Philip Lijnzaad

Mechanisms of dexamethasone-induced bone toxicity in developing bone: a single-cell perspective

This study investigates dexamethasone-induced bone toxicity in developing bones using single-cell transcriptomics in mice, revealing reduced osteoblast and chondrocyte populations and disrupted B cell development.

Cdk8 directly regulates glycolysis via phosphorylation of Gcr2

This study identifies Gcr2 as a Cdk8 substrate, showing its phosphorylation is critical for activating glycolysis genes.

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

The paper measures genome-wide off-rates of the yeast transcription factor Abf1 and shows how these dynamics relate to functional outcomes like transcriptional dependency and RNA polymerase II roadblocking.

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

CHETAH identifies cell types in scRNA-seq data using hierarchical clustering and reference data, offering accuracy and specificity, especially for unknown cell types.

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern

The paper compares genetic interaction patterns between gene-specific transcription factors and signaling genes in yeast, finding inversion is more common in transcription factors due to differential regulation.

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq

Sharq preprocesses single cell RNA-seq data from fastq files to gene expression tables, addressing amplification biases and providing quality control diagnostics.