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RIKEN Quantitative Biology Center

Laboratory for Biochemical Simulation

Team Leader: Koichi Takahashi (Ph.D.)
Koichi  Takahashi(Ph.D.)

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.

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. Yachie, N., Robotic Biology Consortium (including Takahashi K), & Natsume, T.:
    "Robotic crowd biology with Maholo LabDroids"
    Nat. Biotechnol. 35, 310-312 (2017)
  2. Iwamoto, K., Shindo, Y., & Takahashi, K.:
    "Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway"
    PLoS Comput. Biol. 12(11), e1005222 (2016)
  3. Shindo, Y., Iwamoto, K., Mouri, K., Hibino, K., Tomita, M., et al.:
    "Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling"
    Nat. Commun. 7, 10485 (2016)
  4. Takahashi, K., Itaya, K., Nakamura, M., Koizumi, M., Arakawa, N., et al.:
    "A generic software platform for brain-inspired cognitive computing"
    Proc Comput Sci (2015)
  5. Karr, J. R., Takahashi, K. & Funahashi, A.:
    "The principles of whole-cell modeling"
    Curr. Opin. Microbiol. 27, 18-24 (2015)
  6. Watabe, M., Arjunan, S. N. V., Fukushima, S., Iwamoto, K., Kozuka, J., et al.:
    "A Computational Framework for Bioimaging Simulation"
    PLoS One 10, e0130089 (2015)
  7. Shimo, H., Arjunan, S. N. V., Machiyama, H., Nishino, T., Suematsu, M., et al.:
    "Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes"
    PLoS Comput. Biol. 11, UNSP e1004 (2015)
  8. Kaizu, K., Ronde, W., Paijmans, J., Takahashi, K., Tostevin, F. & Wolde, P. R.:
    "The Berg-Purcell Limit Revisited"
    Biophys. J. 106, 976-985 (2014)
  9. Hihara, S., Pack, C., Kaizu, K., Tani, T., Hanafusa, T., et al.:
    "Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells"
    Cell Reports 2, 1645-1656 (2012)
  10. *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)

Lab Members

Principal Investigator

Koichi Takahashi
Team Leader

Core Members

Kazunari Kaizu
Senior Scientist
Satya Nanda Vel Arjunan
Research Scientist
Masaki Watabe
Research Scientist
Wei Xiang Chew
International Program Associate
Kozo Nishida
Technical Staff I
Koji Ochiai
Technical Staff I

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