RIKEN Center for Biosystems Dynamics Research Laboratory for Developmental Dynamics
Team Director: Shuichi Onami (D.V.M., Ph.D.)
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
Related Links
Lab Members
Principal investigator
- Shuichi Onami
- Team Director
Core members
- Soya Shinkai
- Senior 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