Journal Papers

• 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. Environ. Sci. Technol. in press
• 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. Comput. Biol. Med. in press
• Kazuhiro Maeda, Hiroyuki Kurata. Automatic Generation of SBML Kinetic Models from Natural Language Texts using GPT. Int. J. Mol. Sci. 2:72962023, 2023.
• Sho Tsukiyama, Md Mehedi Hasan, Hiroyuki Kurata. CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction. Comput. Struct. Biotechnol. J. 21:644-654, 2023.
• Hiroyuki Kurata. Dynamic models for the whole human metabolic system. Precision Medicine 6:70-74. 2023.
• Kazuhiro Maeda, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, Hiroyuki Kurata. MLAGO: Machine learning-aided global optimization for parameter estimation of kinetic modeling. BMC Bioinformatics 23:455, 2022.
• Hiroyuki Kurata, Sho Tsukiyama. ICAN: interpretable cross-attention network for identifying drug and target protein interactions. PLoS ONE 17: e0276609, 2022. bioRxiv https://doi.org/10.1101/2022.08.04.502877
• Sho Tsukiyama, Hiroyuki Kurata. Cross-attention PHV: Prediction of human and virus protein-protein interactions using cross-attention–based neural networks. Comput. Struct. Biotechnol. J. 20:5564-5573, 2022.
• Hiroyuki Kurata, Sho Tsukiyama, Balachandran Manavalan. iACVP: Markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model Briefings in Bioinformatics https://doi.org/10.1093/bib/bbac265
• Md Mehedi Hasan, Sho Tsukiyama, Hiroyuki Kurata, Xiaowen Liu, Balachandran Manavalan, Hong-Wen Deng. Deepm5C: A deep learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy. Molecular Therapy 30:2856-2867, 2022.
• Yuto Ariji, Tetsuo Hayashi,Ryosuke Ideta, Ryuichiro Koga, Satoshi Murai, Tomoki Naka, Ryusei Ifuku, Fumihiro Towatari, Hiroaki Sakai, Hiroyuki Kurata, Takeshi Maeda. Identification of a reliable sacral sparing examination to assess the ASIA Impairment Scale in patients with traumatic spinal cord injury. J Spinal Cord Med 30:1-7, 2022.
• Sho Tsukiyama, Md Mehedi Hasan, Hong-Wen Deng, Hiroyuki Kurata. BERT6mA: Prediction of DNA N6-Methyladenine site using deep learning-based approaches. Briefings in Bioinformatics 23:1–15, 2022.
• Mst Shamima Khatun, Md Ashad Alam, Watshara Shoombuatong, Md Nurul Haque Mollah, Hiroyuki Kurata, Md Mehedi Hasan. Recent development of bioinformatics tools for microRNA target prediction. Current Medicinal Chemistry 29:865-880, 2022.
• ABM Shamim UL Hasan, Supravat Dey, Hiroyuki Kurata, Abhyudai Singh. Robust in-phase synchronization in repressor-based coupled gene oscillators. IFAC-PapersOnLine 54:574-579, 2021.
• Kazuhiro Maeda, Fred C. Boogerd, Hiroyuki Kurata. A real-coded genetic algorithm software for parameter estimation of kinetic models. IPSJ Transaction on Bioinformatics 4:30-35, 2021.
• Shamim Ul Hasan ABM, Dey S, Kurata H, Singh A. Stochastic comparison of synchronization in activator- and repressor-based coupled gene oscillators. bioRxiv DOI: 10.1101/2021.07.08.451708.
• Md Mehedi Hasan, Md Ashad Alam, Watshara Shoombuatong, Hong-Wen Deng, Balachandran Manavalan, Hiroyuki Kurata. NeuroPred-FRL: An Interpretable Prediction Model for Identifying Neuropeptide using Feature Representation Learning. Briefings in Bioinformatics 22:bbab167, 2021. https://doi.org/10.1093/bib/bbab167
• Sho Tsukiyama, Md. Mehedi Hasan, Satoshi Fujii, Hiroyuki Kurata. LSTM-PHV: Prediction of human-virus protein-protein interactions by LSTM with word2vec. Briefings in Bioinformatics 22:bbab228, 2021. doi: 10.1093/bib/bbab228, bioRxiv, https://doi.org/10.1101/2021.02.26.432975.
• Andi Nur Nilamyani, Firda Nurul Auliah, Mohammad Ali Moni, Watshara Shoombuatong, Md Mehedi Hasan, Hiroyuki Kurata. PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites Using Integrating Multiple Sequence Features. Int. J. Mol. Sci. 22:2704, 2021.
• Firda Nurul Auliah, Andi Nur Nilamyani, Watshara Shoombuatong, Md Ashad Alam, Md. Mehedi Hasan, Hiroyuki Kurata. PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations. Int. J. Mol. Sci. 22:2120, 2021.
• Hiroyuki Kurata. Virtual metabolic human dynamic model for pathological analysis and therapy design for diabetes. iScience, 24:102101, 2021. bioRxiv 2020/269399
• Md. Mehedi Hasan, Watshara Shoombuatong, Hiroyuki Kurata, Balachandran Manavalan. Critical evaluation of web-based DNA N6-methyladenine site prediction tools. Briefings in Functional Genomics 20:258–272, 2021.
• Md. Mehedi Hasan, Mst. Shamima Khatun, Watshara Shoombuatong, Hiroyuki Kurata. IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations. J. Comput. Aided Mol. Des. 35:315-323, 2021.
• Md. Mehedi Hasan, Shaherin Basith, Mst. Shamima Khatun, Gwang Lee, Balachandran Manavalan, Hiroyuki Kurata. Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. Briefings in Bioinformatics 22:bbaa202, 2021. DOI:10.1093/bib/bbaa202
• Mst. Shamima Khatun, Md. Mehedi Hasan, Watshara Shoombuatong, Hiroyuki Kurata. ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations. J. Comput. Aided Mol. Des. 34: 1229–1236, 2020.
• Md. Mamunur Rashid, Hiroyuki Kurata. Coupling protocol of interlocked feedback oscillators in circadian clocks. Journal of the Royal Society Interface 17: 20200287, 2020.
• Hiroyuki Kurata. Kinetic models for the whole human metabolic system. The CELL (Japanese) 52:376-379, 2020.
• Mst. Shamima Khatuna, Watshara Shoombuatong, Md. Mehedi Hasan, Hiroyuki Kurata. Evolution of sequence-based bioinformatics tools for protein-protein interaction prediction. Current Genomics 21: 454-463, 2020.
• Yuto Ariji, Tesuo Hayashi, Ryuichiro Koga, Satoshi Murai, Fumihiro Towatari, Hiroaki Sakai, Hiroyuki Kurata, Takeshi Maeda. 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. Spinal Cord 58: 1158–1165, 2020.
• Md. Mamunur Rashid, Swakkhar Shatabda, Md. Mehedi Hasan, Hiroyuki Kurata. Recent development of machine learning methods in microbial phosphorylation sites. Current Genomics 21:194-203, 2020.
• Md. Mehedi Hasan, Balachandran Manavalan, Watshara Shoombuatong, Hiroyuki Kurata. i4mC-Mouse: improved identification of N4-methylcytosine sites in the mouse genome using multiple encoding schemes. Comput. Struct. Biotechnol. J. 18:906-912, 2020.
• Yu Matsuoka, Hiroyuki Kurata. Computer-aided rational design of efficient NADPH production system by Escherichia coli pgi mutant using a mixture of glucose and xylose. Front. Bioeng. Biotech. 8:277, 2020.
• Md. Mehedi Hasan, Balachandran Manavalan, Watshara Shoombuatong, Mst. Shamima Khatun, Hiroyuki Kurata. i6mA-Fuse: improved and robust prediction of DNA 6mA sites in the Rosaceae genome by fusing multiple feature representation. Plant Mol. Biol. 103: 225–234, 2020.
• Md. Mehedi Hasan, Balachandran Manavalan, Mst Shamima Khatun, Hiroyuki Kurata. i4mC-ROSE, A Bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome. Int. J. Biol. Macromol. 157:752-758, 2020.
• Hiroyuki Kurata. Self-replenishment cycles generate a threshold response. Sci. Rep. 9:17139, 2019.
• Md. Mehedi Hasan, Balachandran Manavalan, Mst. Shamima Khatuna, Hiroyuki Kurata. Prediction of S-nitrosylation Sites by Integrating Support Vector Machine and Random Forest. Mol. Omics 15:451, 2019.
