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.

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.