Michael Beda Stadler

Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration

The paper identifies how cell heterogeneity and YAP1 inactivation drive tissue patterning during intestinal regeneration through feedback mechanisms.

The genetic architecture of the human bZIP family

The paper systematically mutagenizes human bZIP domains and uses deep mutational scanning to quantify interactions, revealing complex genetic architecture and enabling synthetic bZIP design.

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin

The paper creates a comprehensive atlas of transcription factor interactions in S. pombe using experimental methods and introduces a web tool for exploring the data.

Preventing CpG island hypermethylation in oocytes safeguards mouse development

This study shows that KDM2A and KDM2B prevent aberrant DNA methylation in mouse oocytes, which is critical for early embryonic development.

einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

einprot provides an R package for reproducible analysis of quantitative proteomics data, generating reports with interactive visualizations and customizable workflows.

Convergence of multiple RNA-silencing pathways on GW182/TNRC6

The paper identifies TRIM71's mechanism of mRNA silencing through recruitment of TNRC6/GW182 and shows competition among silencing pathways.

mutscan - a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data

mutscan provides an R package for end-to-end analysis of MAVE data, supporting statistical modeling and visualization of variant effects.

monaLisa: an R/Bioconductor package for identifying regulatory motifs

monaLisa identifies transcription factors from experimental data by integrating with Bioconductor packages for motif analysis.

Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance

The paper uses single-cell RNA sequencing to study hippocampal development in DOT1L-mutant mice, identifying distinct neural stem cell populations and their developmental trajectories, revealing DOT1L's role in cell state preservation and hippocampal maturation.

REPRESSION BY HDAC3 AND DAX1 MEDIATES LINEAGE RESTRICTION OF EMBRYONIC STEM CELLS

This study identifies Hdac3 and Dax1 as repressors that restrict mESCs from transdifferentiating into extraembryonic endoderm by silencing Gata6 enhancers, while Nr5a2 and Esrrb promote this conversion.

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

This study compares RNA velocity results across different quantification tools for droplet scRNA-seq data, showing significant differences in abundance estimates and their impact on velocity analysis.

Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map

This study compares cell-type development and transcriptomes in human retinal organoids and adult retinas, finding convergence in transcriptomes and cell-type-specific disease gene expression.