asano, Katsura

  • 第51回 BMIRC研究会

    2017.05.09

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    Type:Seminar, workshop

    第51回BMIRC研究会
    Latest news about Entrepreneurship and Innovation from Silicon Valley
    日時:2017年5月9日 14:40-16:10
    場所:九州工業大学飯塚キャンパスグローバルコミュニケーションラウンジ
    CEO, Silicon Valley Ventures Co., Ltd
    Visiting professor, Yamaguchi University
    森若幸次郎, John Kojiro Moriwaka

  • 第49回 BMIRC研究会

    2017.04.19

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    Type:Seminar, workshop

    第49回BMIRC研究会
    グローバルイノベーターになるために身につけたい3つのスキルとは?
    日時:2017年4月19日 16:20-17:50
    場所:九州工業大学飯塚キャンパスグローバルコミュニケーションラウンジ
    株式会社シリコンバレーベンチャーズ
    代表取締役社長(兼), CEO 山口大学客員教授
    森若幸次郎, John Kojiro Moriwaka

  • 第48回 BMIRC研究会

    2017.02.21

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    Type:Seminar, workshop

    第48回BMIRC研究会
    バイオメディカルデザイン演習発表会
    日時:2017年2月21日(火)13:00-14:30
    場所:九州工業大学飯塚キャンパス グローバルコミュニケーションラウンジ

  • 第47回 BMIRC研究会

    2017.01.10

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    Type:Seminar, workshop

    第47回BMIRC研究会
    2016年度シリコンバレー研修報告会&アントレプレナーシップワークショップ
    日時:2017年1月10日(火)13:00-16:00
    場所:九州工業大学飯塚キャンパス グローバルコミュニケーションラウンジ

  • 第45回 BMIRC研究会

    2016.12.19 - 2016.12.20

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    Type:Seminar, workshop

    デザイン思考ワークショップ
    (第45回BMIRC研究会)
    九州工業大学大学院情報工学府 上熊須悦子 日時:2016年12月19-20日18:00 - 20:00
    場所:九州工業大学飯塚キャンパス 講義棟1303

  • 第44回 BMIRC研究会

    2016.11.04

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    Type:Seminar, workshop

    第44回BMIRC研究会 (情報工学実践セミナー対応、GCE特別セミナー)
    「シリコンバレーへ行って、起業しよう」
    「安定志向よりデザイン思考」
    1 デザイン思考とアントレプレナーシップを学んで(2015年シリコンバレー研修旅行報告)
    バイオメディカルデザインコース 上熊須悦子
    2 就職するより起業しろ
    株式会社シリコンバレーベンチャーズ
    代表取締役社長(兼), CEO 山口大学客員教授
    森若幸次郎, John Kojiro Moriwaka 日時:2016年11月4日(月)13:00-15:00
    場所:九州工業大学飯塚キャンパス グローバルコミュニケーションラウンジ

  • 第43回 BMIRC研究会

    2016.09.26

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    Type:Seminar, workshop

    バイオメディカルデザイン演習発表会
    (第43回BMIRC研究会)
    日時:2016年9月26日(月)5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス 大学院セミナー室7F
    1.毛細血管の画像解析による健康状態の数値化
    小川信也、福田圭寿、梶原成道
    2. 高齢者・負傷者の排泄環境改善のためのニーズ調査
    植木勇太,ラフマンシャハナ,武内僚佑,安延勇紀

  • 第42回 BMIRC研究会

    2016.07.21

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    Type:Seminar, workshop

    デザイン思考と医療ビジネス入門(第42回BMIRC研究会)
    (情報工学実践セミナー対応)
    「バイオメディカルインフォマティクスの起業化」
    アメリエフ株式会社社長 
    山口昌雄 

    日時:2016年7月21日(木)
      場所:九州工業大学飯塚キャンパス 1303講義室
    14:40-16:10:アメリエフのこれまでと、今後の発展に向けて
    16:20-17:50:研究者から起業家への転身について

