Ryuichiro Nakato

ChromBERT identifies chromatin state motifs using a BERT-based model pre-trained on human chromatin data, revealing biologically relevant patterns across multiple tasks.

This study identifies Smc5/6's role in organizing transcription-induced positive DNA supercoils by initiating loop extrusion at cohesin-dependent boundaries.

The paper shows Morc1 re-silences activated transposons in gonocytes by establishing heterochromatin, preventing their disruptive effects on the transcriptome.

The paper shows nutrient fluctuations induce dedifferentiation of enteroendocrine cells into intestinal stem cells in Drosophila, promoting adaptive intestinal growth.

This study shows that transcription and replication create chromosome loop boundaries by blocking cohesin progression, shaping S-phase chromosomes in yeast.

The paper identifies a new subset of cohesin binding sites, DICs, with distinct functions in transcriptional regulation across human cell types.

This study investigates how cohesin and related factors regulate 3D genome structure and gene expression by analyzing depletion effects on chromatin, transcriptome, and epigenome data.

The paper introduces a method to detect gene communities and identify mutually exclusive gene pairs from sparse scRNA-seq data, showing improved sensitivity in capturing cellular heterogeneity.

PHi-C simulates dynamic 3D genome features from Hi-C data, aligning with live-cell imaging observations and providing physical insights.

The paper characterizes the transcriptomic and epigenomic landscape of nine human endothelial cell types, identifying EC-specific enhancers and marker genes, and highlights the role of HOX genes in vascular development and disease.

This study uses CRISPR/Cas9 to generate NIPBL mutants and shows that the N-terminus of NIPBL is critical for transcriptional regulation by interacting with MAU2.

The paper introduces SSP, a tool to assess ChIP-seq data quality by measuring signal-to-noise ratio and peak reliability without peak calling, showing it is sensitive and robust across different factors and sequencing depths.