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Laboratory for Biochemical Simulation

Primary paper

  • Shindo, Y., Iwamoto, K., Mouri, K., Hibino, K., Tomita, M., Kosako, H., et al.
    "Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling"
    Nat. Commun. 7, 10485 (2016) doi:10.1038/ncomms10485
  • Takahashi, K., Itaya, K., Nakamura, M., Koizumi, M., Arakawa, N., Tomita, M., et al.
    "A generic software platform for brain-inspired cognitive computing"
    Proc Comput Sci (2015)
  • Karr, J. R., Takahashi, K. & Funahashi, A.
    "The principles of whole-cell modeling"
    Curr. Opin. Microbiol. 27, 18-24 (2015) doi:10.1016/j.mib.2015.06.004
  • Watabe, M., Arjunan, S. N. V., Fukushima, S., Iwamoto, K., Kozuka, J., Matsuoka, S., et al.
    "A Computational Framework for Bioimaging Simulation"
    PLoS One 10, e0130089 (2015) doi:10.1371/journal.pone.0130089
  • Shimo, H., Arjunan, S. N. V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., et al.
    "Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes"
    PLoS Comput. Biol. 11, UNSP e1004 (2015) doi:10.1371/journal.pcbi.1004210
  • Feig, M., Harada, R., Mori, T., Yu, I., Takahashi, K. & Sugita, Y.
    "Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology"
    J. Mol. Graph. Model. 58, 1-9 (2015) doi:10.1016/j.jmgm.2015.02.004
  • Maeshima, K., Kaizu, K., Tamura, S., Nozaki, T., Kokubo, T. & Takahashi, K.
    "The physical size of transcription factors is key to transcriptional regulation in chromatin domains"
    J. Phys. Condens. Matter 27, 064116 (2015) doi:10.1088/0953-8984/27/6/064116
  • Nishida, K., Ono, K., Kanaya, S. & Takahashi, K.
    "KEGGscape: a Cytoscape app for pathway data integration"
    F1000Research 3, 144 (2014) doi:10.12688/f1000research.4524.1
  • Kaizu, K., Ronde, W., Paijmans, J., Takahashi, K., Tostevin, F. & Wolde, P. R.
    "The Berg-Purcell Limit Revisited"
    Biophys. J. 106, 976-985 (2014) doi:10.1016/j.bpj.2013.12.030
  • Hayashi, K., Pack, C. G., Sato, M. K., Mouri, K., Kaizu, K., Takahashi, K., et al.
    "Viscosity and drag force involved in organelle transport: Investigation of the fluctuation dissipation theorem"
    Eur. Phys. J. E 36, 136 (2013) doi:10.1140/epje/i2013-13136-6
  • Aoki, K., Takahashi, K., Kaizu, K. & Matsuda, M.
    "A Quantitative Model of ERK MAP Kinase Phosphorylation in Crowded Media"
    Sci. Rep. 3, 1541 (2013) doi:10.1038/srep01541
  • Nozaki, T., Kaizu, K., Pack, C., Tamura, S., Tani, T., Hihara, S., et al.
    "Flexible and dynamic nucleosome fiber in living mammalian cells"
    Nucleus 4, 349-356 (2013) doi:10.4161/nucl.26053
  • Hihara, S., Pack, C., Kaizu, K., Tani, T., Hanafusa, T., Nozaki, T., et al.
    "Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells"
    Cell Reports 2, 1645-1656 (2012) doi:10.1016/j.celrep.2012.11.008
  • Mugler, A., Bailey, A. G., Takahashi, K. & Wolde, P. R.
    "Membrane Clustering and the Role of Rebinding in Biochemical Signaling"
    Biophys. J. 102, 1069-1078 (2012) doi:10.1016/j.bpj.2012.02.005
  • Takahashi, K., Tanase-Nicola, S. & Wolde, P. R.
    "Spatio-temporal correlations can drastically change the response of a MAPK pathway"
    Proc. Natl. Acad. Sci. U.S.A. 107, 2473-2478 (2010) doi:10.1073/pnas.0906885107
  • Takahashi, K., Arjunan, S. N. V. & Tomita, M.
    "Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico"
    FEBS Lett. 579, 1783-1788 (2005) doi:10.1016/j.febslet.2005.01.072
  • Takahashi, K., Kaizu, K., Hu, B. & Tomita, M.
    "A multi-algorithm, multi-timescale method for cell simulation"
    Bioinformatics 20, 538-546 (2004) doi:10.1093/bioinformatics/btg442

Book

  • Addy, N. & Takahashi, K.
    "Foundations of E-Cell Simulation Environment Architecture"
    In Arjunan, S.N.V., Dhar, P. & Tomita, M.(Eds.) E-Cell System – Basic Concepts and Applications. Landes Biosciences (2013)