Updated on 2023/07/29

 
MAEDA Kazuhiro
 
Scopus Paper Info  
Total Paper Count: 0  Total Citation Count: 0  h-index: 6

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
Assistant Professor
External link

Research Interests

  • 代謝ネットワーク

  • ハイパフォーマンスコンピューティング

  • スーパーコンピュータ

  • システム生物学

  • 生化学パラメータ推定

Degree

  • Kyushu Institute of Technology  -  Doctor of Information Engineering   2011.03

Biography in Kyutech

  • 2019.12
     

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

  • 2015.03
    -
    2019.11
     

    Kyushu Institute of Technology   Frontier Research Academy for Young Researchers   Specially Appointed Assistant Professor  

Papers

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

    Kazuhiro Maeda, Hiroyuki Kurata

    International Journal of Molecular Sciences   2023.04

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

    DOI: https://doi.org/10.3390/ijms24087296

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

    Kazuhiro Maeda, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, Hiroyuki Kurata

    BMC Bioinformatics   2022.11

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

    DOI: 10.1186/s12859-022-05009-x

    DOI: 10.1186/s12859-022-05009-x

  • Simulation of the crosstalk between glucose- and acetaminophen metabolism in a liver zonation model "jointly worked" Reviewed International journal

    Kazuhiro Maeda, Shuta Hagimori, Masahiro Sugimoto, Yasuyuki Sakai, Masaki Nishikawa

    Frontiers in Pharmacology   2022.08

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

    DOI: 10.3389/fphar.2022.995597

  • RCGAToolbox: 動力学モデルのパラメーター推定 のための実数値遺伝的アルゴリズムソフトウェア

    前田和勲,Fred C. Boogerd,倉田博之

    IPSJ SIG Technical Report   2022.03

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publishing type:Research paper (conference, symposium, etc.)

  • RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models Reviewed

    Kazuhiro Maeda, Fred C. Boogerd, Hiroyuki Kurata

    IPSJ Transactions on Bioinformatics   2021.09

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

    DOI: 10.1101/2021.02.15.431062

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

    5 ( 1 )   2019.12

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

    DOI: 10.1038/s41540-019-0091-6

    Scopus

    Other Link: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85064343332&origin=inward

  • 動力学パラメータ推定問題:大腸菌アンモニア輸送-同化ネットワークの事例

    前田和勲

    IPSJ SIG Technical Report   2019.09

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    Authorship:Lead author   Language:Japanese   Publishing type:Research paper (conference, symposium, etc.)

  • libRCGA: 動力学モデルの高速なパラメータ推定のための遺伝的アルゴリズムライブラリ

    前田和勲, Fred C. Boogerd, 倉田博之

    IPSJ SIG Technical Report   2018.09

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    Authorship:Lead author   Language:Japanese   Publishing type:Research paper (conference, symposium, etc.)

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

    440   21 - 31   2018.03

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

    DOI: 10.1016/j.jtbi.2017.12.014

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    Other Link: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85038957457&origin=inward

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

    11 ( 0 )   31 - 40   2018.01

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

    DOI: 10.2197/ipsjtbio.11.31

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/130007483197

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

    122 ( 1 )   111 - 116   2016.07

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

    DOI: 10.1016/j.jbiosc.2015.12.001

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

    15 ( 1 )   2016.06

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

    DOI: 10.1186/s12934-016-0511-x

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    Other Link: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84975299249&origin=inward

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

    8 ( 5 )   2014.12

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

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

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

    47 ( 1 )   1 - 9   2014.01

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

    DOI: 10.1252/jcej.13we152

    Scopus

    CiNii Article

    Other Link: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84892734889&origin=inward

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

    37 ( 9 )   1925 - 1927   2014.01

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

    DOI: 10.1007/s00449-014-1167-8

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  • 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

