Research Articles – 石原研究室 Ishihara Lab.

X. Yan, G. Ogita, S. Ishihara and K. Sugimura. Bayesian parameter inference for epithelial mechanics. submitted accepted in J. Theor. Biol. / bioRxiv
R. Nishide and S. Ishihara. Oscillatory and chaotic pattern dynamics driven by surface curvature. submitted arXive:e2403,12442
R. Nishide and S. Ishihara. Weakly nonlinear analysis of Turing pattern dynamics on curved surfaces. submitted arXive:e2403.12444
E. Gauquelin, K. Kuromiya, T. Namba, K. Ikawa, Y. Fujita, S. Ishihara# and K. Sugimura# (# corresponding authors). Mechanical convergence in mixed populations of mammalian epithelial cells. Eur. Phys. J. E. 47, 21 (2024)
S. Yamashita, S. Ishihara and F. Graner. Apical constriction requires patterned apical surface remodeling to synchronize cellular deformation. eLife https://doi.org/10.7554/eLife.93496.1 (2024) / bioRxiv
N. Saito and S. Ishihara, Active Deformable Cells Undergo Cell Shape Transition Associated with Percolation of Topological Defects. Science Advances, 10 eadi8433 (2024) / arXive
K. Ikawa#, S. Ishihara, Y. Tamori, and K. Sugimura#. (# corresponding authors) Attachment/detachment of cortical myosin regulates cell junction exchange during cell rearrangement. Current Biology, 33 (2), 263-275. e4 (2023)
R. Nishide and S. Ishihara, Pattern Propagation Driven by Surface Curvature. Phys. Rev. Lett., 128, 224101 (2022)　Editors’ suggestion. On the cover
G. Ogita, T. Kondo, K. Ikawa, T. Uemura, S. Ishihara#, and K. Sugimura# (# Corresponding authors) Image-based parameter inference for epithelial mechanics. PLoS Comput. Biol. 18(6): e1010209 (2022).
M. Tateno and S. Ishihara, Interfacial-curvature-driven coarsening in mass-conserved reaction-diffusion systems. Phys. Rev. Res. 3, 023198 (2021)
S. Nakayama, T. Yano , T. Namba, S. Konishi, M. Takagishi, E. Herawati, T. Nishida, Y. Imoto, S. Ishihara, M. Takahashi, K. Furuta, K. Oiwa, A. Tamura, S. Tsukita. Planar cell polarity induces local microtubule bundling for coordinated ciliary beating. J. Cell Biol. 220 (7), e20201003 (2021)
T. Namba, S. Ishihara. Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells. PLoS Compt. Biol.16 (2), e1007649 (2020)
V. Nier, G. Peyret, J. d’Alessandro, S. Ishihara, B. Ladoux, and P. Marcq. Kalman inversion stress microscopy. Biophys. J. 115, 1808-1816 (2018)
S. Ishihara, P. Marcq, and K. Sugimura. From cells to tissue: A continuum model of epithelial mechanics. Phys. Rev. E 96 022418 (2017)
E. Herawati*, D.Taniguchi*, H. Kanoh, K. Tateishi, S. Ishihara and S. Tsukita. (*equal contribution) Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton. J. Cell Bilol. 214, 571-586 (2016)
T. Torisawa*, D. Taniguchi*, S. Ishihara, and K. Oiwa. (*equal contribution) Spontaneous Formation of a Globally Connected Contractile Network in a Microtubule-Motor System. Biophys. J. 111, 373-385 (2016) On the cover
H. Nogucci and S. Ishihara. Collective dynamics of active filament complexes. Phys. Rev. E 93, 052406 (2016)
V. Nier, S. Jain, C. T. Lim, S. Ishihara, B. Ladoux, P. Marcq. Inference of Internal Stress in a Cell Monolayer. Biophys. J 110, 1625-1635 (2016)
B. Guirao, S. U. Rigaude, F. Bosveld, A. Bailles, J. Lopez-Gay, S. Ishihara, K. Sugimura, F. Graner, Y. Bellaïche. Unified quantitative characterization of epithelial tissue development. eLife 4:e08519 (2015)
A. Nakajima, S. Ishihara, D. Imoto and S. Sawai. Rectified directional sensing in long-range cell migration. Nat. Comm., 5, 5367 (2014)
N. Saito, S. Ishihara and K. Kaneko. Evolution of Genetic Redundancy : The Relevance of Complexity in Genotype-Phenotype Mapping. New J. Phys. 16, 063013 (2014)