  • 第40回 BMIRC研究会

    2016.06.23

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    Type:Seminar, workshop

    第40回BMIRC研究会(情報工学実践セミナー対応)
    「免疫・生体応答を制御するシステムの探究」
    理化学研究所統合生命医科学研究センター
    統合細胞システム研究チーム 上級研究員
    篠原 久明 PhD 
    日時:2016年6月23日(木)16:20-17:50 (6時間目)
    場所:九州工業大学飯塚キャンパス大学院セミナー室(5階)

  • 第39回 BMIRC研究会

    2016.05.20

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    Type:Seminar, workshop

    第39回BMIRC研究会(情報工学実践セミナー対応)
    「光合成および様々な生物学の現象の解析およびシミュレーションへのヒル式およびミカエリス・メンテン式の派生式の利用」
    北九州市立大学国際光合成産業化研究センター長・教授
    河野智謙 
    日時:2016年5月20日(金)16:20-17:50 (5時間目)
    場所:九州工業大学飯塚キャンパスN712

  • 第38回 BMIRC研究会

    2016.05.02

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    Type:Seminar, workshop

    第38回BMIRC研究会
    「実験と数理モデルによるNF-κBシグナル伝達システムの解析」
    理化学研究所統合生命医科学研究センター研究員
    井上健太郎 PhD
    日時:2016年5月2日(月)14:40から
    場所:九州工業大学飯塚キャンパスN712

  • 九工大発イノベーションとアントレプレナーシップ

    2016.03.18

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    Type:Seminar, workshop

    九工大発イノベーションとアントレプレナーシップ
    プレゼンター:
    松永守央 九州工業大学学長
    倉田博之 九州工業大学BMIRCセンター長
    Ashir Ahmed 九州大学システム情報科学研究院准教授
    森若ジョン幸次郎 Silicon Valley Ventures CEO
    渡邉陽平 文部科学省 産学連携・地域支援課長補佐 日時:2016年3月18日(月)14:00 - 17:30
    場所:九州工業大学飯塚キャンパス2201講義室

  • 第37回 BMIRC研究会

    2016.03.11

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    Type:Seminar, workshop

    バイオメディカルデザイン演習II発表会(第37回BMIRC研究会) 日時:2016年3月11日(月)13:00 - 14:30 (3時間目)
    場所:九州工業大学飯塚キャンパス大学院セミナー室(7階)

  • 第36回 BMIRC研究会

    2015.12.21

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    Type:Seminar, workshop

    イノベーションと起業家精神
    GCEシリコンバレー研修旅行報告
    九州工業大学大学院情報工学府修士1年
    上熊須悦子、栗原健、楠田隼人、植木勇太  概要:11月22-28日のシリコンバレーの先進医療ベンチャー企業訪問、スタンフォード大学バイオデザインプログラムでの発表について報告する。
    日時:2015年12月21日(月)16:20 - 17:00 (4時間目)
    場所:九州工業大学飯塚キャンパス1301講義室

  • 第35回 BMIRC研究会

    2015.12.18

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    Type:Seminar, workshop

    アミノ酸インフォマティクス技術を活用した、健康寿命の延伸と医療費削減に資する事業の創出
    味の素株式会社 イノベーション研究所  
    Ajinomoto Certified Professional 田中孝幸
    (PhD, 生命情報工学科OB) 概要:血液中のアミノ酸濃度を測定し、健康状態や病気の可能性を解析するサービス(アミノインデックス®)を一例として、医療・福祉の課題解決に向けたバイオインフォマティクス事業開発をご紹介します。
    日時:2015年12月18日(金)13:00-14:30 (3時間目)
    場所:九州工業大学飯塚キャンパス1305講義室



