Patrick Kemmeren

The paper introduces PIGI, a pathway-informed framework to detect genetic interactions in pediatric cancer, identifying 35 new candidate gene pairs with potential synthetic lethal interactions.

The paper identifies prevalent and pathogenic complex structural variations in pediatric solid tumors, linking them to adverse clinical outcomes and potential therapeutic targets.

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.

Trecode provides a FAIR-compliant platform for managing and analyzing omics data in clinical and research settings, ensuring reproducibility and data reuse.

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.

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

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