Antje Hirsekorn

The paper identifies CRISPRa-responsive enhancers and their target genes in a 2 Mb region around PHOX2B using TESLA-seq, revealing both known and novel regulatory relationships.

The paper predicts RNA degradation and translation levels from RBP binding data using machine learning, finding in vivo binding sites are more important than predicted ones.

The paper identifies RNA-binding proteins and RNA decay factors that regulate aldosterone production kinetics in steroidogenic cells through coordinated transcription and decay mechanisms.

ORFquant quantifies translation at the open reading frame level using Ribo-seq, revealing alternative ORFs and gene-specific protein production differences across human cell lines.

The paper uses sci-ATAC-seq and a new tool, ScregSeg, to analyze chromatin dynamics in zebrafish embryos, revealing roles of npas4l/cloche in cell and regulatory states.

The paper identifies functional miRNA::mRNA interactions in Drosophila using AGO CLIP experiments and quantifies their impact on gene expression and translation.

The paper compares DNase-seq and ATAC-seq for open chromatin and TF footprinting, showing protocol-specific biases affect performance and reproducibility.

The paper identifies FACT as a conserved reprogramming barrier in C. elegans and humans that maintains cell identity by modulating chromatin accessibility.

The paper investigates transcription initiation directionality in metazoans, finding species-specific sequence asymmetry and independent initiation events at promoters and enhancers.

The paper classifies human coding and non-coding genes based on RNA metabolism profiles, revealing distinct metabolic patterns and functional subsets of lncRNAs.

RiboTaper identifies actively translated open reading frames using spectral analysis of Ribo-seq data, revealing novel ORFs and validating peptide products in HEK293 cells.