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 | 3814 | 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 | 1086 | 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 | 315 | 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 | 310 | 2010 |
A multi-algorithm, multi-timescale method for cell simulation K Takahashi, K Kaizu, B Hu, M Tomita Bioinformatics 20 (4), 538-546, 2004 | 248 | 2004 |
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 | 212 | 2020 |
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 | 199 | 2012 |
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 | 191 | 2003 |
The berg-purcell limit revisited K Kaizu, W De Ronde, J Paijmans, K Takahashi, F Tostevin, ... Biophysical journal 106 (4), 976-985, 2014 | 159 | 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 | 111 | 2002 |
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 | 96 | 2017 |
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 | 91 | 2012 |
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 | 87 | 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 | 86 | 2015 |
The principles of whole-cell modeling JR Karr, K Takahashi, A Funahashi Current opinion in microbiology 27, 18-24, 2015 | 81 | 2015 |
KEGGscape: a Cytoscape app for pathway data integration K Nishida, K Ono, S Kanaya, K Takahashi F1000Research 3, 2014 | 79 | 2014 |
Robotic crowd biology with Maholo LabDroids N Yachie, T Natsume Nature biotechnology 35 (4), 310-312, 2017 | 77 | 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 | 62 | 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 | 59 | 2016 |
Flexible and dynamic nucleosome fiber in living mammalian cells T Nozaki, K Kaizu, CG Pack, S Tamura, T Tani, S Hihara, T Nagai, ... Nucleus 4 (5), 349-356, 2013 | 52 | 2013 |