Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics

Strategic Objective

Creation of the technology systems to have absolute control of cells and cell populations by reproducing cell kinetics in silico/in vitro in order to achieve an integrated understanding of life phenomena and realize safe and highly effective treatments among other benefits

Research Supervisor

Tadashi Yamamoto (Professor, Okinawa Institute of Science and Technology (OIST))


Living organisms are in dynamical balance between their responses to environmental stimuli and their ability of maintaining homeostasis. Through observation, experimentation and measurement of biological phenomena conducted by macromolecules including chromosomes, proteins, and lipids at levels of cell-free system, cells and cell populations, the researches of this research area is expected to gain an integrated understanding of dynamical balance of the living organisms in both spatial and temporal dimensions. At the same time, the research of this research area aim to create technologies that can control biological phenomena.
The research should elucidate an operating principle of dynamic and complex biological phenomena that has been hard to address by traditional approaches. To do so, the research needs to utilize rapidly growing high-speed/super-resolution technologies for measurement/analysis, and to integrate life sciences with cutting edge fields of mathematics, physics, chemistry, engineering, information science and computer sciences. We promote leading researches with interdisciplinary views for comprehensive understanding of dynamic systems of the living organisms using modeling and simulation based on mathematical science.

The logo of CREST Biodynamics

Design concept

This round, blue and yellow logo symbolizes the challenges that approximates and expresses the nonlinearity and the hierarchy of a biological dynamics, and consequently, enabling control and design of the regulatory mechanisms of biological phenomena.


・2016.11.24 [FEATURED] Diversification of Neu differentiation factor and epidermal growth factor signaling by combinatorial receptor interactions by Prof. Shinya Kuroda (Science. Signaling).

・2016.08.01 [FEATURED] Neural circuit mechanism how petty experiences become long-term memories when surprising events happen by Prof. Kaoru Inokuchi (Nat. Commun.) Click here for more information.

・2016.06.21 [FEATURED] New insight into Atopic Dermatitis: Claudin-1 dose-dependently regulates the changes of dermatitis by Prof. Sachiko Tsukita (PNAS) Click here for more information.

・2015.07.07 JST CREST-PRESTO joint international symposium ~Structural Biological Dynamics: From Molecules to Life with 60 trillion Cells~ will be held on November 5-6, 2015.
We look forward to meeting you at the symposium in Tokyo.

・2015.07.01 ICSB 2015, jointly organizing with A*star, Singapore will be held on November 23-26, 2015.

・2015.04.07 Prof. Kageyama received the the FY2015 Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology. Conglaturations!

・2015.04.02 [FEATURED] Artificial Association of Pre-Stored Information by Prof. Kaoru Inokuchi (Cell reports). Click here for more information.

・2014.08.15 [FEATURED] Reconstruction of molecular network from cellular big data by Prof. Shinya Kuroda (Cell reports). Click here for more information.

・2014.07.18 [FEATURED] Role of synaptic phosphatidylinositol 3-kinase in a behavioral learning response in C. elegans by Prof. Yuichi Iino (Science).

・2014.04.28 Prof. Hamada received the medal of honor with purple ribbon (shiju hosho) . Conglaturations!

・2014.03.15 Briefing of Research Area by Prof. Yamamoto & Prof. Tokihiro was held at Gakushuin University. Click for handouts & movie.

・2013.11.01 [FEATURED] Oscillatory control of determination factors for multipotency versus fate choice in mouse neural progenitors by Prof. Ryoichiro KAGEYAMA (Science). Click here for more information.

・2013.09.20 Prof. Yamamoto had participated in the ICSB2013 at Copenhagen and subsequently visited Heidelberg University BioQuant & COS.

・2013.08.02 [FEATURED] Robust information transmission of cellular signaling pathways by Prof. Shinya KURODA. Click here for more information.

・2013.07.26 [FEATURED] Yes, that’s the taste!- Neural mechanisms of taste memory of the soil nematode – by Prof. Yuichi IINO. Click here for more information.

