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RIKEN Center for Computational Science Biomedical Computational Intelligence Unit

Unit Leader: Yasushi Okuno (Ph.D.)

Research Summary

Yasushi Okuno (Ph.D.)
  • 1.Elucidation of structure, dynamics, and function of biomolecules by integrating of simulation, AI and experiments
  • 2.Development of network approach for elucidation of disease mechanisms and identification of target molecules for drug discovery
  • 3.Development of AI and simulation technologies for translational research between clinical and basic research

Main Research Fields

  • Medicine, Dentistry & Pharmacy

Related Research Fields

  • Informatics
  • Complex Systems
  • Interdisciplinary Science & Engineering


  • Medicine
  • Drug Discovery
  • Artificial Intelligence
  • Simulation
  • Translational Research

Selected Publications

  • 1. Nakamura K, Kojima R, Uchino E, Ono K, Yanagita M, Murashita K, Itoh K, Nakaji S, Okuno Y:
    "Health improvement framework for actionable treatment planning using a surrogate Bayesian model"
    Nature Communications. 12:3088, 2021.
  • 2. Matsumoto S, Ishida S, Araki M, Kato T, Terayama K, Okuno Y:
    "Extraction of protein dynamics information from cryo-EM maps using deep learning"
    Nature Machine Intelligence. 3:153-160, 2021.
  • 3. Tanaka, Y, Higashihara, K, Nakazawa, M.A, Yamashita F, Tamada Y, Okuno Y
    "Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection"
    Scientific Reports. 11:11241, 2021.
  • 4. Kojima R, Ishida S, Ohta, M, Iwata H, Honma T, Okuno Y:
    "kGCN: a graph-based deep learning framework for chemical structure"
    Journal of Cheminformatics. 12:32, 2020.
  • 5. Tanaka Y, Tamada Y, Ikeguchi M, Yamashita F, Okuno Y:
    "System-based differential gene network analysis for characterizing sample-specific subnetwork"
    Biomolecules. 10(2):306, 2020.
  • 6. Tokuhisa, A, Kanada, R, Chiba, S, Terayama K, Isaka Y, Ma B, Kamiya N, Okuno Y
    "Coarse-grained diffraction template matching model to retrieve multiconformational models for biomolecule structures from noisy diffraction patterns"
    Journal of Chemical Information and Modeling. 60(6): 2803-2818, 2020.
  • 7. Matsumoto S, Araki M, Isaka Y, Ono F, Hirohashi K, Ohashi S, Muto M, Okuno Y:
    "E487K-induced disorder in functionally relevant dynamics of mitochondrial aldehyde dehydrogenase 2"
    Biophysical Journal. 119(3):628-637, 2020.
  • 8. Ishida S, Terayama K, Kojima R, Takasu K, Okuno Y:
    "Prediction and interpretable visualization of retrosynthetic reactions using graph convolutional networks"
    Journal of Chemical Information and Modeling. 59 (12):5026-5033, 2019.
  • 9. Terayama K, Tamura R, Nose Y, Hiramatsu H, Hosono H, Okuno Y, Tsuda K:
    "Efficient construction method for phase diagrams using uncertainty sampling"
    Physical Review Materials. 3(3):033802, 2019.
  • 10. Terayama K, Iwata H, Araki M, Okuno Y, Tsuda K:
    "Machine learning accelerates MD-based binding-pose prediction between ligands and proteins"
    Bioinformatics. 34(5):770-778, 2018.

Related Links

Lab Members

Principal investigator

Yasushi Okuno
Unit Leader

Core members

Atsushi Tokuhisa
Senior Scientist
Biao Ma
Research Scientist

Contact Information

7-1-26, Minatojima-minami-machi,
Chuo-ku, Kobe,Hyogo
650-0047, Japan
Email: yasushi.okuno [at] riken.jp