Koen H.M. Prange

scOmnom: scalable end-to-end single-cell RNA-seq analysis with auditable resolution selection

scOmnom provides a scalable, semi-automated workflow for single-cell RNA-seq analysis, enabling auditable clustering-resolution selection and annotation refinement across large datasets.

Sex-stratified adipose-liver circuits in human MASLD

This study identifies sex-specific transcriptional differences in liver and visceral adipose tissue in MASLD and shows coordinated cross-tissue states.

A CROP-seq screen of histone modifying enzymes reveals histone demethylase Kdm5c regulates inflammatory macrophage activation.

The paper uses CROP-seq to identify histone modifying enzymes regulating inflammatory macrophage activation, finding Kdm5c modulates inflammatory responses by balancing baseline and inducible activation.

Identification of endothelial-to-mesenchymal transition gene signatures in single-cell transcriptomics of human atherosclerotic tissue

The paper identifies gene signatures of endothelial-to-mesenchymal transition in human atherosclerotic tissue using combined in vitro and single-cell transcriptomic data.

Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.

The paper identifies sex-stratified gene regulatory networks in atherosclerotic plaques, showing female plaques are enriched with myofibroblast-like smooth muscle cell networks.