Mana Umeda

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

The paper investigates NF-κB super-enhancers in B cells, finding they enhance transcriptional variability and gene expression through cis-regulatory interactions and NF-κB binding sites.

Local states of chromatin compaction at transcription start sites control transcription levels

The paper identifies local chromatin compaction states at transcription start sites (TSSs) as determinants of transcription levels by correlating weak compaction with RNA polymerase binding.

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

Millefy visualizes cell-to-cell heterogeneity in read coverage of scRNA-seq data using heat maps and dynamic reordering to highlight genomic variations.

A NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data

The paper introduces an NMF-based method to identify overlooked differentially expressed gene regions in single-cell RNA-seq data, finding novel transcripts related to neural stem/progenitor cell differentiation.

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

This study investigates transcriptional bursting kinetics in mESCs using scRNA-seq and identifies regulatory factors and pathways influencing gene expression noise.