  • 第34回 BMIRC研究会

    2015.12.10

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    Type:Seminar, workshop

    第34回BMIRC研究会
    生物システムの安定性と可塑性:理論と実験からのアプローチ
    理化学研究所・生命システム研究センター 
    チームリーダ 古澤力 (PhD) 日時:2015年12月10日(木)14:40-16:10 (4時間目)
    場所:九州工業大学飯塚キャンパス1303講義室


  • 第33回 BMIRC研究会

    2015.10.23

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    Type:Seminar, workshop

    第33回BMIRC研究会
    製薬企業における理系人の働き方
    興和株式会社 臨床解析部部長
    菅波秀規 (生物化学システム工学科1995年度卒業OB) 日時:2015年10月23日(金)13:00-14:30 (3時間目)
    場所:九州工業大学飯塚キャンパス1305講義室

  • 第32回 BMIRC研究会

    2015.09.30

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    Type:Seminar, workshop

    バイオメディカルデザイン演習報告会(第32回BMIRC研究会)
    日時:2015年9月30日(水)13:00-14:30 (2時間目)
    場所:九州工業大学飯塚キャンパス大学院セミナー室(2階)

  • 第31回 BMIRC研究会

    2015.07.24

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    Type:Seminar, workshop

    BMIRC研究開発投資相談会(第31回BMIRC研究会:非公開)

  • 第30回 BMIRC研究会

    2015.07.17

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    Type:Seminar, workshop

    デザイン思考と医療ビジネス入門招待講演 (第30回BMIRC研究会)
    オリンパス株式会社 執行役員事業開発室長 斉藤吉毅 日時:2015年7月17日(金)
    14:40-16:10:医療機器の開発について - 内視鏡の開発(消化管癌に対する手術のイノベーション)
    16:20-17:50:医療機器の規制と品質保証
    場所:飯塚キャンパス総合研究棟 大学院セミナー室N712
    講演概要:
    1. 医療機器産業の現状(世界市場、日本市場、疾病動向)
    2. 内視鏡について
    3. 消化管癌の手術へのイノベーション
    4. 内視鏡の開発に歴史
    5. 内視鏡の将来来像
    6. 医療機器の規制と品質保証

  • 第29回 BMIRC研究会

    2015.06.26

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    Type:Seminar, workshop

    デザイン思考と医療ビジネス入門招待講演
    福岡県庁保健医療介護部薬務課 高橋佳子 日時:2015年6月26日(金)
    14:40-16:10:医薬品医療機器等の法について(I)
    16:20-17:50:医薬品医療機器等の法について(II)
    場所:飯塚キャンパス総合研究棟 大学院セミナー室N511

  • 第28回 BMIRC研究会

    2015.06.25

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    Audience: College students

    Type:Seminar, workshop


    eIF5類似タンパク質5MPによる翻訳制御
    カンザス州立大学生物学科教授 浅野桂 日時:2015年6月25日(木)16:20-17:50

    場所:飯塚キャンパス 2102講義室

  • 九州工業大学大学院情報工学府バイオメディカルデザインコースのキックオフミーティング

    2015.03.03

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    Type:Seminar, workshop

    九飯塚医療イノベーション推進会議(飯塚市、飯塚病院、飯塚研究開発機構、九州工業大学)では、米国シリコンバレーと連携して、医療機関や医療、看護、介護に関する隠れたニーズを発見して、そのニーズを解決するデザイン思考の研究開発に取り組んでいます。2015年度大学院情報工学府にバイオメディカルデザインコースを設置し、医療機器や医療情報システムのイノベーションを行うグローバルリーダーを養成し、飯塚から医療イノベーションを起こします。
    日時:2015年3月3日 13:00から18:00
    場所:九州工業大学飯塚キャンパス 2201講義室
    主催:飯塚医療イノベーション推進会議
    共催:九州工業大学バイオメディカルインフォマティクス研究開発センター(BMIRC)
    http://www.bmirc.jp/bmd/2015/

