Frank C. P. Holstege

Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS

This paper develops a method to detect tumor-specific gene fusions in pediatric cancer by integrating RNA-seq and WGS, identifying 165 high-confidence fusions and their structural variants.

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.

An extensively optimized chromatin immunoprecipitation protocol for quantitatively comparable and robust results

The paper optimizes a ChIP protocol to improve quantitative comparability and reproducibility across samples.

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.

Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

The paper shows that RSC remodeler and pioneer factors work independently to position the +1 nucleosome at yeast promoters, facilitating transcription initiation through DNA sequence-directed action.

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.