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

    研究報告バイオ情報学(BIO)   2013 ( 7 )   1 - 6   2013.09

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

    アンモニアは大腸菌にとって最適な窒素源である.大腸菌は,TCA 回路の中間代謝物である α-ケトグルタル酸にアンモニアを付加し,グルタミン酸とグルタミンを合成する.細胞内の窒素のほとんどはこの 2 つの代謝物に由来するものである.このような理由から,大腸菌がどのようにアンモニアを同化し,グルタミン酸とグルタミンの合成を制御しているのか明らかにすることは重要である.我々は,大腸菌アンモニア同化システムの新しいダイナミックモデルを構築した.動力学パラメータ推定では,推定値と測定値の差が最小になるように遺伝的アルゴリズムにペナルティ戦略を組み合わせた.我々のモデルは,近年発表されたメタボロームデータを定量的に再現できる.最近,グルタミン酸合成酵素に対するアスパラギン酸の競争阻害の重要性が指摘されたが,本稿ではその検証も行う.また GOGAT 欠損株と GOGAT 欠損サプレッサー変異株の解析も行う.アンモニアが豊富な条件では,グルタミン酸の過剰な蓄積によってサプレッサー変異株は野生株よりも増殖が遅いことが予測された.

    CiNii Article

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

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

    36 ( 3 )   333 - 344   2013.03

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

    DOI: 10.1007/s00449-012-0789-y

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

    15 ( 5 )   699 - 709   2013.01

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

    DOI: 10.1093/bib/bbt048

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  • CADLIVE optimizer: web-based parameter estimation for dynamic models Reviewed

    7   2012.08

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

    DOI: 10.1186/1751-0473-7-9

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  • A symmetric dual feedback system provides a robust and entrainable oscillator Reviewed

    7 ( 2 )   2012.02

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

    DOI: 10.1371/journal.pone.0030489

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

    18 ( 1 )   53 - 90   2012.01

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

    DOI: 10.1162/artl_a_00049

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

    34 ( 4 )   433 - 446   2011.05

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

    DOI: 10.1007/s00449-010-0486-7

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

    272 ( 1 )   174 - 186   2011.03

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

    DOI: 10.1016/j.jtbi.2010.12.012

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

    2   2 - 14   2009.12

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

    DOI: 10.2197/ipsjtbio.2.2

    Scopus

    CiNii Article

    Other Link: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=77951099999&origin=inward

  • Robustness Analysis of Interlocked Feedbacks of Circadian Rhythm

    MAEDA KAZUHIRO, KURATA HIROYUKI

    2009 ( 15 )   1 - 5   2009.05

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

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110007990808

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

    32 ( 2 )   283 - 288   2009.02

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

    DOI: 10.1007/s00449-008-0244-2

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

    4 ( 2 )   377 - 389   2009.01

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

    DOI: 10.11185/imt.4.377

    CiNii Article

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

  • 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

    前田 和勲, 倉田 博之

    情報処理学会研究報告バイオ情報学(BIO)   2008 ( 86 )   9 - 12   2008.09

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

    ダイナミックシミュレーションは環境ストレスや遺伝的変化に対してロバストネスを生み出す生化学ネットワークのメカニズムの解明に不可欠である。しかし、これまでに行われた多くのシミュレーションや解析は特定の速度パラメータ値に依存している。速度パラメータの正確な測定は困難であるので、特定のパラメータ値に依存するのではなく、パラメータ値の変化が与える影響を考慮した解析が必要である。これを可能にするためには細胞内の挙動を再現しうる全ての速度パラメータ値を広い探索空間から偏りなく探し出さなければならない。本稿では、ランダム探索と進化的探索を組み合わせた新しいパラメータ探索法、Two-phase search 法を提案する。そして、この手法が偏りなく効率的に速度パラメータを探索できることを示す。Dynamic simulations are essential for understanding the mechanism of how biochemical networks generate robust properties to environmental stresses or genetic changes. However, typical dynamic modeling and analysis yield only local properties regarding a particular choice of plausible values of kinetic parameters. Global and firm analyses are needed that consider how the changes in parameter values affect the results. A typical solution is to systematically analyze the dynamic behaviors in large parameter space by searching all plausible parameter values without any biases. In this paper, we propose the two-phase search method that consists of a random search and an evolutionary search to effectively explore all possible solution vectors of kinetic parameters satisfying the target dynamics. It enables a nonbiased and high-speed parameter search for dynamic models of biochemical networks.

