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RIKEN Center for Biosystems Dynamics Research Laboratory for Developmental Dynamics

Team Leader: Shuichi Onami (D.V.M., Ph.D.)

Research Summary

Shuichi  Onami(D.V.M., Ph.D.)

The development of multicellular organisms is a spatially and temporally dynamic process. A single cell, the fertilized egg, divides many times to generate many functionally different cells, each of which is brought to a specific position to produce complex multicellular structures, i.e. organs and the body. An effective approach to such spatially and temporally dynamic processes is an approach that combines quantitative techniques with modeling and computer simulations. To understand the mechanism of organism development, we are developing mathematical models for developmental systems like the C. elegans embryo, mouse embryo and three-dimensional cell culture systems, by combining molecular cell biology and genome science with biophysics and computer science methods.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Informatics


  • Data-driven modeling
  • Computer simulation
  • Bioimage informatics
  • C. elegans
  • Database

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

  • 1. Azuma, Y., Okada, H., and Onami, S.:
    "Systematic analysis of cell morphodynamics in C. elegans early embryogenesis"
    Frontiers in Bioinformatics 3, 1082531 (2023). doi: 10.3389/fbinf.2023.1082531
  • 2. Shinkai, S., Itoga, H., Kyoda, K., and Onami, S.:
    "PHi-C2: interpreting Hi-C data as the dynamic 3D genome state"
    Bioinformatics 38(21), 4984-4986 (2022). doi: 10.1093/bioinformatics/btac613
  • 3. Iida, S., Shinkai, S., Itoh, Y., Tamura, S., Kanemaki, M. T., Onami, S., and Maeshima, K.:
    "Single nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells"
    Science advances 8(22), eabn5626 (2022). doi: 10.1126/sciadv.abn5626
  • 4. Hirata, T., Tohsato, Y., Itoga, H., Shioi, G., Kiyonari, H., Oka, S., Fujimori, T., and Onami, S.:
    "NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons"
    Cell Reports Methods 1(3), 100012 (2021). doi: 10.1016/j.crmeth.2021.100012
  • 5. Swedlow, J. R., Kankaanpää, P., Sarkans, U., Goscinski, W., Galloway, G., Malacrida, L., Sullivan, R. P., Härtel, S., Brown, C. M., Wood, C., Keppler, A., Paina, F., Loos, B., Zullino, S., Longo, D. L., Aime, S., and Onami, S.:
    "A global view of standards for open image data formats and repositories"
    Nature Methods 18(12), 1440-1446 (2021). doi: 10.1038/s41592-021-01113-7
  • 6. Shinkai, S., Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Taniguchi, Y., and Onami, S.:
    "PHi-C: deciphering Hi-C data into polymer dynamics"
    NAR Genomics and Bioinformatics 2(2), lqaa020 (2020). doi: 10.1093/nargab/lqaa020
  • 7. Takayama, J., and Onami, S.:
    "The sperm TRP-3 channel mediates the onset of a Ca2+ wave in the fertilized C. elegans oocyte"
    Cell Reports 15(3), 625-637 (2016). doi: 10.1016/j.celrep.2016.03.040
  • 8. Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami, S.:
    "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena"
    Bioinformatics 32(22), 3471-3479 (2016). doi: 10.1093/bioinformatics/btw417
  • 9. Kyoda, K., Adachi, E., Masuda, E., Nagai, Y., Suzuki, Y., Oguro, T., Urai, M., Arai, R., Furukawa, M., Shimada, K., Kuramochi, J., Nagai, E., and Onami, S.:
    "WDDD: Worm developmental dynamics database"
    Nucleic Acids Research 41(0), D732-D737 (2013). doi: 10.1093/nar/gks1107
  • 10. Kimura, A., and Onami, S.:
    "Computer simulations and image processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration"
    Developmental Cell 8, 765-775 (2005). doi: 10.1016/j.devcel.2005.03.007

Related Links

Lab Members

Principal investigator

Shuichi Onami
Team Leader

Core members

Soya Shinkai
Senior Scientist
Ko Sugawara
Research Scientist
Akiko Hatakeyama
Research Scientist
Chentao Wen
Special Postdoctoral Researcher
Yukihiko Kubota
Visiting Scientist
Yukako Tohsato
Visiting Scientist
Hiroya Itoga
Technical Scientist
Koji Kyoda
Technical Scientist
Miguel Miranda
Technical Scientist
Shiori Onoue
Student Trainee
Isseki Maeda
Student Trainee
Hatsumi Okada
Technical Staff I
Rie Furushima
Technical Staff I
Haruna Yamamoto
Technical Staff II
Emi Fujisawa
Temporary Staffing


Position Deadline
Seeking a Research Part-time Woker (BDR-23-072) Open until filled
Seeking a Research Scientist, or Postdoctoral Researcher (BDR-23-068) Open until filled
Seeking a Research Scientist, Postdoctoral Researcher, or Technical Scientist (BDR-23-067) Open until filled
Seeking a Technical Staff (BDR-23-002) Open until filled

Contact Information

2-2-3 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan

Email: sonami [at] riken.jp