  • 第27回 BMIRC研究会

    2014.12.11

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    Type:Seminar, workshop

    The Smart Walking Cane Project: Combining Education, Research and Development
    九州工業大学助教 ステファンホルスト
    日時:12月11日(木)、5限(16:20-17:50)
    場所:飯塚キャンパス 総合研究棟 N512

  • 生命情報工学研究系セミナー (第26回 BMIRC研究会)

    2014.12.05

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    Type:Seminar, workshop

    発育鶏卵による次世代型動物実験法の開発と制癌剤の創薬研究
    宇都義浩
    徳島大学大学院ソシオテクノサイエンス研究部
    ライフシステム部門&フロンティア研究センター 教授
    日時:12月5日(金)、3限(13:00-14:30)
    場所:飯塚キャンパス 講義棟1305

  • 第25回 BMIRC研究会

    2014.11.07

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    Type:Seminar, workshop

    マイクロ流体チップの医療・バイオ応用
    坂本憲児
    九州工業大学 情報工学研究院 マイクロ化総合技術センター 助教
    日時:11月7日(金)、5限(16:20-17:50)
    場所:飯塚キャンパス総合研究棟 大学院セミナー室N712

  • 第24回 BMIRC研究会

    2014.10.16

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    Type:Seminar, workshop

    バイオマスの超臨界水ガス化への化学工学的アプローチ
    松村幸彦
    広島大学 大学院工学研究院 エネルギー・環境部門 教授
    日時:10月16日(木)、2限(10:30-12:00)
    場所:九州工業大学 飯塚キャンパス研究棟 E726(生命情報工学科会議室)

  • 第23回 BMIRC研究会

    2014.10.08

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    Audience: College students

    Type:Seminar, workshop

    オミックスデータ解析と機械学習によるインシリコ創薬
    山西芳裕 (九州大学生体防御医学研究所・高等研究院准教授)
    日時:10月8日(水)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス総合研究棟N712
    共催:日本バイオインフォマティクス学会

  • 第22回 BMIRC研究会

    2014.10.06

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    Type:Seminar, workshop


    飯塚発バイオベンチャー企業:ペットの遺伝子検査サービス
    大里義治(有限会社 カホテクノ)
    日時:10月6日(月)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス 講義棟1301

  • 第21回 BMIRC研究会

    2014.08.06

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    Type:Seminar, workshop

    核小体ストレス応答を起点とした新規がん関連分子の同定と創薬
    河原康一(鹿児島大学大学院医歯学総合研究科分子腫瘍学分野)
    有馬一成(鹿児島大学大学院理工学研究科理学系生命化学専攻有機生化学講座)
    日時:8月6日(水)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス総合研究棟5階大学院セミナー室N511
    幹事:倉田博之 BMIRC

  • 第20回BMIRC研究会

    2014.08.05

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    Audience: College students

    Type:Seminar, workshop

    センサーと神経工学
    アストロサイト領域の条件変化とシナプス伝達
    桂林秀太郎(福岡大学薬学部助教) 
    マイクロデバイスを用いた神経系細胞の刺激計測技術
    安田隆(九州工業大学生命体工学研究科教授)
    日時:8月5日(火)16:00~18:00
    場所:九州工業大学若松キャンパス研究棟講義室2


  • 第19回BMIRC研究会

    2014.07.25

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    Type:Seminar, workshop


    デザイン思考とクリエイティビティでイノベーションを生む仕組み
    森若幸次郎 (株式会社モリワカ 専務取締役) 日時:7月25日(金)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス総合研究棟N712

  • 第18回BMIRC研究会

    2014.07.22

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    Type:Seminar, workshop

    医療イノベーションを起こすためのデザイン思考
    BMIRC 倉田博之 日時:7月22日(火)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス総合研究棟N712

  • 第17回BMIRC研究会

    2014.07.16

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    Type:Seminar, workshop

    化学反応ネットワークのSensitivityをFunction-freeに決定する
    望月敦史(理化学研究所 主任研究員/CREST, JST) 日時:7月16日(水) 16:20-17:50
    場所:九州工業大学飯塚キャンパス 1101講義室
    主催:日本バイオインフォマティクス学会九州地域部会、BMIRC