    CiNii Article

    Other Link: https://ci.nii.ac.jp/naid/110006967151

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

    35 ( 20 )   2007.11

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

    DOI: 10.1093/nar/gkm769

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  • Global Optimization of Large-scale Dynamic Biomolecular Network Model

    MAEDA KAZUHIRO, YOSHIDA KEISUKE, KURATA HIROYUKI

    IPSJ SIG Notes   2007 ( 86 )   91 - 94   2007.09

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

    CiNii Article

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

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Conference Prsentations (Oral, Poster)

  • A hybrid approach for kinetic parameter estimation based on machine learning and global optimization

    Kazuhiro Maeda, Aoi Hatae, Yukie Sakai and Hiroyuki Kurata

    IIBMP2022 

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    Event date: 2022.09.13 - 2022.09.15   Language:English  

  • RCGAToolbox: 動力学モデルのパラメーター推定 のための実数値遺伝的アルゴリズムソフトウェア

    前田和勲、Fred C. Boogerd、倉田博之

    第69回 情報処理学会 バイオ情報学研究会 

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    Event date: 2022.03.11   Language:Japanese  

  • RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models

    Kazuhiro Maeda, Fred C. Boogerd, and Hiroyuki Kurata

    ISMB/ECCB 2021 

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    Event date: 2021.07.29   Language:English  

  • RCGAToolbox: 生化学システムの動力学パラメータ推定のためのツールボックス

    前田和勲、倉田博之

    IIBMP2020 

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    Event date: 2020.09.01   Language:Japanese  

  • The ‘rubber band method’ of ranking network mechanisms rather than claimi the single best: E. coli's active ammonium transport is 130 times better than the passive transport network

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

    ICSB2019 

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    Event date: 2019.11.01   Language:English  

  • 大腸菌アンモニア輸送-同化ネットワークの定量的動力学モデルの構築

    前田和勲, Hans V. Westerhoff, 倉田博之, and Fred C. Boogerd

    第71回日本生物工学会大会 

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    Event date: 2019.09.18   Language:Japanese  

  • 制約付き最適化に基づくパラメータ推定を用いた大腸菌アンモニア輸送-同化の動力学モデリング

    前田和勲, Hans V. Westerhoff, 倉田博之, and Fred C. Boogerd

    IIBMP2019 (ハイライトトラック) 

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    Event date: 2019.09.10   Language:Japanese  

  • 動力学パラメータ推定問題:大腸菌アンモニア同化-輸送ネットワークの事例

    前田和勲

    第59回 情報処理学会 バイオ情報学研究会 

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    Event date: 2019.09.08   Language:Japanese  

  • Ranking E. coli’s ammonium transport and assimilation networks

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

    AIMMS Meeting 

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    Event date: 2019.04.18   Language:English  

  • Ranking E. coli’s ammonium transport and assimilation networks by how they fit diverse experiments

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

    BioSB 2019 

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    Event date: 2019.04.02 - 2019.04.03   Language:English  

  • Ranking E. coli’s ammonium transport and assimilation networks by how they fit diverse experiments

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

    AMSA Meeting 

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    Event date: 2019.03.28   Language:English  

  • 大腸菌アンモニア輸送-同化システムのシミュレーション

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

    定量生物学の会 第9回年会 

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    Event date: 2019.01.13 - 2019.01.14   Language:Japanese  

  • 大腸菌AmtBはアンモニアの能動輸送体か?それとも受動輸送体か?

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

    The 41th Annual Meeting of the Molecular Biology Society of Japan 

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    Event date: 2018.11   Language:Japanese  

  • 制約付き最適化を使った動力学パラメータ推定手法の提案と大腸菌アンモニア同化-輸送ネットワークへの応用

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

    生命科学系フロンティアミーティング 2018  生命情報科学若手の会

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    Event date: 2018.10.05   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頑健性と調節可能性の解析

    前田和勲、倉田博之

    IIBMP2018 

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    Event date: 2018.09.19 - 2018.09.21   Language:Japanese  

  • libRCGA: 動力学モデルの高速なパラメータ推定のための遺伝的アルゴリズムライブラリ

    前田和勲、Fred C. Boogerd、倉田博之

    第55回 情報処理学会 バイオ情報学研究会 

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    Event date: 2018.09.18   Language:Japanese  