K. Sugimura# and S. Ishihara#. (#corresponding authors) The mechanical anisotropy in a tissue promotes ordering in hexagonal cell packing. Development, 140 4091-4101 (2013)
D. Taniguchi, S. Ishihara, T. Oonuki, M. Honda-Kitahara, K. Kaneko and S. Sawai. Phase geometries of two-dimensional excitable waves govern self-organized morphodynamics of amoeboid cells. PNAS 110(13)5016-5021
N. Saito, S. Ishihara and K. Kaneko. The Baldwin effect under multi-peaked fitness landscapes: Phenotypic fluctuation accelerates evolutionary rate. Phys. Rev. E, 87, 052701 (2013)
K. Sugimura, Y. Bellaïche, F. Graner, P. Marcq and S. Ishihara. Robustness of force and stress inference in an epithelial tissue. Conf Proc IEEE Eng Med Biol Soc, 10.1109/EMBC.2013.6610100.
S. Ishihara, K. Sugimura, S.J. Cox, I. Bonnet, Y. Bellaïche and F. Graner. Comparative study of non-invasive force and stress inference in tissue. Eur. Phys. J. E 36, 45 (2013), in topical issue `Physical constraints of morphogenesis and evolution’, selected for front cover of the journal
Y. Kondo, K. Kaneko and S. Ishihara. Identifying dynamical systems with bifurcations from noisy partial observation. Phys. Rev. E 87, 042716 (2013)
H. Sano, P.S. Kunwar, A.D. Renault, V. Barbosa, I.B.N. Clark, S. Ishihara, K. Sugimura and R. Lehmann. The Drosophila actin regulator ENABLED regulates cell shape and orientation during gonad morphogenesis. PLoS One 7: e52649 (2012)
S. Ishihara# and K. Sugimura#. (#corresponding authors) Bayesian inference of force dynamics during morphogenesis. J. Theor. Biol., 313: 201-211 (2012).
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A. Nakajima and S. Ishihara. Kinetics of the cellular Potts model revisited. New Jour. Phys. 3, 033035 (2011)
M. Otsuji, Y. Terashima, S. Ishihara, S. Kuroda and K. Matsushima. A Conceptual Molecular Network for Chemotactic Behaviors Characterized by Feedback of Molecules Cycling Between the Membrane and the Cytosol. Sci. Signal. 3, ra89 (2010)
A. Nakajima, T. Isshiki, K. Kaneko and S. Ishihara. Robustness under Functional Constraint: The Genetic Network for Temporal Expression in Drosophila Neurogenesis. PLoS Compt Biol 6(4): e1000760 (2010)
K. Fujimoto, S. Ishihara and K. Kaneko. Network Evolution of Body Plans. PLoS One 3(7): e2772 (2008)
S. Ishihara and T. Shibata. Mutual interaction in network motifs robustly sharpens gene expression in developmental processes. J. Theor. Biol. 252 131-144 (2008)
M. Otsuji, S. Ishihara, C. Co, K. Kaibuchi, A. Mochizuki and S. Kuroda. A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity. PLoS Comput Biol 3(6): e108. (2007)
S. Ishihara, M. Otsuji and A. Mochizuki. Transient and steady state of mass-conserved reaction-diffusion systems. Phys. Rev. E 75 015203(R) (2007)
S. Ishihara and K. Kaneko Turing pattern with proportion preservation. J. Theor. Biol. 238 683-693 (2006)
S. Ishihara, K. Fujimoto and T. Shibata. Cross-talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes to Cells 10 1025- (2005)
S. Ishihara and K. Kaneko. Magic number 7 ± 2 in networks of threshold dynamics. Phys. Rev. Lett. 94 058102 (2005)
S. Ishihara and K. Kaneko. Simple Dynamical Model with History Dependence. J. Phys. Soc. Jpn. 71 2357- (2002)

石原秀至「質量保存の下での反応拡散系のダイナミクス」 (第5回生物数学の理論とその応用,研究会報告)京都大学数理解析研究所講究録 1663, 41-46, 2009-09
石原秀至「Network motifによる遺伝子発現調節」(動的システムの情報論4-シグナル伝達とコミュニケーション-,研究会報告)物性研究 84 624 (2005)
石原秀至　「多重定常状態の履歴依存性」(修士論文(2000年度))物性研究 77 153 (2001)

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