CV

Overview

Assistant Professor at the Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba. My research aims to treat life phenomena as a hierarchical system of morphology, psychology, and behavior and to quantify them as information. Specifically, I work on quantification of morphology using deep generative models, quantification of psychological state (e.g., social stress) using mathematical models, and quantitative analysis of behavior based on inter-individual interactions, with the goal of understanding universal principles that describe the state and dynamics of life.

Contact

  • Email: mtsutsumi[at]tara.tsukuba.ac.jp
  • Address: Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan

Education

  • Ph.D. in Science, Graduate School of Science, The University of Tokyo (Apr 2020 - Sep 2023)
  • M.S. in Science, Graduate School of Science, The University of Tokyo (Apr 2018 - Mar 2020)
  • B.S. in Science, Department of Physics, Faculty of Science, The University of Tokyo (Apr 2014 - Mar 2018)

Professional Appointments

  • Assistant Professor, Life Science Center for Survival Dynamics (TARA), University of Tsukuba (Dec 2025 - Present)
  • Visiting Researcher, Graduate School of Medicine, Nagoya University (Dec 2025 - Present)
  • Designated Assistant Professor, Graduate School of Medicine, Nagoya University (Oct 2024 - Nov 2025)
  • Designated Researcher, Graduate School of Integrated Sciences for Life, Hiroshima University (Oct 2023 - Sep 2024)
  • Graduate Student Research Associate, RIKEN (Apr 2020 - Mar 2023)

Publications (Selected)

  • Disentanglement of batch effects and biological signals across conditions in the single-cell transcriptome
    Shunta Sakaguchi, Masato Tsutsumi, Kentaro Nishi, Naoki Honda. bioRxiv (2025)
  • Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation
    Yui Uchida, Masato Tsutsumi, Shunsuke Ichii, Naoki Irie, Chikara Furusawa. Evolution & Development (2024)
  • A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape
    Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa. npj Systems Biology and Applications (2023)
  • A method for morphological feature extraction based on variational auto-encoder: an application to mandible shape
    Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa. Preprint (2022)

Invited Talks (Selected)

  • Development of quantitative analysis methods for biological morphology using deep learning
    Japan Society for Industrial and Applied Mathematics Annual Meeting (2024)
  • Development of quantitative analysis methods for biological morphology using deep learning
    Online Seminar Series “Future of Evolutionary Biology with AI” (2024)
  • Development of quantitative analysis methods for biological morphology using deep learning
    8th Theoretical Immunology Workshop (2024)

Conference Presentations (Selected)

  • Behavioral analysis of double mutant Drosophila larvae using DOLO (Drosophila tracking with YOLO)
    1st Systems Behavioral Science Workshop (2025)
  • Estimation of psychological state transitions during/after emergency declarations using energy landscape analysis
    SSTB2025 - Spring School for Theoretical Biology (2025)
  • Proposal of morphological quantitative analysis methods using deep learning
    Annual Meeting of the Japanese Society for Mathematical Biology (2024)
  • Quantification of mouse behavior under social defeat stress using mathematical models
    CPSY TOKYO (2024)

Grants & Awards

  • Takeda Science Foundation Medical Research Grant (2025)

Teaching

  • Basic Medical Seminar, Nagoya University (2024)
  • Medical Data Science I, Nagoya University (2025)

For the full publication and presentation list, see the Publications page and researchmap.