Yohei Kondo

Epithelial mechanics in a three-dimensional cell vertex model with local junctional constraints

This paper develops a 3D cell vertex model with local junctional constraints to study epithelial mechanics, showing it reproduces near-zero Poisson's ratio and robust mechanical responses under disorder.

Inferring division-associated stochasticity from time-series single-cell transcriptomes

This paper introduces scDIVIDE, a framework to infer division rates and cellular dynamics from time-series scRNA-seq data, showing it accurately captures birth rates in biological processes.

Spatially resolved mapping of tau amplification rates via differentiable simulation of prion-like propagation

The paper infers spatially resolved tau amplification rates from tau PET data using a differentiable reaction-diffusion framework and links these rates to amyloid PET and gene expression patterns.

ZO-1 shuttles between tight junctions and podosomes by riding ERK activation waves during collective cell migration

This study shows ZO-1 moves between tight junctions and podosomes during collective cell migration, regulated by ERK activity, and contributes to cell adhesion and movement.

Intensity Modulation of Trichromatic Split Fluorescent Proteins for Live Cell Mapping

The paper introduces Caterpie, a live cell labeling system using split fluorescent proteins to enable high-fidelity identification of multiple cell populations with 97% accuracy.

Filament-resolved simulations reproduce self-organization of lamellipodia and filopodia

The paper develops a filament-resolved model of actin self-organization, showing how Arp2/3 and fascin concentrations determine lamellipodia, filopodia, and reticulated meshwork morphologies.

Inverse modeling unveils governing law of mechano-chemical dynamics of epithelial migration

The paper develops a machine-learning framework to infer governing equations of mechano-chemical dynamics in epithelial migration from live-cell imaging data, revealing cell-cell heterogeneity in migratory rules.

Quantification of Cyclin-CDK dissociation constants in living cells using fluorescence cross-correlation spectroscopy with green and near-infrared fluorescent proteins.

This study measures cyclin-CDK dissociation constants in living cells using FCCS with optimized fluorescent proteins, revealing insights into cyclin-CDK binding redundancy.

Inverse signal importance in real exposome: How do biological systems dynamically prioritize multiple environmental signals?

The paper introduces a machine learning framework, ISI, to infer how organisms prioritize environmental signals from time-series data, applied to medaka fish gonadal development under natural conditions, revealing dynamic signal importance and gene expression correlations.

Self-organization of spermatogenic wave coordinates sustained sperm production in the mouse testis

The paper uses live imaging and mathematical modeling to show how self-organization of cell turnover in mouse testes sustains sperm production through phase waves and retinoic acid signaling.

Emergence of Bow-tie Architecture in Evolving Feedforward Networks

This paper shows that bow-tie architecture emerges in evolving feedforward networks due to weak initial molecular interactions, not adaptive advantages.

Improvement of phycocyanobilin synthesis for genetically encoded phytochrome-based optogenetics.

The paper improves a PCB synthesis system for a PhyB-PIF optogenetic tool, enabling stable expression and light-inducible dimerization in cells.