  • 飯塚医工情報連携の先進的事例(第16回BMIRC研究会)

    2014.06.24

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    Type:Seminar, workshop

    飯塚市、飯塚病院、飯塚研究開発機構、九州工業大学は、医工情報連携によるイノベーションを推進し、次代の成長産業の育成を目指しています。飯塚地域からの医療イノベーションの先進的実例を紹介し、医工情報連携を進めるための議論を深めていきます。
    日程: 6月24日(火) 15:00-18:00
    場所: 九州工業大学飯塚キャンパス 2101講義室
    主催: 九州工業大学バイオメディカルインフォマティクス研究開発センター(BMIRC)
    共催: 日本バイオインフォマティクス学会九州地域部会 
    連絡先: 倉田博之(BMIRC)
    15:00-15:05 開会のあいさつ
    15:05-15:45レーザーを用いた血流画像化法(LSFG)を医療機器にするまで
    藤居仁(ソフトケア有限会社、九州工業大学名誉教授) 
    15:45-16:15 情報工学の経皮吸収型製剤設計への応用 ~研究と起業~
    森大輔(バイオコムシステムズ株式会社、代表取締役)
    16:20-16:50知識処理技術を活用した地域医療連携支援の取組みー退院支援業務のシステム化を例としてー
    梅田政信(九州工業大学 情報創成研究系)
    16:50-17:20 消化管内走行カプセル―体内を動き回るカプセルが医療を変えるー
    伊藤高廣(九州工業大学 機械情報研究系、 BMIRC)
    17:30-18:00 ディスカッション

  • 第15回 BMIRC研究会

    2014.06.09

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    Type:Seminar, workshop

    演題:試験管内の概日リズムの同期と共鳴
    講師:九州大学 芸術工学研究院 伊藤浩史
    日時:6月9日(月)、5限(16:20-17:50)
    場所:九州工業大学飯塚キャンパス総合研究棟N511

  • BMIRC-RCBT 共同講演会

    2014.05.13

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    Type:Lecture

    (第14回BMIRC研究会)
    ・日時:5月13日(火)、5限(16:20-17:50)
    ・場所:九州工業大学飯塚キャンパス総合研究棟N511
    ・タイトル:「Unstructured/Structured Interactionを標的にした創薬(2)」
    ・講師:株式会社PRISM Pharma社長 小路弘行
    http://www.kyutech.ac.jp/ura/topics/entry-3061.html

  • 第13回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会

    2014.04.30

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    Type:Seminar, workshop

    ・日時:4月30日(水)、3時間目(13:00-14:00)
    ・場所:飯塚キャンパス 総合研究棟2階大学院セミナー室
    ・世話人:永山勝也(情報工学研究院 機械情報工学系)
    13:00-13:30: 臓器工学(Whole Organ Engineering)
    九州大学 大学院 工学研究院 化学工学部門 教授 井嶋博之 
    13:30-14:00: 臓器工学に基づく肝臓構築の試みと実用化に向けた課題
    九州大学 大学院 工学研究院 化学工学部門 助教 白木川奈菜

  • 情報処理学会第37回バイオ情報学研究会

    2014.03.05

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    Audience: General

    Type:Seminar, workshop

    ・日程:平成26年3月5日(水) 14:00から18:00
    ・会場:九州工業大学飯塚キャンパス総合研究棟大学院セミナー室N712
         820-8502 飯塚市川津680-4
    ・連催:九州工業大学バイオメディカルインフォマティクス研究開発センター(BMIRC)
    ・テーマ:『バイオインフォマティクスとシステム生物学』および『一般』
    ・招待講演:プロモーター配列の合理的な設計に挑む
     矢田哲士 (九州工業大学情報工学研究院)

