Team Leader
Tatsuo Shibata
Ph.D.
Laboratory for Physical Biology
LocationKobe / Developmental Biology Buildings
E-mailtatsuo.shibata[at]riken.jp
Please replace [at] with @.
Open Positions
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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (2012)
doi: 10.1242/jcs.108373
