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Laboratory for Biochemical Simulation

Koichi Takahashi


Team Leader

Koichi Takahashi (Ph.D.)

Takahashi of RIKEN

Intracellular biochemical reaction networks give rise to all living organisms on earth. Modeling and simulating these biochemical pathways is a key technology towards the next generation of life sciences. Our Team has been developing computational methods, including Green's function reaction dynamics and microscopic lattice reaction-diffusion method, and a cell simulation platform called the E-Cell System. We are also working on the application of artificial intelligence and machine learning techniques to mitigate overwhelming complexity in modeling cellular systems.

Research Topics

  • Development of biochemical network simulation techniques
  • Spatio-temporal architectures of intracellular signaling pathways
  • Enzyme kinetics under intracellular macromolecular crowding
  • E-Cell cell simulation software platform
  • Computational platforms for AI-driven science

Selected Publications

  • 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
  • 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
  • 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
  • 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
  • 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., 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