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2020 – today
- 2024
[j22]Md. Harun-Or-Roshid
, Kazuhiro Maeda, Le Thi Phan, Balachandran Manavalan, Hiroyuki Kurata:
Stack-DHUpred: Advancing the accuracy of dihydrouridine modification sites detection via stacking approach. Comput. Biol. Medicine 169: 107848 (2024)- 2022
- [j21]Sho Tsukiyama, Md. Mehedi Hasan, Hong-Wen Deng, Hiroyuki Kurata:
BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches. Briefings Bioinform. 23(2) (2022) - [j20]Hiroyuki Kurata, Sho Tsukiyama, Balachandran Manavalan:
iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model. Briefings Bioinform. 23(4) (2022) - [j19]Kazuhiro Maeda, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, Hiroyuki Kurata:
MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling. BMC Bioinform. 23(1): 455 (2022) - 2021
- [j18]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 Bioinform. 22(3) (2021) - [j17]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 Bioinform. 22(6) (2021) - [j16]Sho Tsukiyama, Md. Mehedi Hasan, Satoshi Fujii, Hiroyuki Kurata:
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. Briefings Bioinform. 22(6) (2021) - [j15]Md. Mehedi Hasan, Md. Ashad Alam, 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(3): 315-323 (2021) - [j14]Michihiro Hara, Takao Umeda, Hiroyuki Kurata:
Fabrication and Characterisation of Organic EL Devices in the Presence of Cyclodextrin as an Interlayer. Sensors 21(11): 3666 (2021) - 2020
- [j13]Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata:
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. Genom. Proteom. Bioinform. 18(5): 593-600 (2020) - [j12]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(12): 1229-1236 (2020)
2010 – 2019
- 2019
- [j11]A. B. M. Shamim Ul Hasan, Hiroyuki Kurata, Sebastian Pechmann:
Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation. BMC Bioinform. 20(1): 734 (2019) - 2018
- [c7]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. BIBE 2018: 122-125 - [c6]Md. Mehedi Hasan, Hiroyuki Kurata:
iLMS, Computational Identification of Lysine-Malonylation Sites by Combining Multiple Sequence Features. BIBE 2018: 356-359 - 2014
- [j10]Hiroyuki Kurata, Kazuhiro Maeda, Toshikazu Onaka, Takenori Takata:
BioFNet: biological functional network database for analysis and synthesis of biological systems. Briefings Bioinform. 15(5): 699-709 (2014) - [j9]Kazuhiro Maeda, Hiroyuki Kurata:
Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. BMC Syst. Biol. 8(S-5): S1 (2014) - 2013
- [j8]Shuhei Yoshida, Takaaki Matsubara, Hiroyuki Kurata, Shuma Horiuchi, Manabu Yamamoto:
Multi-Dimensional Shift Multiplexing Technique with Spherical Reference Waves. IEICE Trans. Electron. 96-C(12): 1520-1524 (2013) - 2012
- [j7]Koichi Masaki, Kazuhiro Maeda, Hiroyuki Kurata:
Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System. Artif. Life 18(1): 53-90 (2012) - [j6]Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi, Hiroyuki Kurata:
CADLIVE optimizer: web-based parameter estimation for dynamic models. Source Code Biol. Medicine 7: 9 (2012)
2000 – 2009
- 2009
- [j5]Quanyu Zhao, Hiroyuki Kurata:
Genetic modification of flux for flux prediction of mutants. Bioinform. 25(13): 1702-1708 (2009) - [j4]Kazuhiro Maeda, Hiroyuki Kurata:
Two-phase Search (TPS) Method: Nonbiased and High-speed Parameter Search for Dynamic Models of Biochemical Networks. Inf. Media Technol. 4(2): 377-389 (2009) - 2007
- [j3]Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda, Kazuyuki Shimizu:
Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst. Biol. 1: 31 (2007) - 2006
- [j2]Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C. Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash:
Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. PLoS Comput. Biol. 2(7) (2006) - [c5]Tanaka Shin, Hiroyuki Kurata, Takeshi Ohashi:
Effective and Fast Optimization for a Dynamic Model of the Drosophila Circadian Oscillator. SMC 2006: 3596-3601 - 2005
- [j1]Weijiang Li, Hiroyuki Kurata:
A grid layout algorithm for automatic drawing of biochemical networks. Bioinform. 21(9): 2036-2042 (2005) - [c4]Tanaka Shin, Hiroyuki Kurata, Takeshi Ohashi:
Reverse Engineering for a Dynamic Model of the Drosophila Circadia Oscillator. CIMCA/IAWTIC 2005: 625-631 - [c3]Tanaka Shin, Hiroyuki Kurata, Takeshi Ohashi:
Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli. SMC 2005: 2078-2083 - 2002
- [c2]Hana El-Samad, Mustafa Khammash, Hiroyuki Kurata, John Doyle:
Robustness analysis of the heat shock response in E. coli. ACC 2002: 1742-1747 - 2001
- [c1]Hiroyuki Kurata, Hana El-Samad, Tau-Mu Yi, Mustafa Khammash, John Doyle:
Feedback regulation of the heat shock response in E. coli. CDC 2001: 837-842
Coauthor Index
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