Laboratory for Developmental Dynamics, RIKEN BDR
We are pleased to announce that a new paper by Koji Kyoda, a Research Scientist in Onami lab, et al. was published in PLOS ONE.
In this paper, we developed the BD5, a new binary data format based on HDF5. It can be used to represent quantitative data of biological dynamics obtained from bioimage informatics techniques and mechanobiological simulations. BD5 allows fast access to quantitative data and fast transfer of files containing large quantitative data.
A press release introducing the PHi-C, an original simulation method of the Hi-C data analysis by Dr. Soya Shinkai, has been issued.
We have discovered a formula that links the contact probability in Hi-C matrix data and the interaction parameter of the polymer network model. Using Hi-C matrix data as input, the PHi-C method allows for the simulation of the dynamic 3D genome in living cells.
Read the full press release article regarding PHi-C in Japanese on RIKEN website.
Soya Shinkai, et al. (2020) PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genom. Bioinform. doi: 10.1093/nargab/lqaa020
The 2020 OME Community Meeting was held virtually. Team Leader Dr. Onami gave a video talk regarding SSBD:tdatabase and SSBD:repository.
To check his presentation, please visit our MULTIMEDIA page.
Or visit https://www.openmicroscopy.org/events/ome-community-meeting-2020/.
We are pleased to announce that a new paper by Soya Shinkai , a Research Scientist in Onami lab, and Takeshi Sugawara at University Tokyo, et al. was published in Biophysical Journal.
In this paper, we characterize the dynamic viscoelastic properties of a chromosome by using Hi-C data. Boundaries of known megabase-scale chromatin domains are more rigid than sequences inside these domains. The dynamic and hierarchical emergence of chromatin domains depends on the rheological feature of a chromosome.
An article in Nature featured image data sharing in Life Science.
Our SSBD: database /repository was introduced as one of the representative databases with IDR and BioImage Archive.
Onami Lab was featured on Japanese online magazine HILLS LIFE DAILY.
BIOIMAGE INFORMATICS
生命科学を革新するバイオイメージ・インフォマティクス
(in Japanese)