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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. 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, lqaa020 (2020). doi: 10.1093/nargab/lqaa020
  • 2. Shinkai, S., Sugawara, T., Miura, H., Hiratani, I., and Onami, S.:
    "Microrheology for Hi-C data reveals the spectrum of the dynamic 3D genome organization"
    Biophysical Journal 118(9), 2220-2228 (2020). doi: 10.1016/j.bpj.2020.02.020
  • 3. Onoue, Y., Kyoda, K., Kioka, M., Baba, K., Onami, S., and Koyamada, K.:
    "Development of an integrated visualization system for phenotype character networks"
    2018 IEEE Pacific Visualization Symposium (PacificVis), pp. 21-25 (2018). doi: 10.1109/PacificVis.2018.00012
  • 4. Azuma, Y., and Onami, S.:
    "Biologically constrained optimization based cell membrane segmentation in C. elegans embryos"
    BMC Bioinformatics 18, 307 (2017). doi: 10.1186/s12859-017-1717-6
  • 5. 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
  • 6. 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
  • 7. Kyoda, K., Tohsato, Y., Ho, K. H. L., and Onami, S.:
    "Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data"
    Bioinformatics 31(7), 1044-1052 (2015). doi: 10.1093/bioinformatics/btu767
  • 8. Azuma, Y., and Onami, S.:
    "Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images"
    BMC Bioinformatics 14, 295 (2013). doi: 10.1186/1471-2105-14-295
  • 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

Yusuke Azuma
Research Scientist
Koji Kyoda
Research Scientist
Soya Shinkai
Research Scientist
Bakhtiyor Nosirov
Research Scientist
Akiko Hatakeyama
Research Scientist
Yuki Yamagata
Research Scientist
Yukihiko Kubota
Visiting Scientist
Yukako Tohsato
Visiting Scientist
Akihiro Mori
Visiting Scientist
Hiroya Itoga
Technical Scientist
Kenneth Hung Lit Ho
Technical Scientist
Shiori Onoue
Junior Research Associate
Momoko Imakubo
Student Trainee
Natsumi Ota
Student Trainee
Fangfang Wang
Technical Staff II
Hatsumi Okada
Technical Staff II
Rie Furushima
Technical Staff II

Contact Information

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

Email: sonami [at] riken.jp