• Mst. Shamima Khatun, Md. Mehedi Hasan, Hiroyuki Kurata. iAntiTB: Efficient computational model for identification of anti-tubercular peptides by integrating of the amino acid patterns and properties. FEBS Lett. 593:3029-3039, 2019.
• ABMSU Hasan, H. Kurata, S Pechmann. Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation. BMC Bioinformatics 20:734, 2019.
• Md. Mehedi Hasan, Md. Mamunur Rashid, Mst. Shamima Khatun, Hiroyuki Kurata. Computational identification of microbial phosphorylation sites by the enhanced characteristics of sequence information. Sci. Rep. 9:8258, 2019.
• Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata. iLBE, A Bioinformatics Tool for the Identification of Linear B-Cell Epitopes by Integrating Sequence and Evolutionary Features. Genomics Proteomics Bioinformatics 18:593-600, 2020.
• Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, 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 Application 5:14, 2019.
• Mst. Shamima Khatun, Md. Mehedi Hasan, Hiroyuki Kurata. PreAIP: Prediction of anti-inflammatory peptides by integrating multiple complementary features. Front. Genet. 10:129, 2019.
• Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata. Large-scale assessment of bioinformatics tools for lysine succinylation sites. Cells 8(2):95, 2019.
• Md Shamsuddin Khan, Christopher I Cazzonelli, Hiroyuki Kurata, Chun Guang Li, Md Bahadur Badsha, Gerald Muench, Amin M Majid. Advancing herbal medicine through metabolic pathway analysis in plants and animals for routine pharmacological assessments. Advances in Integrative Medicine S106, 2019.
• Md Shamsuddin Khan, Christopher I Cazzonelli, Hiroyuki Kurata, Md Bahadar Badsha, Chun Guang Li, Gerald Muench, Amin Malik Majid. Metabolic similarity of plant and human: implications for efficacy and regulatory compliance of herbal therapies. Australian Herbal Insight 028-037, 2019.
• Kazuhiro Maeda, Fred C. Boogerd, Hiroyuki Kurata. libRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models. IPSJ Transaction on Bioinformatics 11:31-40, 2018.
• Md. Mehedi Hasan, Hiroyuki Kurata. GPSuc: Global prediction of generic and species-specific succinylation sites by aggregating multiple sequence features. PLoS ONE 13:e0200283, 2018
• Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata. A comprehensive review of in silico analysis for protein S-sulfenylation sites. Protein Peptide Lett. 25:815-821, 2018.
• Kazuhiro Maeda, Hiroyuki Kurata. Long negative feedback loop enhances period tunability of biological oscillators. J. Theor. Biol. 440:21–31, 2018.
• Hiroyuki Kurata, Yurie Sugimoto. Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures. J. Biosci. Bioeng. 125:251-257, 2018.
• Yohei Kamijo, Kohichi Kawahara, Takuma Yoshinaga, Hiroyuki Kurata, Kazunari Arima, Tatsuhiko Furukawa. A novel isolation method for cancer prognostic factors via the p53 pathway by a combination of in vitro and in silico analyses. Oncoscience 5:88-98, 2018.
• Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata. Computational modeling of lysine post-translational modification: an overview. Curr. Synthetic Sys. Biol. 6:1, 2018.
• Md. Mehedi Hasan, Guo Dianjing, Hiroyuki Kurata. Computational identification of protein S-sulfenylation sites by incorporating the multiple sequence features information. Mol. Biosyst. 13:2545-2550, 2017.
• Yu Matsuoka, Hiroyuki Kurata. Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations. Biotechnol. Biofuels 10:183, 2017.
• A B M Shamim Ul Hasan, Hiroyuki Kurata. Mathematical comparison of memory functions between mutual activation and repression networks in a stochastic environment. J. Theor. Biol. 427:28–40, 2017.
• Hiroyuki Masunaga, Yurie Sugimoto, Shigeyuki Magi, Ryunosuke Itasaki, Mariko Okada-Hatakeyama, Hiroyuki Kurata. Robustness analysis of the detailed kinetic model of an ErbB signaling network by using dynamic sensitivity. PLoS ONE 12(5): e0178250, 2017.
• Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata. Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli. Microb. Cell Fact. 15:112, 2016.
• Yu Matsuoka, Nusrat Jahan, Hiroyuki Kurata. S-system-based Analysis of the Robust Properties Common to Many Biochemical Network Models. Bioproc. Biosyst. Eng. 39:735–746, 2016.
• Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka,Takushi Oga,Takeshi Omasa. Metabolic analysis of antibody producing Chinese hamster ovary cell culture under different stresses conditions. J. Biosci. Bioeng. 122:117-24, 2016.
• Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kazuhiro Maeda, Hiroyuki Kurata. Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants. J. Biosci. Bioeng. 122:111–116, 2016.
• Senna Sakai, Hiroto Izumi, Yukiko Yoshiura, Yoshifumi Nakayama,Takahiro Yamaguchi, Yoshikazu Harada, Chiho Koi, Hiroyuki Kurata, Yasuo Morimoto. In vitro evaluation of a combination treatment involving anticancer agents and an aurora kinase B inhibitor. Oncology Letters 12: 4263-4269, 2016.
• Kazuhiro Maeda, Hiroyuki Kurata, Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. BMC Syst. Biol., 8 (Suppl 5): S1, 2014.
• Md. Bahadur Badsha, Ryo Tsuboi, Hiroyuki Kurata, Complementary elementary modes for fast and efficient analysis of metabolic networks. Biochem. Eng. J., 90:121–130, 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. Bioproc. Biosyst. Eng., 37:1925–1927, 2014.
• Hiroyuki Kurata, Kazuhiro Maeda, Yu Matsuoka, Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes. J. Chem. Eng. Japan, 90:121–130, 2014.
• Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata, BioFNet: Biological functional network database for analysis and synthesis of biological systems. Briefings in Bioinformatics, 15:699-709, 2014.
• Ruilian Yao, Hiroyuki Kurata, Kazuyuki Shimizu, Effect of cra gene mutation on the metabolism of Escherichia coli for a mixture of multiple carbon sources. Advances in Bioscience and Biotechnology, 4:477-486, 2013.
• Md. Bahadur Badsha, Md. Nurul Haque Mollah, Nusrat Jahan, Hiroyuki Kurata, Robust Complementary Hierarchical Clustering for Gene Expression Data Analysis by β-Divergence. J. Biosci. Bioeng., 116:397-407, 2013.
• Kazuhiro Maeda, Keisuke Yoshida, Hiroyuki Kurata, Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks.  Bioproc. Biosyst. Eng., 36:333–344, 2013.
• Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi, Hiroyuki Kurata, CADLIVE Optimizer: Web-based Parameter Estimation for Dynamic Models, Source Code for Biology and Medicine, 7:9, 2012.
• Kentaro Inoue, Shinichi Shimozono, Hideaki Yoshida, Hiroyuki Kurata, Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps. PLoS ONE, 7: e37739, 2012.
• Kazuhiro Maeda, Hiroyuki Kurata, A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator. PLoS ONE, 7: e30489, 2012.
• Koichi Masaki, Kazuhiro Maeda, Hiroyuki Kurata, Biological design principles of complex feedback modules in the E. coli ammonia assimilation system. Artificial Life, 18:53-90, 2012.
• Kentaro Inoue, Sayaka Tomeda, Shinpei Tonami, Yuki Shimokawa, Masayo Ono, Hiroyuki Kurata, CADLIVE Converter for constructing a biochemical network map. Biochem. Eng. J., 54:200–206, 2011.
