RIKEN Center for Biosystems Dynamics Research Laboratory for Developmental Dynamics

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

Japanese Page

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.

Main Research Fields

Biological Sciences

Related Research Fields

Informatics

Keywords

Data-driven modeling
Computer simulation
Bioimage informatics
C. elegans
Database

Selected Publications

1. Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., and Onami, S.:
"SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data"
Nucleic Acids Res. gkae860 (2024). doi: 10.1093/nar/gkae860
2. Shinkai, S., Onami, S., and Miyaguchi, T.:
"Generalized Langevin dynamics for single beads in linear elastic networks"
Phys. Rev. E 110(4), 044136 (2024). doi: 10.1103/PhysRevE.110.044136
3. Nozaki, T., Shinkai, S., Ide, S., Higashi, K., Tamura, S., Shimazoe, M. A., Nakagawa, M., Suzuki, Y., Okada, Y., Sasai, M., Onami, S., Kurokawa, K., Iida, S., and Maeshima, K.:
"Condensed but liquid-like domain organization of active chromatin regions in living human cells"
Sci. Adv. 9(14), eadf1488 (2023). doi: 10.1126/sciadv.adf1488
4. Hirata, T., Tohsato, Y., Itoga, H., Shioi, G., Kiyonari, H., Oka, S., Fujimori, T., and Onami, S.:
"NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons"
Cell Rep. Methods 1(3), 100012 (2021). doi: 10.1016/j.crmeth.2021.100012
5. Swedlow, J. R., Kankaanpää, P., Sarkans, U., Goscinski, W., Galloway, G., Malacrida, L., Sullivan, R. P., Härtel, S., Brown, C. M., Wood, C., Keppler, A., Paina, F., Loos, B., Zullino, S., Longo, D. L., Aime, S., and Onami, S.:
"A global view of standards for open image data formats and repositories"
Nat. Methods 18(12), 1440-1446 (2021). doi: 10.1038/s41592-021-01113-7
6. 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 Genom. Bioinform. 2(2), lqaa020 (2020). doi: 10.1093/nargab/lqaa020
7. 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(3), 625-637 (2016). doi: 10.1016/j.celrep.2016.03.040
8. 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
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 Res. 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"
Dev. Cell 8, 765-775 (2005). doi: 10.1016/j.devcel.2005.03.007

Lab Members

Principal investigator

Shuichi Onami: Team Director

Core members

Soya Shinkai: Senior Research Scientist
Ko Sugawara: Research Scientist
Chentao Wen: Special Postdoctoral Researcher
Yukihiko Kubota: Visiting Scientist
Yukako Tohsato: Visiting Scientist
Hiroya Itoga: Technical Scientist
Koji Kyoda: Technical Scientist
Shiori Onoue: Research Associate
Isseki Maeda: Student Trainee
Hatsumi Okada: Technical Staff I
Hiroki Nakajima: Technical Staff I
Rie Furushima: Technical Staff I
Haruna Yamamoto: Technical Staff II
Emi Fujisawa: Research Part-time Worker I
Soya Hagiwara: Research Part-time Worker II

Careers

Position	Deadline
Seeking a Research Scientist, Postdoctoral Researcher, or Technical Scientist (BDR-23-067)	Open until filled

Contact Information

2-2-3 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan
Email: sonami@riken.jp