Koichi Takahashi
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ...
Bioinformatics 19 (4), 524-531, 2003
E-CELL: software environment for whole-cell simulation.
M Tomita, K Hashimoto, K Takahashi, TS Shimizu, Y Matsuzaki, F Miyoshi, ...
Bioinformatics (Oxford, England) 15 (1), 72-84, 1999
Space in systems biology of signaling pathways–towards intracellular molecular crowding in silico
K Takahashi, SNV Arjunan, M Tomita
FEBS letters 579 (8), 1783-1788, 2005
Spatio-temporal correlations can drastically change the response of a MAPK pathway
K Takahashi, S Tănase-Nicola, PR Ten Wolde
Proceedings of the National Academy of Sciences 107 (6), 2473-2478, 2010
A multi-algorithm, multi-timescale method for cell simulation
K Takahashi, K Kaizu, B Hu, M Tomita
Bioinformatics 20 (4), 538-546, 2004
E-Cell 2: multi-platform E-Cell simulation system
K Takahashi, N Ishikawa, Y Sadamoto, H Sasamoto, S Ohta, A Shiozawa, ...
Bioinformatics 19 (13), 1727-1729, 2003
Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells
S Hihara, CG Pack, K Kaizu, T Tani, T Hanafusa, T Nozaki, S Takemoto, ...
Cell reports 2 (6), 1645-1656, 2012
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
The berg-purcell limit revisited
K Kaizu, W De Ronde, J Paijmans, K Takahashi, F Tostevin, ...
Biophysical journal 106 (4), 976-985, 2014
Computational challenges in cell simulation: a software engineering approach
K Takahashi, K Yugi, K Hashimoto, Y Yamada, CJF Pickett, M Tomita
IEEE Intelligent Systems 17 (5), 64-71, 2002
Membrane clustering and the role of rebinding in biochemical signaling
A Mugler, AG Bailey, K Takahashi, PR Ten Wolde
Biophysical journal 102 (5), 1069-1078, 2012
Density imaging of heterochromatin in live cells using orientation-independent-DIC microscopy
R Imai, T Nozaki, T Tani, K Kaizu, K Hibino, S Ide, S Tamura, K Takahashi, ...
Molecular biology of the cell 28 (23), 3349-3359, 2017
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
M Feig, R Harada, T Mori, I Yu, K Takahashi, Y Sugita
Journal of Molecular Graphics and Modelling 58, 1-9, 2015
The principles of whole-cell modeling
JR Karr, K Takahashi, A Funahashi
Current opinion in microbiology 27, 18-24, 2015
The physical size of transcription factors is key to transcriptional regulation in chromatin domains
K Maeshima, K Kaizu, S Tamura, T Nozaki, T Kokubo, K Takahashi
Journal of Physics: Condensed Matter 27 (6), 064116, 2015
KEGGscape: a Cytoscape app for pathway data integration
K Nishida, K Ono, S Kanaya, K Takahashi
F1000Research 3, 2014
Robotic crowd biology with Maholo LabDroids
N Yachie, T Natsume
Nature biotechnology 35 (4), 310-312, 2017
A quantitative model of ERK MAP kinase phosphorylation in crowded media
K Aoki, K Takahashi, K Kaizu, M Matsuda
Scientific reports 3 (1), 1541, 2013
Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling
Y Shindo, K Iwamoto, K Mouri, K Hibino, M Tomita, H Kosako, Y Sako, ...
Nature communications 7 (1), 10485, 2016
The E-CELL project: towards integrative simulation of cellular processes
M Tomita, K Hashimoto, K Takahashi, Y Matsuzaki, R Matsushima, K Yugi, ...
Proceedings of the fourth annual international conference on Computational …, 2000
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