・2013.03.20 Briefing of Research Area by Prof. Yamamoto was held at Kyoto University on 20 March. Click for handouts & movie (Japanese only).

・2013.02.27  Briefing of Research Area on March 20, 2013, at Yoshida South Campus, Kyoto University. Please click here for more information.

・2012.12.13 CREST seminar “Towards Deeper Understanding of Biodynamic Principles” at OIST. Please click here for more information.

CRESTMeeting Reports

・2014.10.28-30 CREST-Biodynamics 3rd annual meeting

・2013.11.25-26 CREST-Biodynamics 2nd annual meeting

・2012.12.02-03 CREST-Biodynamics 1st annual meeting

Research Area Advisors

Professor, The University of Tokyo

・Kiyoshi ASAI
Professor, The University of Tokyo

Professor, Kyushu University

・Tsuyoshi KATO
Professor, Kyoto University

・Takashi SUZUKI
Professor, Osaka University

Professor, Kyoto University

Adjunct professor, Kobe University

・Hiroyoshi TOYOSHIBA
Principal Scientist, Takeda Pharmaceutical Co. Ltd.

・Akihiko NAKANO
Professor, The University of Tokyo / Team Leader, RIKEN

Advisor, JT Biohistory Research Hall / NPO All About Science Japan

・Kiyoko FUKAMI
Professor, Tokyo University of Pharmacy and Life Sciences

・Hisao HONDA
Adjunct professor, Kobe University

・Masayoshi MISHINA
Professor, Ritsumeikan University

・Yoshikazu YOSHIDA
Corporate Adviser, SHIMADZU Corp.

Year Started : 2012

Elucidation of operating characteristics of the neural circuit based on observational data of the whole nervous system

Research Director:
Yuichi Iino(Professor, The University of Tokyo)

Elucidation and control of dynamics of oscillatory gene expression in cell proliferation and differentiation

Research Director:
Ryoichiro Kageyama(Professor, Kyoto University)

Temporal coding of cellular dynamical system

Research Director:
Sinya Kuroda(Professor, The University of Tokyo)

Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks

Research Director:
Minoru S.H. Ko(Professor, Keio University)

Investigation of the mechanism of biological pattern formation that may allow us to control the shape of animals

Research Director:
Shigeru Kondo(Professor, Osaka University)

Year Started : 2013

Memory integration process based on cell assembly and neural circuit model

Research Director:
Kaoru Inokuchi(Professor, University of Toyama)

Exploring the principle of tissue organization based on the diversity and heterogeneity of cellular dynamics

Research Director:
Hiroki Kurihara (Professor, The University of Tokyo)

Understanding and Predicting 3D Chromatin Dynamics

Research Director:
Hiroyuki Takeda (Professor, The University of Tokyo)

Elucidation of a novel unified epithelial system defined by the reciprocal regulation of cell-cell adhesion and the apical cytoskeleton and its use for manipulating the epithelial barrier

Research Director:
Sachiko Tsukita (Professor, Osaka University)

Mechanics of generating and sensing flow by cilia

Research Director:
Hiroshi Hamada (Director, RIKEN Center for Developmental Biology)

Solving complex network systems based on theories to connect structure and dynamics

Research Director:
Atsushi Mochizuki (Chief Scientist, RIKEN)

Year Started : 2014

Direct Visualization for RNA Silencing Prcess by Novel Single Molecule Methods : Basis and Appllication

Research Director:
Sotaro Uemura(Professor, Graduate School of Science, The University of Tokyo)

Understanding synapse dynamics through nanoscale structural analyses

Research Director:
Shigeo Okabe(Professor, Graduate School of Medicine, The university of Tokyo)

Chronometabolism: Molecular analysis of biological timing

Research Director:
Hitoshi Okamura(Professor, Graduate School of Pharmaceutical Sciences, Kyoto University)

Spontaneous pattern formation ex vivo

Research Director:
Takashi Miura(Professor, Graduate School of Medical Sciences, Kyushu University)

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