• Kazuhiro Maeda, Yuya Fukano, Shunsuke Yamamichi, Daichi Nitta, Hiroyuki Kurata, An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks. Bioproc. Biosyst. Eng., 34:433–446, 2011
• Kazuhiro Maeda, Hiroyuki Kurata, Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks. J. Theor. Biol., 272:174–186, 2011.
• Kentaro Inoue, Weijiang Li and Hiroyuki Kurata, Diffusion Model Based Spectral Clustering For Protein-Protein Interaction Networks. PLoS ONE, 5:e12623, 2010.
• Quanyu Zhao, Hiroyuki Kurata, Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis. J. Biosci. Bioeng., 110:254-261, 2010.
• Quanyu Zhao, Hiroyuki Kurata, Genetic modification of flux for flux prediction of mutants. Bioinformatics, 25: 1702-1708, 2009
• Kazuhiro Maeda, Hiroyuki Kurata, Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks. IPSJ Transaction on Bioinformatics, 2:2-14, 2009
• Quanyu Zhao, Hiroyuki Kurata, Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng., 107: 84–89, 2009
• Emi Shiraishi, Kazuhiro Maeda Hiroyuki Kurata, A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits. Bioproc. Biosyst. Eng., 32:283–288, 2009.
• Li W., Kurata H., Visualizing Global Properties of Large Complex Networks. PLoS ONE, 3: e2541, 2008.
• Quanyu Zhao, Hiroyuki Kurata, Estimation of Intracellular Flux Distribution under Underdetermined and Uncertain Conditions by Maximum Entropy Principle. Chin. J. Biotech., 24:2135−2136 2008.
• Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata, Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol. Syst. Biol., 4:160, 2008.
• H. Kurata, T. Tanaka, and F. Ohnishi, Mathematical identification of critical reactions in the interlocked feedback model. PLoS ONE, 2(10): e1103, 2007.
• Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao, Extended CADLIVE: a novel graphical notation for designing a biochemical network map that enables computational pathway analysis. Nucleic Acids Res. 35(20):e134, 2007.
• Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda and Kazuyuki Shimizu, Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst. Biol., 1:31, 2007.
• Kouichi Masaki, Hiroyuki Kurata, A simple model of positive feedback of the nitrogen assimilation system in E. coli. IPSJ Transactions on Mathematical Modeling and Its Applications, 48:104-109, 2007.
• H. Kurata*, H. El Samad*, R. Iwasaki, H. Othake, J.C. Doyle, I. Grigorova, C. Gross, and M. Khammash, Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. PLoS Comp. Biol., 2: e59, 2006　*Both contributed equally.
• Hiroyuki Kurata, Kouichi Masaki, Yoshiyuki Sumida, Rei Iwasaki, CADLIVE Dynamic Simulator: Direct Link of Biochemical Networks to Dynamic Models. Genome Res., 15: 590-600, 2005.
• H. El-Samad*, H. Kurata*, J.C. Doyle, C. A. Gross, M. Khammash, Surviving heat shock: Control strategy for robustness and performance. Proc. Natl. Acad. Sci. U S A, 102:2736-41, 2005. *Both contributed equally.
• Weijiang Li and Hiroyuki Kurata, A Grid Layout Algorithm for Automatic Drawing of Biochemical Networks. Bioinformatics, 21: 2036-2042, 2005.
• Hiroyuki Kurata, Natsumi Shimizu, Kanako Misumi, Statistical And Integrative Approach For Constructing Biological Network Maps. Genome Informatics, 15:161-170, 2004.
• Hiroyuki Kurata, Nana Matoba, Natsumi Shimizu, CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res., 31: 4071-4084, 2003.
• Akashi, H. Kurata, H., Seki, M., Taira, K., Furusaki, S. Screening for transgenic plant cells that highly express a target gene from genetically mixed cells. Biochem. Eng. J., 10:175-182, 2002.
• Akashi H, Miyagishi M, Kurata H, Nagata T, Taira K. A simple and rapid system for the quantitation of RNA interference in plant cultured cells. Nucleic Acids Res. Suppl., (1):235-6, 2001.
• Kurata, H. Mochizuki, A., Okuda, N., Seki, M., Furusaki,S. Intermittent light irradiation with second- or hour- scale periods controls anthocyanin production by strawberry cells. Enzyme Microb. Technol. 26: 621-629, 2000.
• Nara, Y., Kurata, H. Seki, M, Taira, K. Grucocorticoid-induced expression of a foreign gene by the GVG system in transformed tobacco BY-2. Biochem. Eng. J., 6: 185-191, 2000.
• Kurata, H. and Taira, K. Two-phase partition method for simulating a biological system at an extremely high speed. Genome Informatics, 11: 185-195, 2000.
• Kurata, H., Kaizuka, Y., Seki, M., Furusaki, S. Mathematical model analyzes light-controlled expression of the CHS promoter in BY-2 cells. Biochem. Eng. J., 4: 65-72, 1999.
• Ohtake, H., Tsuji, T. and Kurata, H. Software of living systems. Kagaku Kougaku Ronbunshu, 25:169-176, 1999.
• Kurata, H., Furusaki, S., Kado, C. I. Light-enhanced target gene expression in tobacco BY-2 by the combination of overexpressed phytochrome and therbcS3A promoter. Biotechnol. Lett,, 20: 463-468, 1998.
• Kurata, H., Takemura, T., Furusaki, S., Kado, C. I. Light-controlled expression of a foreign gene using the chalcone synthase promoter in tobacco BY-2 cells. J. Ferment. Biotechnol., 86: 317-323, 1998.
• Kurata, H., Achioku, T., Furusaki, S. The light/dark cycle operation with an hour-scale period enhances caffeine production by Coffea arabica cells. Enzyme Microb. Technol., 23: 518-523, 1998.
• Kurata, H., Achioku, K., Okuda, N., Furusaki, S. The intermittent light irradiation with a second-scale interval enhances caffeine production by C. arabica cells. Biotechnol.Prog.,14: 797-799, 1998.
• Kurata, H., Matsumura, S., Furusaki, S. Light irradiation causes physiological and metabolic changes for purine alkaloid production by Coffea arabica cells. Plant Sci., 123: 197-203, 1997.
• Kurata, H., Kawai, A., Seki, M., Furusaki, S. Increased Alkaloid Production in a Suspension Culture of Coffea arabica Cells Using Adosorption Column for Product Removal. J. Ferment. Bioeng. 78: 117-119, 1994.
• Kurata, H., Seki, M., Furusaki, S. Light Effect to Promote Secondary Metabolite Production of Plant Cell Culture. Advances in Plant Biotechnology, D.D.Y. Ryuand S. Furusaki (eds.), Elsevier (Amsterdam). 103-133, 1994.
• Furusaki, S., Seki, M., Kurata, H., Furuya, T. The effect of light irradiation on secondary metabolic production by Coffea arabica cells, T. Yoshida &Tanner (Eds.). Springer-Verlag.  271-282, 1993.
• Kurata, H., Furusaki, S. Nonisotropic scattering model for estimation of light absorption rates in suspension culture of Coffea arabica cells. Biotechnol. Prog. 9: 86-92, 1993.
• Kurata, H., Furusaki, S. Immobilized Coffea arabica Cell Culture Using a Bubble-Column Reactor with Controlled Light Intensity. Biotechnol. Bioeng. 42: 494-502, 1993.
• Kurata, H., Seki, M., Furusaki, S., Furuya, T. Influence of light irradiation rates and irradiation modes on caffeine production and cell growth in suspension culture of Coffea arabica cells. J. Chem. Eng. Japan 24: 783-788, 1991.
• Kurata, H., Seki, M., Furusaki, S., Furuya, T. Effect of light on caffeine production by plant cells of Coffea arabica. Ann. N. Y. Acad. Sci. 613: 538-541, 1990.
• Nakao, S., Osada, H., Kurata, H., Tsuru, M., Kimura, S. Separation of proteins by charged ultrafiltration membranes. Desalination, 70: 191-205, 1988.

