Mette Skou Bentsen

SC-Framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets

SC-Framework provides a unified, containerized environment for single-cell data analysis to improve reproducibility and scalability.

PEAKQC: Periodicity Evaluation in scATAC-seq data for quality assessment

PEAKQC evaluates single-cell ATAC-seq quality using wavelet-based convolution of fragment length distribution patterns, improving downstream analysis by filtering low-quality cells.

Endocardial HDAC3 is required for myocardial trabeculation

This study shows that endocardial HDAC3 is essential for myocardial trabeculation by regulating TGFβ3 expression through miR-129-5p repression in mice.

Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data

This paper introduces DENIS, a framework for de novo motif discovery from ATAC-seq footprints to identify uncharacterized transcription factor binding.

The homeobox transcription factor DUXBL controls exit from totipotency

This study identifies DUXBL as a key factor promoting the silencing of the 2C transcriptional program during exit from totipotency.

Scanpro: robust proportion analysis for single cell resolution data

Scanpro is a tool for differential proportion analysis in single-cell data, supporting both replicated and unreplicated datasets.

TF-COMB - discovering grammar of transcription factor binding sites

TF-COMB identifies co-occurring transcription factors and their binding grammar using ChIP-seq data and ATAC-seq footprinting.

i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results

i2dash creates customizable, interactive web dashboards for visualizing omics data, integrating with R-based analysis pipelines and supporting single-cell RNA-seq workflows.

multicrispr: fast gRNA designer enables prime editing and parallel targeting of thousands of targets

multicrispr is a gRNA design tool that enables efficient and specific gRNA creation for CRISPR-based applications like Prime Editing and large-scale screening.

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

TOBIAS enables genome-wide analysis of TF binding dynamics using ATAC-seq data, revealing complex TF interactions during zygotic genome activation in humans and mice.

UROPA GUI: A web platform for genomic region annotation

The paper introduces a web-based GUI for the UROPA tool to simplify genomic region annotation for biologists and clinicians.