  • 九州工業大学 講演会

    2014.02.19

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    Type:Lecture

    医工情報連携 人材育成を目指して -アメリカ・シリコンバレーの先進事例-
    ・日  時 2月19日 水曜日 10:30 ~ 14:30
    ・場  所 九州工業大学 情報工学部 総合研究棟大学院セミナー室N711
    ・TV中継 戸畑キャンパス AVホール 若松キャンパス TV会議室
    ・発表者 
    ・Dr. Michael Needels Fogarty Institute for Innovation (FII)
    ・Dr. Eric Pifer   El Camino Hospital 
    ・井桁洋貴 氏    飯塚病院
    ・池野文昭 博士(MD)  Stanford University

  • 第12回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会

    2013.12.16

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    Type:Seminar, workshop

    テーマ:工学と解析で連携可能な医療研究の紹介
    日時:12月16日(月)13:00~14:30
    会場:九州工業大学情報工学部、飯塚キャンパス 総合研究棟大学院セミナー室N511
    交通: http://www.iizuka.kyutech.ac.jp/public/access/
    キャンパスマップ 12の建物: http://www.iizuka.kyutech.ac.jp/public/map/
    世話人 永山 勝也 (九工大 情報工学研究院 機械情報工学系)
    13:00-13:30 がんスフェロイド増殖試験の評価と予測をめざす仮想培養系の基礎研究
    立野 玲子 (東京都医学総合研究所、病院連携研究)
    13:30-14:00 歯科再生医療と微小循環
    松尾 雅斗 (神奈川歯科大学大学院 口腔科学講座・歯科形態学)
    14:00-14:30 毛細血管の形態学とシミュレーションモデル
    三浦 一郎 (順天堂大学医学部、人体病理病態学講座)
    14:30-14:35 総評
    倉田 博之 (バイオメディカルインフォマティクス研究開発センター長)

  • 第11回バイオメディカルインフォマティクス研究開発センター研究会

    2013.07.22

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    Type:Seminar, workshop

    演題: 開始コドンの厳密な選択とその異常からくる病理について
    講演者: 浅野桂 カンザス州立大学
    日時: 7月22日(月)14:40から
    場所: 九州工業大学 飯塚キャンパス 総合研究棟 2階 大学院セミナー室
    主催:BMIRC
    共催:日本バイオインフォマティクス学会九州地域部会
    参加費:無料
    世話人:倉田博之 (BMIRC) kurata@bio.kyutech.ac.jp

  • 第11回バイオメディカルインフォマティクス研究開発センター研究会

    2013.07.22

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    Type:Seminar, workshop

    演題: 開始コドンの厳密な選択とその異常からくる病理について
    講演者: 浅野桂 カンザス州立大学
    日時: 7月22日(月)14:40から
    場所: 九州工業大学 飯塚キャンパス 総合研究棟 2階 大学院セミナー室
    主催:BMIRC
    共催:日本バイオインフォマティクス学会九州地域部会
    参加費:無料
    世話人:倉田博之 (BMIRC) kurata@bio.kyutech.ac.jp

  • 第10回バイオメディカルインフォマティクス研究開発センター研究会

    2013.04.19

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    Type:Seminar, workshop

    14:40-16:00
    場所: 九州工業大学 飯塚キャンパス 総合研究棟 7階 大学院セミナー室
    Title: Interactively learning segmentation model complexity using max-margin interval regression.
    講演者: Toby Dylan Hocking (東工大)

  • 第9回バイオメディカルインフォマティクス研究開発センター研究会

    2013.01.29

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    Type:Seminar, workshop

    15:00から16:00
    場所: 九州工業大学 飯塚キャンパス 総合研究棟 5階 大学院セミナー室
    演題:ブーリアンネットワークとスケールフリーネットワークの制御
    講演者: 阿久津達也 (京都大学)

  • 第8回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会

    2012.12.14

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    Type:Seminar, workshop

    5時間目(16:20-17:50)
    場所:飯塚キャンパス 総合研究棟5階大学院セミナー室N511
    演題:「遺伝子発現を統合的に理解する」
    講師:秋田県立大学 小西智一