Proceedings

• Md. Mehedi Hasan, Hiroyuki Kurata, Identification of redox-sensitive cysteines using sequence profile information. Proceedings of the 10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2020), Kyoto, Japan, 2020
• Mst. Shamima Khatun, Md. Mehedi Hasan, Md. Nurul Haque Mollah, Hiroyuki Kurata, SIPMA: a systematic identification of protein–protein interactions in Zea mays using autocorrelation features in a machine-learning framework. The 18th IEEE International Conference on BioInformatics and BioEngineering, 122-125,Taichung, Taiwan, Oct 29-31, 2018.
• Md. Mehedi Hasan, Hiroyuki Kurata, iLMS, computational identification of lysine-malonylation sites by combining multiple sequence features. The 18th IEEE International Conference on BioInformatics and BioEngineering, 356-359, Taichung, Taiwan, Oct 29-31, 2018.
• Hiroyuki Kurata, Virtual cell metabolism for systems and synthetic biology. Proceedings of International Conference on Bioinformatics and Biostatistics for Agriculture, Health and Environment Rajshahi, Bangladesh, 20-23 January, 2017.
• A B M Shamim Ul Hasan,Hiroyuki Kurata, Gene expression noise can induce stochastic bimodality, even multimodality in deterministically monostable description with non-cooperative binding. Proceedings of International Conference on Bioinformatics and Biostatistics for Agriculture, Health and Environment Rajshahi, Bangladesh, 20-23 January, 2017.
• A B M Shamim Ul Hasan,Hiroyuki Kurata, Robustness of Memory Functions between Competitive Gene Regulatory Networks. Proceedings of Asian Congress on Biotechnology 2015 (SAES2016), 21, Kitakyushu, 17–18 Dec 2016.
• Yu Matsuoka, Hiroyuki Kurata, Modeling of the redox regulation in response to the change in the oxygen level for Escherichia coli. Proceedings of Asian Congress on Biotechnology 2015 (SAES2016) , 7, Kitakyushu, 17–18 Dec 2016.
• Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata, A detailed kinetic model of E. coli central metabolism in a batch culture. Proceedings of the 4th International Symposium on Applied Engineering and Sciences(ACB2015) , Kuala Lumpur, Malaysia, Nov. 15-19, 2015.
• Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa, Effect of NaCl and Trehalose Condition on Antibody Producing CHO Cell Culture. Proceedings of Asian Congress on Biotechnology 2015 (ACB2015) , Kuala Lumpur, Malaysia, Nov. 15-19, 2015.
• Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata, Developing a kinetic model of the E. coli ammonium assimilation network. Proceedings of the 16th International Conference on Systems Biology, Singapore, Nov. 23-26, 2015.
• Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata, Toward a quantitative in silico model for the E. coli ammonium assimilation system. Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human, 25, Iizuka, March 5-6, 2015.
• Kazuhiro Maeda, Hiroyuki Kurata, Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. Proceedings of GIW/ISCB-Asia 2014, Tokyo, Japan, December 15-17, 2014.
• Md Bahadur Badsha, Hiroyuki Kurata, Integration of omics into metabolic flux distribution by complementary elementary mode analysis for large-scale metabolic networks. Proceedings of 3rd International Conference and Exhibition on Metabolomics & Systems Biology, San Antonio, USA, March 24-26, 2014.
• Hiroyuki Kurata, Aim and scope of the BMIRC at Kyutech. Proceedings of the Second BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering , 8, Iizuka, Feb 19-20, 2014.
• Hiroyuki Kurata, Bioalgorithms for rational design of biological systems, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering , 25, Iizuka, February 28, 2013
• Md. Bahadur Badsha, Nusrat Jahan, Md. Nurul Haque Mollah, Hiroyuki Kurata, Metabolic Engineering for Systematic Organization and Analysis of Complex Metabolic Networks, Proceedings of the International Conference on Statistical Data Mining for Bioinformatics Health Agriculture and Environment, 22-24, University of Rajshahi, Bangladesh, December 2012
• Md. Bahadur Badsha, Nusrat Jahan, Md. Nurul Haque Mollah, Hiroyuki Kurata, Sequential Extraction of Several Gene-sets with Proper Groups of Individuals for Gene Expression Data Analysis, Proceedings of the International Conference on Statistical Data Mining for Bioinformatics Health Agriculture and Environment, University of Rajshahi, Bangladesh, 22-24 December 2012.
• Hiroyuki Kurata, Soma Tabata, Quanyu Zhao, Computational framework for integration of metabolic flux analysis with its associated omics data. Proceedings of the14th International Biotechnology Symposium and Exhibition (IBS2012), Deagu, Korea, September 18, 2012.
• Hiroyuki Kurata, Soma Tabata, Quanyu Zhao, Computational framework for integration of metabolic flux analysis with its associated omics data. Proceedings of the 8th Asia-Pacific Conference on Algal Biotechnology and 1st International Conference on Coastal Biotechnology, 55, Adelaide, Australia, July 9, 2012
• Hiroyuki Kurata, Quanyu Zhao,　Maximum entropy principle optimizes the large-scale elementary modes for a broad raqgne of genetic mutants. Asian Congress on Biotechnology, Shanghai, May 11-15, 2011.
• Quanyu Zhao, Hiroyuki Kurata, Elementary model-based prediction of the flux distribution for a variety of genetic mutants. Proceedings of APBioCHEC’2009, (J Biosci Bioeng, 108:S165, 2009) Kobe, November 24-28, 2009.
• Hiroyuki Kurata, Module-based analysis of the robustness generated by complex feedback regulations in biological networks. ICROS-SICE International Joint Conference 2009, Fukuoka International Congress Center, Fukuoka, JAPAN, August 18-21, 2009
• Kentaro Inoue, Tetsuya Shimabara, Toshikazu Onaka, Erika Fujiura, Hiroyuki Kurata, Extended CADLIVE: Computer-aided rational design of living systems.The proceedings of the 2008th annual conference of the Japanese Society for Bioinformatics, Osaka, S02-1-2, 2008
• Kazuhiro Maeda, Hiroyuki Kurata, Searching multiple sets of kinetic parameters values reproducing target experimental data in dynamic biochemical models.The proceedings of the 2008th annual conference of the Japanese Society for Bioinformatics, Osaka, S063-1-2, December 15-16, 2008
• Hiroyuki Kurata, CADLIVE: Computer aided design of biochemical systems. Supplement of Journal of Biotechnology: 13 th International Biotechnology Symposium and Exhibition (IBS2008), Dailen, China, October 12-17, 2008
• Quanyu Zhao, Hiroyuki Kurata, Prediction of flux distribution of mutants by enzyme control fluxes with maximum entropy principal. Supplement of Journal of Biotechnology: 13 th International Biotechnology Symposium and Exhibition (IBS2008), Dailen, China, October 12-17, 2008
• Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata, Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Supplement of Journal of Biotechnology:13 th International Biotechnology Symposium and Exhibition (IBS2008), Dailen, China, October 12-17, 2008
• Kazuhiro Maeda, Hiroyuki Kurata, CADLIVE for Construction and Dynamic Simulation of Biochemical Networks, Proceedings of Asia Pacific Biochemical Engineering Conference, J0013, 4 pages, Taipei, Taiwan, November 4-7, 2007
• Koichi Masaki, Hiroyuki Kurata, Systems Biology of the Nitrogen Assimilation System in E.coli. Proceedings of Asia Pacific Biochemical Engineering Conference, J0108, 4 pages, Taipei, Taiwan, November 4-7, 2007
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator, IEEE InternationalConference on Systems, Man, and Cybernetics, 3596-3601, October 8-11, 2006 Taipei, Taiwan.
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Reverse Engineering for a Dynamic Model of the Drosophila Circadian Oscillator. International Conference on Computational Intelligence for Modelling, Control and Automation, 1:625-631 Vienna, Austria. November, 28-30, 2005.
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli,Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, 2078-2083, Big Island, Hawaii, October 10-12, 2005.
• Yamamichi, S., Kurata, H., A large-scale dynamic simulation of the cell cycle network Proceedings of 7th Asia-Pacific Biochemical Engineering Conference,Jeju Island, Korea, SYS2-05 (4 pages), May 10-15, 2005.
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Optimization of E.coli Heat Shock Response Parameter Tuning Using Distributed and Integrated Genetic Algorithms, Proceedings of the IEEE International Conference on Systems, Man and Cybernetics, 1243-1248, The Hague, The Netherlands, October 10-13, 2004.
• Hiroyuki Kurata, Computer-Aided Design of Metabolic and Gene Regulatory Networks, Proceedings of The 10th APCChE Congress, 2L-06, 8 pages, October 17-21, Kitakyushu, October 19, 2004.
• Hiroyuki Kurata, Map-based analysis for the budding yeast cell cycle network:  Integration of heterogeneous knowledge and data into CADLIVE, Proceedings of The First International Symposium on Systems Biology of Yeast. 23-28, St. Louis, USA. November 9, 2003.
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Dominant direction priority searching method for real-coded genetic algorithm. Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications PDPTA'03, 1113-1119, Las Vegas, Nevada, USA. June 23, 2003.
• El-Samad, M. Khammash, Kurata, H., H. T.-M. Yi, J. C. Doyle, Robustness Analysis of the heat shock response in E. coli. Proceedings of the American Control Conference, Anchorage, AK, pp. 1742-1747. 2002.
• Kurata, H., H. El-Samad, T.-M. Yi, M. Khammash, J. C. Doyle, Feedback regulation of the heat shock response in E. coli. Proceedings of the 40th IEEE Conference on Decision and Control.　837-842, 2001.
• Kurata, H. and Taira, K, Complexity in Regulation Generates Robustness in Bacterial Molecular Networks, Proceedings of the First International Conference on Systems Biology, Tokyo, 167-172, 2000.
• Kurata, H. Kaizuka, Y. Furusaki, S.  Mathematical model of light-enhanced expression of the CHS promoter in tobacco BY-2. 7-th International Conference on Computer Applications in Biotechnology -CAB7-, Osaka, 511-515, 1998.
• Kurata, H., Takemura, T., Furusaki, S., Kado, C. I., Light-controlled expression of the chalcone synthase promoter in tobacco BY-2 cells. Proceedings of 4th Asia-Pacific Biochemical Engineering Conference, Beijing, 1: 97-102, 1997.
• Furusaki, S., Seki, M., Kurata, H. Development of a Photobioreactor for Coffea arabica Cells. Proceedings of 4th Pacific-Rim Biotechnol. Conf., Melbourne, 143-144, 1995.
• Furusaki, S., Kurata, H.  Light effect on alkaloid production and growth of immobilized Coffea arabica cells. Proc. Seminar on Biochem. Eng., Taipei, 45-48. 1993.

