Team Leader
Tatsuo Shibata
Ph.D.
Laboratory for Physical Biology
LocationKobe / Developmental Biology Buildings
E-mailtatsuo.shibata[at]riken.jp
Please replace [at] with @.
Advances in measurement technologies have afforded us glimpses into dynamic functional processes, such as morphogenesis and information processing, in cells and tissues involved in development and regeneration. The truly organic dynamism of the biological phenomena exhibited by living cells, individually or in groups, emerges from the coordinated interaction of numerous molecular and genetic factors, and the need for integrated, systems-based approaches to the study of design and operating principles in such “living” phenomena is becoming increasingly clear. This will require not only technologies for the measurement of such elements but the development of applicable mathematical methods as well. In Laboratory for Physical Biology, we will seek to use concepts and methodology from mathematical sciences such as physics in the study and elucidation of these emerging questions in biology.
Research Theme
- Dynamics of information processes of chemotaxis
- Dynamics of polarization
- Dynamics of gene regulatory networks
Selected Publications
Tarama M, Shibata T.
Pattern formation and the mechanics of a motor-driven filamentous system confined by rigid membranes.
Physical Review Research
4, 043071 Mon Oct 31 00:00:00 JST 2022
doi: 10.1103/PhysRevResearch.4.043071
Wen FL, Kwan CW, Wang YC, Shibata T.
Autonomous epithelial folding induced by an intracellular mechano–polarity feedback loop.
PLOS Computational Biology
17(12), e1009614 Mon Dec 06 00:00:00 JST 2021
doi: 10.1371/journal.pcbi.1009614
Hayakawa M, Hiraiwa T, Wada Y, et al.
Polar pattern formation induced by contact following locomotion in a multicellular system.
eLife
9, e53609 Tue Dec 01 00:00:00 JST 2020
doi: 10.7554/eLife.53609
Kono K, Yoshiura S, Fujita I, et al.
Reconstruction of Par-dependent polarity in apolar cells reveals a dynamic process of cortical polarization.
eLife
8, e45559 Sun Dec 01 00:00:00 JST 2019
doi: 10.7554/eLife.45559.001
Sekine R, Shibata T, Ebisuya M.
Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty.
Nature communications
9(1), 5456 Sat Dec 01 00:00:00 JST 2018
doi: 10.1038/s41467-018-07847-x
Ogura Y, Wen FL, Sami MM, et al.
A Switch-like Activation Relay of EGFR-ERK Signaling Regulates a Wave of Cellular Contractility for Epithelial Invagination.
Developmental cell
46(2), 162-172 Mon Jul 16 00:00:00 JST 2018
doi: 10.1016/j.devcel.2018.06.004
Wen FL, Wang YC, Shibata T.
Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects.
Biophysical journal
112(12), 2683-2695 Tue Jun 20 00:00:00 JST 2017
doi: 10.1016/j.bpj.2017.05.012
Sato K, Hiraiwa T, Maekawa E, et al.
Left–right asymmetric cell intercalation drives directional collective cell movement in epithelial morphogenesis.
Nature Communications
6, 10074 Tue Dec 01 00:00:00 JST 2015
doi: 10.1038/ncomms10074
Sato K, Hiraiwa T, Shibata T.
Cell Chirality Induces Collective Cell Migration in Epithelial Sheets.
Physical Review Letters
115(18), 188102 Sun Nov 01 00:00:00 JST 2015
doi: 10.1103/PhysRevLett.115.188102
Hiraiwa T, Nagamatsu A, Akuzawa N, et al.
Relevance of intracellular polarity to accuracy of eukaryotic chemotaxis.
Physical Biology
11(5), 056002 Mon Dec 01 00:00:00 JST 2014
doi: 10.1088/1478-3975/11/5/056002
Nishikawa M, Horning M, Ueda M, Shibata T.
Excitable Signal Transduction Induces Both Spontaneous and Directional Cell Asymmetries in the Phosphatidylinositol Lipid Signaling System for Eukaryotic Chemotaxis.
Biophysical Journal
106(3), 723-734 Sat Nov 01 00:00:00 JST 2014
doi: 10.1016/j.bpj.2013.12.023
Shibata T, Nishikawa M, Matsuoka S, Ueda M.
Intracellular Encoding of Spatiotemporal Guidance Cues in a Self-Organizing Signaling System for Chemotaxis in Dictyostelium Cells.
Biophysical Journal
105(9), 2199-2209 Sun Dec 01 00:00:00 JST 2013
doi: 10.1016/j.bpj.2013.09.024
Inomata H, Shibata T, Haraguchi T, Sasai Y.
Scaling of Dorsal-Ventral Patterning by Embryo Size-Dependent Degradation of Spemann's Organizer Signals.
Cell
153(6), 1296-1311 Fri Nov 01 00:00:00 JST 2013
doi: 10.1016/j.cell.2013.05.004
Hiraiwa T, Baba A, Shibata T.
Theoretical model for cell migration with gradient sensing and shape deformation.
European Physical Journal E
36(4), 32 9 Tue Oct 01 00:00:00 JST 2013
doi: 10.1140/epje/i2013-13032-1
Baba A, Hiraiwa T, Shibata T.
Directional sensing of deformed cells under faint gradients.
Physical Review E
86(6), 060901 5 Sat Dec 01 00:00:00 JST 2012
doi: 10.1103/PhysRevE.86.060901
Shibata T, Nishikawa M, Matsuoka S, Ueda M.
Modeling the self-organized phosphatidylinositol lipid signaling system in chemotactic cells using quantitative image analysis.
Journal of Cell Science
125(21), 5138-5150 Thu Nov 01 00:00:00 JST 2012
doi: 10.1242/jcs.108373