Team Leader
Shuichi Onami
D.V.M., Ph.D.
Laboratory for Developmental Dynamics
LocationKobe / Developmental Biology Buildings
E-mailsonami[at]riken.jp
Please replace [at] with @.
Open Positions
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