Technical Reports

• Shinichi Shimozono, Kentaro Inoue, Hiroyuki Kurata, Efficient Grid Graph Layout by Approximate Point-set Matching on the Plane, IPSJ SIG Technical Report, 2012-BIO-30 No. 1, 1-3. Iizuka, August 9, 2012. (Oral presentation)
• 前田和勲，倉田博之，大腸菌アンモニア同化システムのダイナミックモデルの構築，情報処理学会研究報告，2012-BIO-30 No. 5, 1-6. 飯塚，8月9日，2012. (Oral presentation)
• Noorlin Mohd Ali, Kentaro Inoue, Soma Tabata, Hiroyuki Kurata, The effect of implementing objective functions in analyzing the changes of enzyme activity profiles. IPSJ SIG Technical Report, 2012-BIO-30 No. 8, 1-2. Iizuka, August 9 2012.(Oral presentation)
• Kazuhiro Maeda, Hiroyuki Kurata, Robustness Analysis of Feedback Systems of Circadian Rhythm, IPSJ SIG Technical Report, 2011-BIO-24 No.7, 1-6, Kyoto, March 10-11, 2011. (Oral presentation)
• Kentaro Inoue, Shinichi Shimozono, Hideaki Yoshida and Hiroyuki Kurata, Hybrid Layout Algorithm using Approximate Pattern Matching in Two Dimensional Space for Biochemical Network Layout, IPSJ SIG Technical Report, 2011-BIO-24 No.6, 1-6, Kyoto, March 10-11, 2011 (Oral presentation)
• Kazuhiro Maeda and Hiroyuki Kurata, Robustness Analysis of Feedback Systems of Circadian Rhythm, IPSJ SIG Technical Report, 2011-BIO-24 No.7, 1-6, Kyoto, March 10-11, 2011 (Oral presentation)
• Kazuhiro Maeday and Hiroyuki Kurata, Robustness Analysis of Interlocked Feedbacks of Circadian Rhythm, IPSJ SIG Technical Report, 2009-BIO-17 No15, 1-5, Okinawa, 2009. (Oral presentation)
• Kentaro Inoue, Weijiang Li, and Hiroyuki Kurata, Modular decomposition based spectrum for protein-protein interaction network, IPSJ SIG Technical Report, 2009-BIO-17 No14, 1-4,  Okinawa, 2009 (Oral presentation)
• 前田和勲，吉田圭介，倉田博之，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，情報処理学会研究報告　数理モデル化と問題解決，MPS-66, 91-94, 2007. (口答発表)
• Maeda, K., Yoshida, K., Kurata, H., Global optimization of large-scale dynamic biomolecular network model, ISPJ SIG Technical Reports, MPS-66, 91-94, 2007. (Oral presentation)
• 中野克俊，岩崎麗，倉田博之，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，情報処理学会研究報告　数理モデル化と問題解決，MPS-66, 95-98, 2007. (口答発表)
• Nakano, K., Iwasaki, R., Kurata, H., A stochastic simulation of diffusion reaction model in embryo development, ISPJ SIG Technical Reports, MPS-66, 95-98, 2007. (Oral presentation)
• 真崎浩一，倉田博之，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シンプルモデル，数理モデル化と問題解決研究報告, 2006-MPS-59, 61-64. 2006. (口答発表)
• Masaki, Kouichi, Kurata Hiroyuki, A simple model of positive feedback of the nitrogen assimilation system in E. coli, ISPJ SIG Technical Reports, 61-64, 2006.(Oral presentation)
• 吉田圭介，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ISPJ Symposium Series, 数理モデル化と問題解決シンポジウム論文集， 97-102, 2004 10月26日　名古屋大学　(口答発表)
• Keisuke Yoshida, Hiroyuki Kurata, Decomposition and Integration of Functional Modules Optimizes a Dynamic Model of Large-Scale Biochemical Networks,ISPJ Symposium Series, 12, 97-102, 2004.
• 山道俊介，大西史高，倉田博之，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　ISPJ Symposium Series, 数理モデル化と問題解決シンポジウム論文集, 名古屋大学12:379-382, 10月27日 2004.　(ポスタ発表)
• Keisuke Yamamichi, Fumitaka Ohnishi, Hiroyuki Kurata, Modeling and system analysis of oscillatory systems in a biological system, ISPJ Symposium Series, 12:379-382, 2004.
• 田中信，倉田博之，大橋健，優勢方向優先探索法を追加した実数値遺伝的アルゴリズムの最適化性能検証, 情報処理学会研究報告 (IPSJ SIG Technical Report)（口答発表)
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Verification of the optimization performance of Real-Coded Genetic Algorithm with Dominant Direction Priority Searching Method. 2003-MPS-47 49-52, 2003.
• 田中信，倉田博之，大橋健，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(IPSJ SIG Technical Report), MPS-45, 9-12, Las Vegas, Nevada, USA, 2003年6月24日(口答発表)
• Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi, Dominant direction priority searching method for real-coded genetic algorithm. 2003-MPS-45 9-12, 2003.
• Kurata, H.　Taira, K. Evolution of Ammonia Assimilation System in E. coli. Technical Report of IEICE, AI2000-12, 17-24, 2000. (口答発表)
• Kurata, H. Complexity generates robustness and high performance in E. coli heat shock response. Technical Report of IEICE, AI99-5, 33-38, 1999. (口答発表)
• Furusaki, S., Kurata, H., Seki, M. Design of Photo-Bioreactor for Producing Useful Secondary Metabolites Using Plant Cells. Rep. Asahi Glass Found. 60: 263-270, 1992.

