Kazuhide Watanabe

Comparative single-cell transcriptomes of dose and time dependent epithelial-mesenchymal spectrums

The paper compares dose- and time-dependent EMT transcriptomes to show stable intermediate states and improved gene detection in dose-dependent experiments.

Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition

This study introduces gsPCA and gsNMF for analyzing transcriptome data, showing they provide interpretable, transferrable, and gene-specific functional insights comparable to existing methods.

Quality assessment of single-cell RNA sequencing data by coverage skewness analysis

The paper introduces SkewC, a method to identify poor quality cells in scRNA-seq by analyzing gene coverage skewness, and validates it across 37,993 cells from 15 protocols.

Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition

The paper uses combinatorial perturbations to study EMT gene regulation, finding that mesenchymal genes show diverse dependencies on TGF-β and ZEB1, with functional differences in motility and cancer survival.