Centers & Labs

RIKEN Quantitative Biology Center

Laboratory for Developmental Dynamics

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

Biological Sciences

Related Research Fields



  • 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., and Onami, S.:
    "Biologically constrained optimization based cell membrane segmentation in C. elegans embryos"
    BMC Bioinformatics 18, 307 (2017).
  2. Takayama, J., Fujita, M., and Onami, S.:
    "In vivo live imaging of calcium waves and other cellular processes during fertilization in Caenorhabditis elegans"
    Bio Protoc. 7, e2205 (2017)
  3. Takayama, J., and Onami, S.:
    "The sperm TRP-3 channel mediates the onset of a Ca2+ wave in the fertilized C. elegans oocyte"
    Cell Rep. 15, 625-637 (2016)
  4. Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami, S.:
    "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena"
    Bioinformatics 33, 3471-3479 (2016)
  5. 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, 1044-1052 (2015)
  6. Azuma, Y., and Onami, S.:
    "Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images"
    BMC Bioinformatics 14, 295 (2013)
  7. 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 Res. 41, D732-D737 (2013)
  8. Shimozawa, T., Yamagata, K., Kondo, T., Hayashi, S., Shitamukai, A., Konno, D., Matsuzaki, F., Takayama, J., Onami, S., Nakayama, H., Kosugi, Y., Watanabe, T. M., Fujita, K., and Mimori-Kiyosue, Y.:
    "Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging"
    Proc. Natl. Acad. Sci. U.S.A. 110, 3399-3404 (2013)
  9. Fujita, M., and Onami, S.:
    "Cell-to-Cell Heterogeneity in Cortical Tension Specifies Curvature of Contact Surfaces in Caenorhabditis elegans Embryos"
    PLoS One 7, 463-471 (2012)
  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"
    Dev. Cell 8, 765-775 (2005)

Lab Members

Principal Investigator

Shuichi Onami
Team Leader

Core Members

Koji Kyoda
Research Scientist
Masashi Fujita
Research Scientist
Jun Takayama
Research Scientist
Yusuke Azuma
Research Scientist
Yukako Tohsato
Research Scientist
Chamidu Atupelage
Postdoctoral Researcher
Kenneth Hung Lit Ho
Technical Staff I
Rie Furushima
Technical Staff I
Akiko Hatakeyama
Technical Staff I
Hatsumi Okada
Technical Staff II

Contact information

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

Email: sonami [at]

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