Reviews and Commentaries

• 倉田博之，情報システム理論の代謝ネットワークへの応用　～ 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紹介 ～，電子情報通信学会情報理論研究報告，112:19-22, ISSN 0913-5685 飯塚，5月25日，2012.
• 倉田博之, コンピュータ支援による生物回路の合理的設計, ソフトウエアバイオロジー, 9:13-17, 2010.
• Quanyu Zhao,　Hiroyuki Kurata, Prediction of Metabolic Fluxes of Klebsiella pneumoniae by Enzyme Control Flux, ソフトウエアバイオロジー,  9:28-31, 2010.
• 井上健太郎，倉田博之, スペクトルクラスタリングによるタンパク質相互作用ネットワークの機能モジュール分解, ソフトウエアバイオロジー, 9:37-41, 2010.
• 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, ソフトウエアバイオロジー, 9:42-45, 2010.   
• 新田大地，倉田博之, 大規模ダイナミックモデルの最適化手法の開発と癌研究への応用, ソフトウエアバイオロジー,  9:46-51, 2010.
• 留田紗彌可，倉田博之, 生命分子ネットワーク統合システムの開発, ソフトウエアバイオロジー,  9:52-55, 2010.
• 新田大地，深野祐哉，山道俊介，倉田博之，出芽酵母の細胞周期モデルの構築と最適化法の考案, ソフトウエアバイオロジー, 9: 21-27, 2009.
• Quanyu Zhao, Hiroyuki Kurata, Integration of enzyme activities into elementary modes for predicting a metabolic flux profile. Software Biology, 7:30-38, 2008
• 真崎浩一,　倉田博之,　大腸菌窒素同化システムポジティブフィードバックの理論解析. ソフトウエアバイオロジー, 6:28-33, 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. ソフトウエアバイオロジー, 6:34-49, 2007
• 白石絵美, 倉田博之, 定常状態近似によるstiffな微分方程式のシミュレーション. ソフトウエアバイオロジー, 6:40-44, 2007
• 井上健太郎, 下川由紀, 倉田博之, 大規模生命分子ネットワークのトポロジカル解析. ソフトウエアバイオロジー, 6:45-49, 2007
• 深野祐哉, 倉田博之, モジュール分割統合法による大規模な細胞周期ネットワークの最適化. ソフトウエアバイオロジー, 6:50-55, 2007
• 田中孝幸, 梶原万梨恵, 岡野隆也, 倉田博之, 概日リズムの数学モデリング及びロバスト解析を行うための方法論開発. ソフトウエアバイオロジー, 6:56-66, 2007
• 倉田博之, CADLIVE:生物機能設計支援システム, バイオサイエンスとバイオインダストリー, 64: 508-511, 2006.
• 倉田博之　システムバイオロジーの現状と未来　生物物理　46:244-250, 2006.
• 倉田博之　有用物質生産のための細胞設計工学　ケミカルエンジニヤリング, 50:907-912, 2005.
• 真崎浩一, 倉田博之　有用物質生産のための細胞設計工学, In:ソフトウエアバイオロジー,　43-47, 化学工学会バイオ部会生物情報分野専門分科会，3月2006.
• 大西史高, 倉田博之　決定論的および確率論的シミュレーションによる概日リズムのシステム解析，In:ソフトウエアバイオロジー,　61-65, 化学工学会バイオ部会生物情報分野専門分科会　3月 2004.
• 真崎浩一,　倉田博之　生命システムの持つマルチフィードバック制御 In:ソフトウエアバイオロジー,　78-83, 化学工学会バイオ部会生物情報分野専門分科会　3月 2004.
• 倉田博之　代謝シミュレーションの新展開, 生物工学会誌 81, 229, 2003.
• 清水奈津美, 倉田博之　コンピュータエイデッドなバイオシステムへの利用　In:ソフトウエアバイオロジー，31-35　化学工学会バイオ部会生物情報分野専門分科会,　3月 2003.
• 岩崎麗, 倉田博之 大腸菌熱ショック応答のフイードバック/フィードフォワード制御　In:ソフトウエアバイオロジー，9-13　化学工学会バイオ部会生物情報分野専門分科会,　3月 2002.
• 井上貴博,　倉田博之 アンモニア同化システム制御の解析　In:ソフトウエアバイオロジー　14-18, 化学工学会バイオ部会生物情報分野専門分科会　3月 2002.
• 倉田博之　私の原典　化学工学　63: 45-46, 1999.
• 倉田博之　細胞のアポトーシスを防ぎ抗体生産の促進、化学と工業　50:630, 1997.
• 倉田博之　植物細胞を用いた有用二次代謝物生産のための光バイオリアクターに関する研究　化学工学　61:(3)　ⅸ, 1996.
• 倉田博之　植物による抗体の生産　化学工学　57:924, 1993.
• Kurata, H., Seki, M., Furusaki, S., Furuya, T. Development of a photobioreactor using immobilized Coffea arabica cells. Kagaku-Kougaku 56: 742-743, 1992.

Books

• 倉田博之, 品質とプロセス管理, BIODESIGNバイオデザイン日本語版，ステファノス・ゼニオス、ジョシュ・マコーワー、ポール・ヨック著，日本医療機器産業連合会, 日本医工ものづくりコモンズ監修,　バイオの杜, 2015.
• 倉田博之, 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），監修：大政健史，シーエムシー出版，86-94, 2015.
• Hiroyuki Kurata, Modularity of biochemical networks, In: Biomedical Engineering and Cognitive Neuroscience for Healthcare: Interdisciplinary Applications, IGI Global, 2012.
• 倉田博之，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，シーエムシー出版，133-140, 2010.
• 倉田博之, 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，シーエムシー出版, 289-300, 2009.
• 倉田博之，宮野悟， システム生物学入門：生物回路の設計原理，（291pages）翻訳：An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon, Chapman&Hall/CRC, 共立出版 2008
• 倉田博之, 生命の仕組みをコンピュータで再現する～バイオテクノロジーや医療に生かされる生命システム，九工大世界トップ技術2,　西日本新聞社, 126-135, 2008
• 倉田博之　バイオインフォマティクス事典，日本バイオインフォマティクス学会編集，共立出版，2006.
• 倉田博之，生命現象のシミュレーション，In: 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，化学工学会バイオ部会編，コロナ社，29-32，2006.
• 宮野悟, 松野浩嗣, 倉田博之,　システム生物学　In:ゲノム研究実験ハンドブック、実験医学別冊, 羊土, 49-54, 2004.　
• 倉田博之, 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エンジニアリング, シーエムシー出版, 289-300, 11月30日2002.
• 倉田博之,　大腸菌熱ショック適応のシステム分析,　In: システムバイオロジーの展開,北野宏明編, シュプリンガー・フェアラーク東京株式会, 199-208, 2001.
• 倉田博之, 多比良和誠, リボザイムの分子設計,　In: シリーズニューバイオフィジックスⅡ　生体ナノマシンの分子設計, 城所俊一編,　共立出版,　185-204, 2000.
• 倉田博之、多比良和誠, 生体で機能するRNA触媒の新展, In: 技術予測レポート第４巻バイオテクノロジー編、（株）日本能率協会総合研究所協力,（株）日本ビジネスレポート発行 2000.

