Koji Kyoda

Divergence of Cortical Force-Generating Mechanisms Underlies Differences in Spindle Behavior between C. elegans and C. inopinata

This study compares spindle behavior in C. elegans and C. inopinata embryos, finding differences in pronuclear migration and spindle oscillations linked to changes in cortical force generation.

Immobilization-free chemotaxis analysis reveals the novel behavioral mode of leaving in Caenorhabditis elegans

This study identifies a novel post-arrival behavior called 'leaving' in C. elegans using an immobilization-free chemotaxis assay, showing it is regulated by the egl-4 gene.

A Computational Framework for Extracting Mechanistic Hypotheses from Quantitative Data of Morphological Dynamics

The paper introduces a computational framework to extract mechanistic hypotheses from morphological dynamics data by analyzing correlations and gene perturbations in C. elegans embryos.

OME-Zarr: a cloud-optimized bioimaging file format with international community support

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

PHi-C2: interpreting Hi-C data as the dynamic 3D genome state

PHi-C2 converts Hi-C data into dynamic 3D genome models using polymer modeling and provides an optimized algorithm and Colab workflow for analysis.

Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos

The paper creates a deep collection of quantitative nuclear division dynamics data from RNAi-treated C. elegans embryos, identifies 8660 reproducible RNAi phenotypes, and suggests 24 functional processes in early embryogenesis.

BD5: an open HDF5-based data format to represent quantitative biological dynamics data

BD5 is a new HDF5-based data format for biological dynamics data that allows fast random access, improving data reuse compared to XML-based BDML.