Team Leader

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.

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

• Yachie, N., Natsume, T., Takahashi, K., Katayama, T., Sakurada, T., Kanda, G. N., et al.
  "Robotic crowd biology with Maholo LabDroids"
  Nat. Biotechnol. 35, 310-312 (2017) doi:10.1038/nbt.3758
• Iwamoto, K., Shindo, Y. & Takahashi, K.
  "Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway"
  PLoS Comput. Biol. 12, e1005222 (2016) doi:10.1371/journal.pcbi.1005222
• 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
• 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