Jacques van Helden

YAAT identifies functionally-related gene groups by integrating co-expression and phylogenetic conservation data, revealing biases in gene set enrichment interpretation.

The paper identifies regulatory motifs in peach using co-expression networks and RSAT::Plants, finding that small promoter regions are optimal for motif discovery.

The paper introduces Var-tools, a framework for predicting the impact of regulatory variants on transcription factor binding, with four case studies demonstrating its functionality.

Sequanix provides a graphical interface for Snakemake workflows to make them more accessible to a broader audience.

SnakeChunks provides modular Snakemake rules for reproducible NGS analyses, demonstrated on RNA-seq and ChIP-seq data.

The paper introduces matrix-clustering, a tool that reduces redundancy and clusters transcription factor binding motifs from multiple sources, improving interpretation of motif collections.