Koichi Takahashi

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Satya ArjunanScientific Software Engineer, Victor Chang Cardiac Research InstituteVerified email at cyros.org
Kazuhiro MaeshimaProfessor, National Institute of Genetics and SOKENDAI (The Graduate University for Advanced StudiesVerified email at nig.ac.jp
Tadasu NozakiPostdoctoral fellow, Harvard UniversityVerified email at fas.harvard.edu
Kazunari IwamotoInstitute for Protein Research, Osaka UniversityVerified email at protein.osaka-u.ac.jp
Chan-Gi PackAsan institute for Life Sciences, Asan Medical Center, University of Ulsan Colleage of MedicineVerified email at amc.seoul.kr
Sorin Tanase NicolaDepartment of Cell and Molecular Biology, Uppsala UniversityVerified email at icm.uu.se
Masataka KinjoLaboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido UniversityVerified email at sci.hokudai.ac.jp
Tohru NatsumeNational Institute of Advanced Industrial Science and Technology (AIST)Verified email at aist.go.jp
Yuki ShindoDartmouth CollegeVerified email at dartmouth.edu
Chew Wei XiangCenter for Genomics RegulationVerified email at crg.eu
Bin HuLos Alamos National LaboratoryVerified email at lanl.gov
Hideo YokotaRIKEN Center for Advanced PhotonicsVerified email at riken.jp
堀之内貴明 (Takaaki Horinouchi)AIRC, AISTVerified email at aist.go.jp
Andrew MuglerAssociate Professor, Department of Physics and Astronomy, University of PittsburghVerified email at pitt.edu
Michael FeigMichigan State UniversityVerified email at msu.edu
Ryuhei HaradaUniversity of TsukubaVerified email at ccs.tsukuba.ac.jp
Shigehiko KanayaProfessor of Computational Systems biology Lab, Nara Institute of Science and Technology (NAIST)Verified email at gtc.naist.jp
Keiichiro OnoUniversity of California, San DiegoVerified email at ucsd.edu
Akira FunahashiProfessor of Systems Biology, Keio UniversityVerified email at bio.keio.ac.jp
Jonathan KarrIcahn School of Medicine at Mount SinaiVerified email at mssm.edu

Koichi Takahashi

RIKEN

Verified email at sfc.keio.ac.jp - Homepage

Computational Systems Biology Laboratory Automation Brain-inspired Computing Architectures Artificial Intelligence


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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	3740	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	1094	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	316	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	308	2010
A multi-algorithm, multi-timescale method for cell simulation K Takahashi, K Kaizu, B Hu, M Tomita Bioinformatics 20 (4), 538-546, 2004	253	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	190	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	184	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	174	2020
The berg-purcell limit revisited K Kaizu, W De Ronde, J Paijmans, K Takahashi, F Tostevin, ... Biophysical journal 106 (4), 976-985, 2014	154	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	112	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	90	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	87	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	81	2015
The principles of whole-cell modeling JR Karr, K Takahashi, A Funahashi Current opinion in microbiology 27, 18-24, 2015	79	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	79	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	68	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	61	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	55	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	52	2000

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