Masahiro Nagano

This paper introduces Swap-seq, a method to systematically delete and quantify the effects of enhancers, silencers, and topological elements on gene expression in human cells.

Species-OT uses Gromov-Wasserstein optimal transport to compare transcriptome geometries across species, identifying gene correspondences and transcriptomic discrepancies.

Translating cells between mouse, macaque and human scRNA-seq with a CycleGAN, without ortholog mapping, preserved developmental time structure, imputed missing states and produced more realistic synthetic cells than scGAN.

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

The paper identifies 'matchmaker' cis-regulatory elements in erythropoiesis that strengthen loops between neighboring elements and are linked to gene expression and cohesin loading.

This study investigates how promoter strength and position influence promoter competition by inserting diverse promoters into the Sox2 locus and measuring their effect on endogenous Sox2 expression.