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Laboratory for Developmental Dynamics

Shuichi Onami


Team Leader

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

Onami of RIKEN

Original HP

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.

Research Topics

  • System analysis of development by using large collections of quantitative dynamic information
  • Mathematical modeling of development
  • Development of technology for measuring developmental dynamics

Selected Publications

  • Azuma, Y. & Onami, S.
    "Biologically constrained optimization based cell membrane segmentation in C. elegans embryos"
    BMC Bioinf. 18, 307 (2017) doi:10.1186/s12859-017-1717-6
  • Takayama, J., Fujita, M. & Onami, S.
    "In vivo live imaging of calcium waves and other cellular processes during fertilization in Caenorhabditis elegans"
    Bio-protocol 7, e2205 (2017) doi:10.21769/BioProtoc.2205
  • Tohsato, Y., Ho, K. H. L., Kyoda, K. & Onami, S.
    "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena"
    Bioinformatics 32, 3471-3479 (2016) doi:10.1093/bioinformatics/btw417
  • Takayama, J. & Onami, S.
    "The Sperm TRP-3 Channel Mediates the Onset of a Ca2+ Wave in the Fertilized C-elegans Oocyte"
    Cell Reports 15, 625-637 (2016) doi:10.1016/j.celrep.2016.03.040
  • Kyoda, K., Tohsato, Y., Ho, K. H. L. & Onami, S.
    "Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data"
    Bioinformatics 31, 1044-1052 (2015) doi:10.1093/bioinformatics/btu767
  • Azuma, Y. & Onami, S.
    "Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images"
    BMC Bioinf. 14 (2013) doi:10.1186/1471-2105-14-295
  • Shimozawa, T., Yamagata, K., Kondo, T., Hayashi, S., Shitamukai, A., Konno, D., et al.
    "Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging"
    Proc. Natl. Acad. Sci. U.S.A. 110, 3399-3404 (2013) doi:10.1073/pnas.1216696110
  • Kyoda, K., Adachi, E., Masuda, E., Nagai, Y., Suzuki, Y., Oguro, T., et al.
    "WDDD: Worm Developmental Dynamics Database"
    Nucleic Acids Res. 41, D732-D737 (2013) doi:10.1093/nar/gks1107
  • Fujita, M. & Onami, S.
    "Cell-to-Cell Heterogeneity in Cortical Tension Specifies Curvature of Contact Surfaces in Caenorhabditis elegans Embryos"
    PLoS One 7, e30224, 463-471 (2012) doi:10.1371/journal.pone.0030224
  • Kimura, A., 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)