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