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Works

  • RCGAToolbox

    2021.02

  • libRCGA

    2018.06

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    Location:https://github.com/kmaeda16/libRCGA  

    libRCGA is a C library for real-coded genetic algorithms (RCGAs). Currently, two RCGAs, UNDX/MGG and REXstar/JGG, are implemented. For constrained optimization problems, the stochastic ranking can be used. RCGAs are paralleled by MPI. For details, see the original paper: Kazuhiro Maeda, Fred C. Boogerd, and Hiroyuki Kurata, libRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models, IPSJ Transactions on Bioinformatics, 11: 31-40, 2018 (https://www.jstage.jst.go.jp/article/ipsjtbio/11/0/11_31/_article/-char/en).

    libRCGA is available from https://github.com/kmaeda16/libRCGA.

Lectures

  • 肝臓のzonationを考慮した薬物代謝動態の数理モデル

    第31回日本医学会総会  2023.04 

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    Language:Japanese   Presentation type:Invited lecture  

  • 動力学シミュレーションを使った生化学システムの理解と設計

    第2回分子サイバネティクス・第46回分子ロボティクス定例研究会  2021.05 

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    Language:Japanese   Presentation type:Invited lecture  

Honors and Awards

  • デジタルコンテンツコンテスト優秀賞(YOKABIO)

    九州工業大学   2021.07.21

    九工大BIOMODチーム YOKABIO

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    Country:Japan

  • デジタルコンテンツコンテスト優秀賞(前田個人)

    九州工業大学   2021.07.21

    前田和勲

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    Country:Japan

  • IPSJ IPSJ Yamashita SIG Research Award

    Information Processing Society of Japan   2020.03.01

    Kazuhiro Maeda

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    Country:Japan

  • 情報処理学会第55回バイオ情報学研究会 SIGBIO優秀プレゼンテーション賞

    情報処理学会 バイオ情報学研究会   2018.09

    前田和勲

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    Country:Japan

  • 情報処理学会第51回バイオ情報学研究会 SIGBIO優秀プレゼンテーション賞

    情報処理学会 バイオ情報学研究会   2017.09

    前田和勲

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    Country:Japan

  • 平成21年度IPSJ論文船井若手奨励賞

    船井情報科学振興財団   2010.03

    前田和勲

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    Country:Japan

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Grants-in-Aid for Scientific Research

  • 腸内細菌代謝の理解と合理的な制御

    Grant number:18K18153  2018.04 - 2022.03   若手研究

  • 大腸菌アンモニア同化制御の定量的ダイナミックモデル構築とシステム的理解

    Grant number:26870432  2014.04 - 2017.03   若手研究(B)

  • 生体分子ネットワークのシステム的理解に基づく抗がん剤投薬スケジューリング法の開発

    Grant number:24800050  2012.08 - 2014.03   研究活動スタート支援

  • 生命システムのアドホックな進化

    Grant number:10J07813  2010.04 - 2012.03   特別研究員奨励費

Other External Funds

  • 機械学習を用いたヒトPPARαに結合するPFASの特徴の解明

    2023.04 - 2024.03

    愛媛大学化学汚染・沿岸環境研究拠点 共同利用・共同研究  

  • libRCGA: 動力学モデルの高速なパラメータ推定のための実数値遺伝的アルゴリズムのC言語ライブラリ

    2018.09

    英文校正・論文掲載費用補助  

  • 生体分子ネットワークの効率的なダイナミックモデル構築手法の開発

    2018.04 - 2018.07

    教育職員海外研修プログラム  

  • 大腸菌のアンモニア同化制御の理解とグルタミン酸発酵向上

    2017.06 - 2017.07

    吉田科学技術財団: 海外研究派遣研究者  

  • 大腸菌アンモニア輸送-同化システムのシミュレーションモデル構築とその制御機構の理解

    2017.02 - 2017.03

    教育職員海外研修プログラム  

Award for Educational Activities

  • 九州工業大学デジタルコンテンツコンテスト優秀賞

    九州工業大学   2021.07.21

  • Project Award: Bronze

    Annual biomolecular design competition for students (BIOMOD)   2019.10.28

  • 第3位(トラベルアワード)

    分子ロボティクス研究会   2019.08.31

Activities of Academic societies and Committees

  • BIOMOD 2023   実行委員