BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.



BDR communicates the appeal and significance of our research to society through the use of various media and activities.



From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Shuichi Onami

Team Leader
Shuichi Onami D.V.M., Ph.D.

Laboratory for Developmental Dynamics

LocationKobe / Developmental Biology Buildings


Please replace [at] with @.

Recruiting graduate students

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

Selected Publications

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 18, 1440-1446 (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

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