Feedback regulation of the heat shock response in E. coli. - Hiroyuki Kurata; Hana El-Samad; Tau-Mu Yi; Mustafa Khammash; John Doyle 001 (CDC, 2001)

Robustness analysis of the heat shock response in E. coli. - Hana El-Samad; Mustafa Khammash; Hiroyuki Kurata; John Doyle 001 (ACC, 2002)

Reverse Engineering for a Dynamic Model of the Drosophila Circadia Oscillator. - Tanaka Shin; Hiroyuki Kurata; Takeshi Ohashi 001 (CIMCA/IAWTIC, 2005)

Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli. - Tanaka Shin; Hiroyuki Kurata; Takeshi Ohashi 001 (SMC, 2005)

A grid layout algorithm for automatic drawing of biochemical networks. - Weijiang Li; Hiroyuki Kurata (Bioinform., 2005)

Effective and Fast Optimization for a Dynamic Model of the Drosophila Circadian Oscillator. - Tanaka Shin; Hiroyuki Kurata; Takeshi Ohashi 001 (SMC, 2006)

Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. - Hiroyuki Kurata; Hana El-Samad; Rei Iwasaki; Hisao Ohtake; John C. Doyle 001; Irina Grigorova; Carol A. Gross; Mustafa Khammash (PLoS Comput. Biol., 2006)

Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. - Hiroyuki Kurata; Quanyu Zhao; Ryuichi Okuda; Kazuyuki Shimizu (BMC Syst. Biol., 2007)

Genetic modification of flux for flux prediction of mutants. - Quanyu Zhao; Hiroyuki Kurata (Bioinform., 2009)

Two-phase Search (TPS) Method: Nonbiased and High-speed Parameter Search for Dynamic Models of Biochemical Networks. - Kazuhiro Maeda; Hiroyuki Kurata (Inf. Media Technol., 2009)

Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System. - Koichi Masaki; Kazuhiro Maeda; Hiroyuki Kurata (Artif. Life, 2012)

CADLIVE optimizer: web-based parameter estimation for dynamic models. - Kentaro Inoue; Kazuhiro Maeda; Yuki Kato; Shinpei Tonami; Shogo Takagi; Hiroyuki Kurata (Source Code Biol. Medicine, 2012)

Multi-Dimensional Shift Multiplexing Technique with Spherical Reference Waves. - Shuhei Yoshida; Takaaki Matsubara; Hiroyuki Kurata; Shuma Horiuchi; Manabu Yamamoto (IEICE Trans. Electron., 2013)

BioFNet: biological functional network database for analysis and synthesis of biological systems. - Hiroyuki Kurata; Kazuhiro Maeda; Toshikazu Onaka; Takenori Takata (Briefings Bioinform., 2014)

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. - Kazuhiro Maeda; Hiroyuki Kurata (BMC Syst. Biol., 2014)

iLMS, Computational Identification of Lysine-Malonylation Sites by Combining Multiple Sequence Features. - Md. Mehedi Hasan 002; Hiroyuki Kurata (BIBE, 2018)

SIPMA: A Systematic Identification of Protein-Protein Interactions in Zea mays Using Autocorrelation Features in a Machine-Learning Framework. - Mst. Shamima Khatun; Md. Mehedi Hasan 002; Md. Nurul Haque Mollah; Hiroyuki Kurata (BIBE, 2018)

Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation. - A. B. M. Shamim Ul Hasan; Hiroyuki Kurata; Sebastian Pechmann (BMC Bioinform., 2019)

iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. - Md. Mehedi Hasan 002; Mst. Shamima Khatun; Hiroyuki Kurata (Genom. Proteom. Bioinform., 2020)

ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations. - Mst. Shamima Khatun; Md. Mehedi Hasan 002; Watshara Shoombuatong; Hiroyuki Kurata (J. Comput. Aided Mol. Des., 2020)

NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning. - Md. Mehedi Hasan 002; Md. Ashad Alam; Watshara Shoombuatong; Hong-Wen Deng; Balachandran Manavalan; Hiroyuki Kurata (Briefings Bioinform., 2021)

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. - Md. Mehedi Hasan 002; Shaherin Basith; Mst. Shamima Khatun; Gwang Lee; Balachandran Manavalan; Hiroyuki Kurata (Briefings Bioinform., 2021)

LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. - Sho Tsukiyama; Md. Mehedi Hasan 002; Satoshi Fujii; Hiroyuki Kurata (Briefings Bioinform., 2021)

IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations. - Md. Mehedi Hasan 002; Md. Ashad Alam; Watshara Shoombuatong; Hiroyuki Kurata (J. Comput. Aided Mol. Des., 2021)

Fabrication and Characterisation of Organic EL Devices in the Presence of Cyclodextrin as an Interlayer. - Michihiro Hara; Takao Umeda; Hiroyuki Kurata (Sensors, 2021)

iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model. - Hiroyuki Kurata; Sho Tsukiyama; Balachandran Manavalan (Briefings Bioinform., 2022)

BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches. - Sho Tsukiyama; Md. Mehedi Hasan 002; Hong-Wen Deng; Hiroyuki Kurata (Briefings Bioinform., 2022)

MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling. - Kazuhiro Maeda; Aoi Hatae; Yukie Sakai; Fred C. Boogerd; Hiroyuki Kurata (BMC Bioinform., 2022)

Stack-DHUpred: Advancing the accuracy of dihydrouridine modification sites detection via stacking approach. - Md. Harun-Or-Roshid; Kazuhiro Maeda; Le Thi Phan; Balachandran Manavalan; Hiroyuki Kurata (Comput. Biol. Medicine, 2024)