Patents

• 倉田博之　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　公開特許公報2000-106295 2000, 4/7
• Kurata, H. Simulator, Method and Recording Medium For Simulating a Biological System. 09/727,699 2000, 12/18 (US Patent)

Invited Talks

• 倉田博之，ヒトコンピュータモデルの開発とその応用，医療ICTに関する座談会，横浜国立大学共同研究推進センター，2012年11月26日.
• 倉田博之，飯塚市の医工学連携，のがみプレジデントホテル，飯塚，2012年10月16日.
• 倉田博之，Integration of omics data into metabolic and gene regulatory networks, 理化学研究所免疫・アレルギー科学総合研究センターセミナー，横浜，2012年9月25日.
• 倉田博之，生体分子ネットワークのダイナミックシミュレーション，理化学研究所免疫・アレルギー科学総合研究センター，横浜，2012年6月15日.
• 倉田博之，メディカルインフォマティクス研究開発センターの紹介，第83回 e-ZUKA TRY VALLEY 産学官交流研究会（ニーズ会）「消化管内走行カプセル研究会フォーラム」，のがみプレジデントホテル，飯塚，2012年3月9日.
• 倉田博之，メディカルインフォマティックスへの化学工学的アプローチ　北九州化学工学懇話会（KACE）第51回講演会, 九州工業大学戸畑キャンパス附属図書館4Ｆ，2011年12月13日.
• Hiroyuki Kurata, Dynamic modeling of gene regulatory and metabolic networks in E. coli, UK-Japan Workshop on Systems Biology, S16, 24-25 October, Tsuruoka, JAPAN, 2011.
• 倉田博之，オミックスデータを代謝システムへ統合するためのパスウエイ解析モデル, 2011年度統計関連学会連合大会, 九州大学伊都キャンパス, 9月6日, 2011
• Hiroyuki Kurata, Use of maximum entropy principle extends the feasibility of elementary mode analysis, UK-Japan Workshop on Systems Biology, 13-14 September, Guildford, UK, 2010
• 倉田博之, バーチャルE.COLIの開発にむけて，山口大学研究推進体「微生物の機能進化と環境適応」第１回研究集会，山口大学大学会館，22 December, 2009 (特別講演)
• Hiroyuki Kurata, Integration of omics data into metabolic networks by elementary modes, UK-Japan Workshop on Systems Biology, 23-24 September, Osaka, 2009
• 倉田博之，生物回路の設計原理に基づく細胞機能の設計，第22回 回路とシステム軽井沢ワークショップ, The 22nd Workshop on Circuits and Systems inKaruizawa, 軽井沢プリンスホテル ウエスト・国際会議場浅間　498-502，4月20-21日，2009
• Hiroyuki Kurata, Computer aided rational design of biochemical systems. The 21st Annual and International Meeting of the Japanese Association for Animal Cell Technology. Fukuoka Japan, November 24-27, 2008.
• 倉田博之, 生命システムのシミュレーションとシステム解析、京都大学大学院医学研究科セミナー,　京都大学芝蘭会館　2008年3月13日.
• Hiroyuki Kurata, Simulation and system analysis of the E. coli nitrogen assimilation system, Systems biology workshop, Iizuka, Japan, July 13, 2007.
• 倉田博之　熱ショック応答の階層的モジュール構造が生み出すロバストネス，第6回計測自動制御学会生物制御調査研究，2006年12月8日，福岡天神イムズ.
• Hiroyuki Kurata, Mathematical Analysis for Robustness in Circadian Clock Systems, Frontier Research System 20th Anniversary International Workshop on Recent Advances in Biological Control, RIKEN, Nagoya, July 29-30, 2006.
• 倉田博之　生命設計原理に基づく生命システムの設計, システムバイオロジー研究会サテライトミーティング, スカイライト・バイオテック本社,秋田，8月31日2006.
• 倉田博之, 有用物質生産のための細胞設計工学, 第17回九州地区若手ケミカルエンジニア討論会, 7月28日,　2006, 山口(ホテル松政)
• Hiroyuki Kurata, Simulation and system analysis of metabolic and gene regulatory networks, The First KIT Bioinformatics Symposium, December 11, 2004,Iizuka, Japan.
• Hiroyuki Kurata, CADLIVE: from biochemical map to dynamic simulations, The First KIT Bioinformatics Workshop, December 10 (9-10), 2004, Iizuka, Japan.
• Hiroyuki Kurata, Map-based analysis for the budding yeast cell cycle network:  Integration of heterogeneous knowledge and data into CADLIVE, Proceedings of The First International Symposium on Systems Biology of Yeast. 23-28, St. Louis, USA. November 9, 2003.
• Hiroyuki Kurata, CADLIVE for designing metabolic and gene regulatory networks, The 9th Symposium of Young Asian Biochemical Engineers' Community,Jeju Island, Korea, November 14, 2003.
• 倉田 博之 大腸菌熱ショック応答システムの複雑な制御が生み出すロバスト性, 第１回システムバイオロジー研究会, 平成15年10月22日, 東京大学医科学研究所
• 倉田 博之「生命分子ネットワークの合理的設計をめざして」, 第25回生命情報学セミナー, 　平成15年7月10日木曜日, 場所：東京医科歯科大学湯島地区医科新棟地下1階 (臨床講堂１).
• 倉田 博之, 生物システムのシミュレーション, 第3回コンピューテーショナルゲノミックス研究会, 平成14年11月5日, 2002. 名古屋大学
• Hiroyuki Kurata, BIOCAD project for synthesis and analysis of gene regulatory networks, US-JAPAN Joint Workshop on Systems Biology of Useful Microorganism, Tsuruoka Town Campus of Keio University, Campus Center. September 18, 2002.
• 倉田博之　NEDOシステム生物学勉強会, 2002年 12月5日, 日本バイオインダストリ-協会（東京）
• Furusaki, S., Seki, M., Kurata, H., Furuya, T. The effect of light irradiation on secondary-metabolite production by Coffea arabica cells. Third U.S.-Japan Conference on Biotechnology, S. Furusaki & D.D.Y. Ryu (Eds.) Davis. 1992.

