Publications

Hiroyuki Kurata* Md. Harun-Or-Roshid, Md Mehedi Hasan, Sho Tsukiyama, Kazuhiro Maeda, Balachandran Manavalan*, MLm5C: a high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models, Methods, in press, *Corresponding authors

Md. Harun-Or-Roshid, Kazuhiro Maeda, Phan Thi Le; Balachandran Manavalan, Hiroyuki Kurata, Stack-DHUpred: Advancing the accuracy of dihydrouridine modification sites detection via stacking approach, Computers in Biology and Medicine, 2024;169:107848.

Kazuhiro Maeda, Masashi Hirano, Taka Hayashi, Midori Iida, Hiroyuki Kurata, Hiroshi Ishibashi*, Elucidating key characteristics of PFAS binding to human peroxisome proliferator-activated receptor alpha: an explainable machine learning approach, Environmental Science & Technology, 2024;58(1):488-497. *Corresponding Author

Kazuhiro Maeda* and Hiroyuki Kurata, Automatic Generation of SBML Kinetic Models from Natural Language Texts using GPT, International Journal of Molecular Sciences, 24(8):7296, 2023   *Corresponding Author

Kazuhiro Maeda*, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, and Hiroyuki Kurata, MLAGO: Machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling, BMC Bioinformatics, 23(1):455, 2022  *Corresponding Author

Kazuhiro Maeda*, Shuta Hagimori*, Masahiro Sugimoto, Yasuyuki Sakai, Masaki Nishikawa, Simulation of the crosstalk between glucose- and acetaminophen metabolism in a liver zonation model, Frontiers in Pharmacology, 13, 2022   *These authors equally contributed to this work.

Kazuhiro Maeda*, Fred C. Boogerd, and Hiroyuki Kurata, RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models , IPSJ Transactions on Bioinformatics, 14, 30-35, 2021 *Corresponding Author, RCGAToolbox can be downloaded  at GitHub

Kazuhiro Maeda, Hans V. Westerhoff*, Hiroyuki Kurata*, and Fred C. Boogerd, Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network, npj Systems Biology and Applications, 5, 14, 2019 *Corresponding Authors

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 *Corresponding Author, libRCGA can be downloaded here and at GitHub

Kazuhiro Maeda*, Hiroyuki Kurata, Long negative feedback loop enhances period tunability of biological oscillators, Journal of Theoretical Biology, 440: 21-31, 2018 *Corresponding Author

Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata, Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli, Microbial Cell Factories, 15(1), 112, 2016

Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kentaro Inoue, Kazuhiro Maeda, Hiroyuki Kurata, Web Application for Genetic Modification Flux with Database to Estimate Metabolic Fluxes of Genetic Mutants, Journal of Bioscience and Bioengineering, 122(1): 111-116, 2016

Kazuhiro Maeda and Hiroyuki Kurata, Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity, BMC Systems Biology, 8(Suppl 5): S1, 2014

Kentaro Inoue, Kazuhiro Maeda, Takaaki Miyabe, Yu Matsuoka, Hiroyuki Kurata, CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis, Bioprocess and Biosystems Engineering, 37(9): 1925-1927, 2014

Hiroyuki Kurata, Kazuhiro Maeda, Yu Matsuoka, Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes, Journal of Chemical Engineering of Japan, 47(1):1-9, 2014

Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata, BioFNet: Biological functional network database for analysis and synthesis of biological systems, Briefings in Bioinformatics, 15(5): 699-709, 2014

Kazuhiro Maeda, Hiroshi Minamida, Keisuke Yoshida, and Hiroyuki Kurata, Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks, Bioprocess and Biosystems Engineering, 36(3):333-344, 2013

Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi, and Hiroyuki Kurata, CADLIVE optimizer: web-based parameter estimation for dynamic models, Source code for Biology and Medicine, 7(9), 2012

Kazuhiro Maeda and Hiroyuki Kurata, A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator, PLoS ONE, 7(2):e30489, 2012

Koichi Masaki, Kazuhiro Maeda and Hiroyuki Kurata, Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System, Artificial Life, 18(1):53-90, 2012

Kazuhiro Maeda and Hiroyuki Kurata, Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks, Journal of Theoretical Biology, 272(1):174-186, 2011

Kazuhiro Maeda, Yuya Fukano, Daichi Nitta, Shunsuke Yamamichi, and Hiroyuki Kurata, An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks, Bioprocess and Biosystems Engineering, 34(4):433-446, 2011

Kazuhiro Maeda and Hiroyuki Kurata, Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks, IPSJ Transactions on Bioinformatics, 2:2-14, 2009

Emi Shiraishi, Kazuhiro Maeda, and Hiroyuki Kurata, A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits, Bioprocess and Biosystems Engineering, 32(2):283-288, 2008

Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao, Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis, Nucleic Acids Research, 35(20):p.e134, 2007

前田和勲、Fred C. Boogerd、倉田博之、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、IPSJ SIG Technical Report, 2022-BIO-69(20):1-6, 2022

前田和勲, 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, IPSJ SIG Technical Report, 2019-BIO-59(5):1, 2019

前田和勲, Fred C. Boogerd, 倉田博之, 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, IPSJ SIG Technical Report, 2018-BIO-55(5):1-6, 2018

前田和勲, 倉田博之, 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, IPSJ SIG Technical Report, 2017-BIO-51(10):1-5, 2017

前田和勲, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, 倉田博之, 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, IPSJ SIG Technical Report, 2013-BIO-35(7):1-6, 2013

Kazuhiro Maeda and Hiroyuki Kurata, Dynamic modeling of ammonia assimilation system in E. coli, IPSJ SIG Technical Report, 2012-BIO-30(5):1-6, 2012

Kazuhiro Maeda and Hiroyuki Kurata, Robustness Analysis of Feedback Systems of Circadian Rhythm, IPSJ SIG Technical Report, 2011-BIO-24(7):1-6, 2011

Kazuhiro Maeda and Hiroyuki Kurata, Robustness Analysis of Interlocked Feedbacks of Circadian Rhythm, IPSJ SIG Technical Report, 2009-BIO-17(15):1-5, 2009

Kazuhiro Maeda and Hiroyuki Kurata, Two-phase search (TPS) method: Nonbiased and efficient parameter search for dynamic models of biochemical networks, IPSJ SIG Technical Report, 2008-BIO-14(86):9-12, 2008

Kazuhiro Maeda, Keisuke Yoshida, and Hiroyuki Kurata, Global Optimization of Large-scale Dynamic Biomolecular Network Model, IPSJ SIG Technical Report, 2007-MPS-66(23):91-94, 2007

前田和勲・吉田圭佑・倉田博之、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、ソフトウェアバイオロジー第６号、化学工学会バイオ部会生物情報分野専門分科会、34-39、2007

前田和勲・倉田博之、概日リズムのマルチパラメータ感度解析、ソフトウェアバイオロジー第９号、化学工学会バイオ部会生物情報分野専門分科会、2010