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The principles of whole-cell modeling.
Karr JR, Takahashi K, Funahashi A. Karr JR, et al. Among authors: takahashi k. Curr Opin Microbiol. 2015 Oct;27:18-24. doi: 10.1016/j.mib.2015.06.004. Epub 2015 Jun 24. Curr Opin Microbiol. 2015. PMID: 26115539 Review.
A Computational Framework for Bioimaging Simulation.
Watabe M, Arjunan SN, Fukushima S, Iwamoto K, Kozuka J, Matsuoka S, Shindo Y, Ueda M, Takahashi K. Watabe M, et al. Among authors: takahashi k. PLoS One. 2015 Jul 6;10(7):e0130089. doi: 10.1371/journal.pone.0130089. eCollection 2015. PLoS One. 2015. PMID: 26147508 Free PMC article.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Multi-Algorithm Particle Simulations with Spatiocyte.
Arjunan SNV, Takahashi K. Arjunan SNV, et al. Among authors: takahashi k. Methods Mol Biol. 2017;1611:219-236. doi: 10.1007/978-1-4939-7015-5_16. Methods Mol Biol. 2017. PMID: 28451982
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.
Shimo H, Arjunan SN, Machiyama H, Nishino T, Suematsu M, Fujita H, Tomita M, Takahashi K. Shimo H, et al. Among authors: takahashi k. PLoS Comput Biol. 2015 Jun 5;11(6):e1004210. doi: 10.1371/journal.pcbi.1004210. eCollection 2015 Jun. PLoS Comput Biol. 2015. PMID: 26046580 Free PMC article.
Flexible and dynamic nucleosome fiber in living mammalian cells.
Nozaki T, Kaizu K, Pack CG, Tamura S, Tani T, Hihara S, Nagai T, Takahashi K, Maeshima K. Nozaki T, et al. Among authors: takahashi k. Nucleus. 2013 Sep-Oct;4(5):349-56. doi: 10.4161/nucl.26053. Epub 2013 Aug 12. Nucleus. 2013. PMID: 23945462 Free PMC article.
Transcriptionally inducible Pleckstrin homology-like domain, family A, member 1, attenuates ErbB receptor activity by inhibiting receptor oligomerization.
Magi S, Iwamoto K, Yumoto N, Hiroshima M, Nagashima T, Ohki R, Garcia-Munoz A, Volinsky N, Von Kriegsheim A, Sako Y, Takahashi K, Kimura S, Kholodenko BN, Okada-Hatakeyama M. Magi S, et al. Among authors: takahashi k. J Biol Chem. 2018 Feb 9;293(6):2206-2218. doi: 10.1074/jbc.M117.778399. Epub 2017 Dec 12. J Biol Chem. 2018. PMID: 29233889 Free PMC article.
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