International Conferences

• Md. Bahadur Badsha, Nusrat Jahan, Hiroyuki Kurata, Identifying Differentially Expressed Genes by Robust Hierarchical Clustering in Microarray Gene Expression Data Analysis, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 31, Iizuka, February 28, 2013.
• Kentaro Inoue, Kazuhiro Maeda, Takaaki Miyabe, Hiroyuki Kurata, CADLIVE Toolbox for MATLAB: Comprehensive Analysis Tool for Dynamic Models in Systems Biology, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 33, Iizuka, February 28, 2013.
• Kazuhiro Maeda, Hiroyuki Kurata, Quasi-multiparameter sensitivity analysis reveals mechanisms to enhance robustness in circadian oscillators, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 34, Iizuka, February 28, 2013.
• Yu Matsuoka, Kazuyuki Shimizu, Hiroyuki Kurata, Modeling of the metabolic regulation of microbe such as Escherichia coli for the transition from aerobic to anaerobic condition, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 35, Iizuka, February 28, 2013.
• Ruilian Yao, Kazuyuki Shimizu, Hiroyuki Kurata, Catabolite regulation and its modulation by the specific gene mutations in Escherichia coli for the case of multiple carbon sources, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 36, Iizuka, February 28, 2013
• Noorlin Mohd Ali, Tsuboi Ryo, Matsumoto Yuta, Koishi Daisuke, Kentaro Inoue, Hiroyuki Kurata, Data Preparation in Analyzing Metabolic Fluxes, Proceedings of the First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering, 37, Iizuka, February 28, 2013.
• Hiroyuki Kurata, Use of elementary mode analysis predicts the flux distributions of a broad range of genetic mutants. The 12-th international Conference on Systems biology, Heidelberg/Mannheim, August 28 - September 1, 2011. (Poster)
• Kazuhiro Maeda,Hiroyuki Kurata, Dual Feedback Loop Architecture is a Robust and Entrainable Oscillator for Circadian Rhythm. The 12-th international Conference on Systems biology, Heidelberg/Mannheim, August 28 - September 1, 2011. (Poster)
• Kazuhiro Maeda, Hiroyuki Kurata,Quasi-Multiparameter Sensitivity Analysis reveals Remarkable Robustness of Dual Feedback Circadian Oscillators. The 11-th international Conference on Systems biology, Edinburgh, October 10-16, 2010. (Poster)
• Kentaro Inoue, Shin Shimozono, Hideaki Yoshida, Sayaka Tomeda, Kazuya Fukami, Shinpei Tonami, Hiroyuki Kurata, CADLIVE: Data Integrator with Network Layout Module. The 11-th international Conference on Systems biology, Edinburgh, October 10-16, 2010. (Poster)
• Kazuhiro Maeda, Yuya Fukano, Daichi Nitta, Shunsuke Yamamichi, Hiroyuki Kurata, An integrative and practical strategy for optimizing a large-scale dynamic model of biochemical systems. The 9-th International Conference on Bioinformatics (InCoB2010), Tokyo, September 26-28, 2010 (Oral presentation)
• Hiroshi Minamida, Kazuhiro Maeda, Hiroyuki Kurata, An optimization aiming for diverse parameter sets of a large-scale and dynamic model of biochemical networks. The 9-th International Conference on Bioinformatics (InCoB2010), Tokyo, September 26-28, 2010 (Poster)
• Souma Tabata, Quanyu Zhao, Hiroyuki Kurata, Development of elementary mode-based algorithms for designing a metabolic system. The 9-th International Conference on Bioinformatics (InCoB2010), Tokyo, September 26-28, 2010 (Poster)
• Kentaro Inoue, Hiroyuki Kurata, A Novel Spectral Clustering of Protein Interaction Networks. The 9-th International Conference on Bioinformatics (InCoB2010), Tokyo, September 26-28, 2010 (InCoB2010 Best Poster Award)
• Kentaro Inoue, Hiroyuki Kurata, Adjustable Diffusion Matrix-Based Spectral Clustering for Protein-Protein Interaction Network. Proceedings of The 20th International Conference on Genome Informatics, P064-1-2, YOKOHAMA, December 14-16, 2009. (Poster)
• Kazuhiro Maeda, Hiroyuki Kurata, Novel Robustness Analysis Reveals Remarkable Robustness of Dual Feedback Loops in a Circadian Clock. Proceedings of The 20th International Conference on Genome Informatics, P065-1-2, YOKOHAMA, December 14-16, 2009. (Poster)
• Daichi Nitta, Hiroyuki Kurata, Module Decomposition and Integration Method Optimizes a Large-Scale Cell Cycle Model. Proceedings of The 20th International Conference on Genome Informatics, P066-1-2, YOKOHAMA, December 14-16, 2009. (Poster)
• Quanyu Zhao, Hiroyuki Kurata, Prediction of Transcriptional Patterns of Gene Deletion Mutants by Modified Control Effective Flux. Proceedings of The 20th International Conference on Genome Informatics, P076-1-2, YOKOHAMA, December 14-16, 2009. (Poster)
• Sayaka Tomeda, Shinpei, Tonami, Kentaro Inoue, Kazuhiro Maeda, Hiroyuki Kurata, Extended CADLIVE: Multi-User Framework and Data Integrator. Proceedings of The 20th International Conference on Genome Informatics, P0004-1-2, YOKOHAMA, December 14-16, 2009. (Software Demonstration)
• Kentaro Inoue, Tetsuya Shimabara, Toshikazu Onaka, Erika Fujiura, Hiroyuki Kurata, Extended CADLIVE: Computer-aided rational design of living systems. The proceedings of the 2th annual conference of the Japanese Society for Bioinformatics, Osaka, S02-1-2, December 15-16, 2008.
• Kazuhiro Maeda, Hiroyuki Kurata, Searching multiple sets of kinetic parameters values reproducing target experimental data in dynamic biochemical models. The proceedings of the 2008th annual conference of the Japanese Society for Bioinformatics, Osaka, S063-1-2,  December 15-16, 2008.
• Kentaro Inoue, Shogo Takagi, Sayaka Tomeda, Masayo Ono, Hiroyuki Kurata, CADLIVE : An integrative system of life information, The 2007 annual conference of Japanese Society for Bioinformatics, S1, December, 17-19, 2007 (Poster)
• Katsutoshi Nakano, Rei Iwasaki, Hiroyuki Kurata, Stochastic simulation of diffusion reaction model in embryo development, The 2007 annual conference of Japanese Society for Bioinformatics,  P021, December, 17-19, 2007 (Poster)
• Koichi Masaki, Hiroyuki Kurata, Systems biology for analysis of nitrogen assimilation system in E. coli, The 2007 annual conference of Japanese Society for Bioinformatics, P022, December, 17-19, 2007 (Poster)
• Yuya Fukano, Daichi Nitta, Hiroyuki Kurata, Optimization of a large-scale cell cycle model using multi-objective GAs, The 2007 annual conference of Japanese Society for Bioinformatics, P025, December, 17-19, 2007 (Poster)
• Kazuhiro Maeda, Hiroyuki Kurata, Parameter search of large-scale dynamic biochemical network models, The 2007 annual conference of Japanese Society for Bioinformatics, P027, December, 17-19, 2007 (Poster)
• Hiroyuki Kurata, CADLIVE:Computer-Aided Design of Living Systems. The 15th annual international conference on intelligent systems for molecular biology,Wien, Austria, July 21-25, 2007. (Oral presentation, software demonstration)
• Koichi Masaki, Hiroyuki Kurata, Hysteresis analysis for the dynamic model of the nitrogen assimilation system in E. coli. The 15th annual international conference on intelligent systems for molecular biology, Wien, Austria, July 21-25, 2007. (Poster)
• Yuki Shimokawa, Kazuhiro Maeda, Kentaro Inoue, Hiroyuki Kurata, CADLIVE: Integration for large-scale network data, The 17th International Conference on Genome Informatics, S02-1-2, Pacifico Yokohama, Japan, December 18-20, 2006. (Software demonstration)
• Koichi Masaki, Hiroyuki Kurata, Sensitivity analysis for the E. coli nitrogen assimilation system, The 17th International Conference on Genome Informatics, P010-1-2, Pacifico Yokohama, Japan,　December 18-20, 2006. (Poster)
• Quanyu Zhao, Hiroyuki Kurata, Comparison of the prediction abilities of FBA, MOMA, and ROOM for a pykF mutant of E. coli, The 17th International Conference on Genome Informatics, P107-1-2, Pacifico Yokohama, Japan, December 18-20, 2006. (Poster)
• Emi Shiraishi, Hiroyuki Kurata, A steady-state approximation-based solver for stiff biochemical models, The 17th International Conference on Genome Informatics, P016-1-2, Pacifico Yokohama, Japan, December 18-20, 2006. (Poster)
• Koichi Masaki, Hiroyuki Kurata, 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, 4P-A-220, Kyoto, June 22, 2006. (Poster)
• Hiroyuki Kurata, Takayuki Tanaka, Fumitaka Ohnishi, Robustness analysis for the mechanism for a temperature-compensated circadian oscillator. The 20th IUBMB International Congress of Biochemistry and Molecular Biology and the 11 th FAOBMB Congress, 4P-A-229, Kyoto, June 22, 2006. (Poster)
• Hiroyuki Kurata, Marie Kajiwara, Yuki Shimokawa, CADLIVE: Computer-Aided Design of Living Systems. The 16th International Conference on Genome Informatics, P114-1-2, Pacifico Yokohama, Japan, December 19-21, 2005. (Software demonstration)

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