Laboratory for Developmental Dynamics | RIKEN BDR

Laboratory for Developmental Dynamics

Team Leader

Shuichi OnamiD.V.M., Ph.D.

Photo of principal investigator

  • Location:Kobe / Developmental Biology Buildings
  • E-mail:sonami[at]riken.jpPlease replace [at] with @.
  • Lab Website

Research Summary

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 Theme

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

Main Publications List

  • Hirata T, Tohsato Y, Itoga H, et al.
    NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons.
    Cell Reports Methods 1, 100012 (2021) doi: 10.1016/j.crmeth.2021.100012
  • Swedlow JR, Kankaanpää P, Sarkans U, et al.
    A global view of standards for open image data formats and repositories.
    Nature Methods (2021) doi: 10.1038/s41592-021-01113-7
  • Shinkai S, Nakagawa M, Sugawara T, et al.
    PHi-C: deciphering Hi-C data into polymer dynamics.
    NAR Genomics and Bioinformatics 2, lqaa020 (2020) doi: 10.1093/nargab/lqaa020
  • Shinkai S, Sugawara T, Miura H, et al.
    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
  • Onoue Y, Kyoda K, Kioka M, et al.
    Development of an integrated visualization system for phenotype character networks.
    2018 IEEE Pacific Visualization Symposium (PacificVis), 21-25 (2018) doi: 10.1109/PacificVis.2018.00012
  • Azuma Y, 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
  • Tohsato Y, Ho KHL, Kyoda K, 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
  • 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(3), 625-637 (2016) doi: 10.1016/j.celrep.2016.03.040
  • Kyoda K, Tohsato Y, Ho KHL, 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
  • Azuma Y, 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
  • Kyoda K, Adachi E, Masuda E, et al.
    WDDD: Worm developmental dynamics database.
    Nucleic Acids Research 41, D732-D737 (2013) doi: 10.1093/nar/gks1107
  • Kimura A, 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