  • 第7回BMIRC主催セミナー

    2012.12.10

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    Type:Seminar, workshop

    テーマ:工学と解析で連携可能な医療研究の紹介
    主催:九州工業大学バイオメディカルインフォマティクス研究開発センター(BMIRC)
    日時:12月10日(月)13:00~16:00
    会場:九州工業大学情報工学部、飯塚キャンパス 総合研究棟大学院セミナー室N711
    交通: http://www.iizuka.kyutech.ac.jp/public/access/
    キャンパスマップ 12の建物: http://www.iizuka.kyutech.ac.jp/public/map/
    12:58-13:00 挨拶
    13:00-13:30 がん治療法の数理・情報学的基盤の研究開発
    立野 玲子 (東京都医学総合研究所、がん治療研究室)
    13:30-14:00 がん悪性化因子GEF-1を標的とする坑がん剤の研究
    小倉  潔 (東京都医学総合研究所、がん治療研究室)
    14:00-14:30 腫瘍微小環境を標的としたがん治療
    齋藤 さかえ (京都大学医学研究科、次世代免疫制御を目指す創薬医学融合拠点)
    14:30-14:40 休憩
    14:40-15:10 歯科再生医療と微小循環
    松尾 雅斗 (神奈川歯科大学、歯学部)
    15:10-15:40 毛細血管と病理について
    三浦 一郎 (順天堂大学医学部、人体病理病態学講座)
    質疑の後 16:00閉会

  • 医⇒学へのプレゼンテーション

    2012.11.02

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    Type:Seminar, workshop


    主催:飯塚市病院、飯塚市、九州工業大学
    テーマ:最新米国医療機器開発の現状と飯塚病院からの課題提案
    日時: 11月2日(金)16:30~19:00
    会場:九州工業大学情報工学部第一会議室
    講師:伊藤高廣ほか

  • 第6回 BMIRC主催セミナー

    2012.09.28

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    Type:Seminar, workshop


    主催:BMIRC
    演題:広島大学工学部における医用画像処理の取り組み:放射線科,眼科,内科
    日時: 9月28日(金)13:00~14:00
    会場:総合研究棟5F大学院セミナー室
    講師:広島大学 准教授 玉木徹

  • 第5回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会

    2012.09.12

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    Type:Seminar, workshop

    日時:9月12日(水)、5時間目(16:20-17:50)
    会場:生命体工学研究科若松キャンパス 2階端末室1(廊下側)
    演題:脳で観察される神経リズムとブレインコンピュータインターフェース
    講師:生命体工学研究科 夏目季代久
    演題:ECDL-based BCIs with motor imagery
    講師:情報工学研究院 山﨑敏正

  • 第30回バイオ情報学研究会開催のお知らせ

    2012.08.09 - 2012.08.10

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    Audience: General

    Type:Seminar, workshop


    主催:情報処理学会バイオ情報学研究会
    連催:九州工業大学バイオメディカルインフォマティクス研究開発センター(BMIRC)
    題目:『バイオメディカルインフォマティクス』および『一般』
    日時:平成24年8月9日(木)~10日(金) 
    会場:九州工業大学情報工学部(飯塚キャンパス)
    詳細:http://www.ipsj.or.jp/katsudou/sig/sighp/bio/

  • 第4回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会開催

    2012.06.28

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    Type:Seminar, workshop

  • 第3回バイオメディカルインフォマティクス研究開発センター(BMIRC)研究会開催

    2012.05.31

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    Type:Seminar, workshop

  • バイオサイエンスのe-learningサイトe-Bioの公開

    2012.05.22

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    Type:Seminar, workshop


    開発責任者:皿井明倫(BMIRC)

  • バイオメディカルインフォマティクス研究開発センター開所式典記念講演祝賀会

    2012.04.20

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    Type:Seminar, workshop

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