RIKEN Center for Biosystems Dynamics Research Laboratory for Biologically Inspired Computing
Team Director: Koichi Takahashi (Ph.D.)
Research Summary
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)
Recent Research Results
Related Links
Lab Members
Principal investigator
- Koichi Takahashi
- Team Director
Core members
- Kazunari Kaizu
- Senior Research Scientist
- Nobuyuki Tanaka
- Senior Technical Scientist
- Koji Ochiai
- Research Scientist
- Eliott Gerard Raymond Jacopin
- Postdoctoral Researcher
- Shiwei Su
- Postdoctoral Researcher
- Kozo Nishida
- Technical Scientist
- Kazuya Azumi
- Technical Staff I
Contact Information
Email: ktakahashi@riken.jp