Ralf A. Bundschuh

This paper introduces Free Energy Spectroscopy (FES) to characterize chromatin compaction by analyzing end-to-end distance and nucleosome stacking interactions, revealing three mechanisms by which linker histones reshape compaction energetics.

This study shows PYM1 regulates EJC occupancy in a gene architecture-dependent manner, affecting mRNA stability and decay, and is exploited by flaviviruses to alter host mRNA regulation.

RBPamp models protein-RNA interactions using RBNS data to predict in vivo binding affinities and eCLIP densities for 79 human RBPs.

This study compares bulk and single-cell RNAseq for identifying differentially expressed genes in adult hippocampal NSCs, finding single-cell methods miss high-fold-change genes but can be optimized for in vivo use.

The paper shows that UPF3A and UPF3B can activate NMD independently of EJC binding in human cells, challenging the idea that UPF3 is solely a bridge between the EJC and UPF complex.

The paper identifies stop codon-proximal 3′UTR introns as a new class of EJC-regulated NMD targets that influence vertebrate development.

The paper shows the exon junction complex (EJC) undergoes a compositional switch from an SR-rich to an SR-devoid form, altering mRNP structure and NMD activity.