Takaki Yamamoto

Takaki Yamamoto

  • AI
    graph neural network
    image recognition
    non-equilibrium physics
    biophysics

  • Department

  • Biography

    • Ph.D. in Physics

    • 2024-

      Toyota Motor Corporation

    • 2024-

      Visiting researcher, RIKEN Center for Biosystems Dynamics Research

    • 2017-
      2024

      Research scientist, RIKEN Center for Biosystems Dynamics Research

    • 2019

      Visiting researcher, Physics Department, Syracuse University (USA).

    • 2014-
      2017

      Ph.D., Department of Physics, Graduate School of Science, the University of Tokyo

    • 2012-
      2014

      M.S., Department of Physics, Graduate School of Science, the University of Tokyo

    • 2011-
      2012

      Department of Chemistry, Graduate School of Science, the University of Tokyo (transitioned to physics after 1 year)

    • 2007-
      2011

      B.S., Department of chemistry & biotechnology, Engineering, the University of Tokyo

  • Publication List/Conference presentation

    Publication

    • [14] Takaki Yamamoto, Tomoki Ishibashi, Yuko Mimori-Kiyosue, Sylvain Hiver, Naoko Tokushige, Mitsusuke Tarama, Masatoshi Takeichi, Tatsuo Shibata,
      “Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton”, bioRxiv, 2023.08.16.553476 (2023).

    • [13] Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi,
      “Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks”, PLOS Computational Biology, 18(9):e1010477 (2022).

    • [12] Takaki Yamamoto, Daniel M. Sussman, Tatsuo Shibata and M. Lisa Manning,
      "Non-monotonic fluidization generated by fluctuating edge tensions in confluent tissues”, Soft matter, 18, 2168 (2022).

    • [11] John Devany, Daniel M. Sussman, Takaki Yamamoto, M. Lisa Manning, Margaret L. Gardel,
      "Cell cycle-dependent active stress drives epithelia remodeling”, Proceedings of National Academy of Science, 118, 10 (2021).

    • [10] Ritsuko Morita, Noriko Sanzen, Hiroko Sasaki, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Takaki Yamamoto, Tatsuo Shibata, Takaya Abe, Hiroshi Kiyonari, Yasuhide Furuta, Itoshi Nikaido, Hironobu Fujiwara,
      "Tracing the origin of hair follicle stem cells”, Nature, 594, 547 (2021).

    • [9] Hiroko Saito, Fumiko Matsukawa-Usami, Toshihiko Fujimori, Toshiya Kimura, Takahiro Ide, Takaki Yamamoto, Tatsuo Shibata, Kenta Onoue, Satoko Okayama, Shigenobu Yonemura, Kazuyo Misaki, Mika Toya, Masatoshi Takeichi,
      “Tracheal motile cilia in mice require CAMSAP3 for the formation of central microtubule pair and coordinated beating”, Molecular Biology of the Cell, 32, 20 (2021).

    • [8] Takaki Yamamoto, Tetsuya Hiraiwa and Tatsuo Shibata,
      “Collective cell migration of epithelial cells driven by chiral torque generation”, Physical Review Research, 2, 043326 (2020).

    • [7] Masayuki Ozawa, Sylvain Hiver, Takaki Yamamoto, Tatsuo Shibata, Srigokul Upadhyayula, Yuko Mimori-Kiyosue, Masatoshi Takeichi,
      “Adherens junction serves to generate cryptic lamellipodia required for collective migration of epithelial cells”, Journal of Cell Biology, 219 (10) (2020).

    • [6] Federico lancia, Takaki Yamamoto, Alexander Ryabchun, Tadatsugu Yamaguchi, Masaki Sano, Nathalie Katsonis,
      “Reorientation behavior in the helical motility of light-responsive spiral droplets”, Nature Communications, 10, 5238 (2019).

    • [5] Takaki Yamamoto and Masaki Sano,
      “Hydrodynamic rotlet dipole driven by spinning chiral liquid crystal droplets”, Physical Review E, 99, 022704 (2019).

    • [4] Takaki Yamamoto and Masaki Sano,
      “Theoretical model of chirality-induced helical self-propulsion”, Physical Review E, 97, 012607 (2018).

    • [3] Takaki Yamamoto and Masaki Sano,
      “Chirality-induced helical self-propulsion of cholesteric liquid crystal droplets”, Soft Matter, 13, 3328 (2017).

    • [2] Takaki Yamamoto, Masafumi Kuroda, and Masaki Sano,
      “Three-dimensional analysis of thermo-mechanically rotating cholesteric liquid crystal droplets under a temperature gradient”, Europhysics Letters, 109, 46001 (2015).

    • [1] Takaki Yamamoto, Junichi Hatano, Takafumi Nakagawa, Shigeru Yamaguchi, and Yutaka Matsuo,
      “Small molecule solution-process bulk heterojunction solar cells with inverted structure using porphyrin donor”, Applied Physics Letters, 102, 013305 (2013).

  • Selected talks

    • Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi, “Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks”, STATPHYS28 (2023)

    • Takaki Yamamoto, Daniel M. Sussman, Tatsuo Shibata and M. Lisa Manning, “Non-monotonic fluidization generated by fluctuating edge tensions in confluent tissues”, RIKEN BDR symposium 2021 (2021).

    • Takaki Yamamoto, Tetsuya Hiraiwa and Tatsuo Shibata, “Collective cell migration of epithelial cells driven by chiral torque generation”, EMBO Workshop Physics of living systems: From molecules to tissues (2021).

    • Takaki Yamamoto and Masaki Sano, “Chirality-induced helical self-propulsion of cholesteric liquid crystal droplets”, STATPHYS26 (France, Lyon) (2016).

  • Commendation/Memberships

    Awards

    • Best poster prize@International WE-Heraeus Physics School on "Model systems for understanding biological processes", Germany (2015)

    • Bronze medal@iGEM 2009: international contest of synthetic biology, USA (2009).

Members List