Yusuke Kijima

Epigenetic regulators partition the genome by evolutionary and developmental constraint

The paper uses single-cell RNA sequencing to analyze mutant phenotypes of epigenetic regulators in mouse embryos, revealing how these regulators partition the genome based on developmental and evolutionary constraints.

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

This study uses a deep-learning model to analyze scRNA-seq data and identifies how folate deficiency disrupts metabolic transitions in developing mouse neural ectoderm, leading to morphological defects.

A multi-kingdom genetic barcoding system for precise target clone isolation

This paper introduces CloneSelect, a multi-kingdom genetic barcoding system that enables precise isolation of target clones using CRISPR base editing to trigger reporter gene expression.

A universal sequencing read interpreter

INTERSTELLAR translates sequencing reads from any structure to any other, enabling analysis by existing tools for similar experiments.

Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

This study compares age-associated transcriptome changes in zebrafish and rat to identify common and species-specific aging features.

The DNA-based global positioning system--a theoretical framework for large-scale spatial genomics

The paper introduces GPS-seq, a theoretical framework for spatial transcriptomics that uses DNA barcodes to enable large-scale, optics-free imaging of tissue sections at single-cell resolution.

Zebrafish Danio rerio trunk muscle structure and growth from a spatial transcriptomics perspective

This study uses spatial transcriptomics to analyze zebrafish trunk muscle structure and growth, identifying spatial gene expression patterns and developmental processes in different muscle types.