Philipp Benner

Fiora predicts compound mass spectra from single fragmentation events using graph neural networks, outperforming existing methods and enabling faster spectral library expansion.

Mistle improves metaproteomics by efficiently searching predicted spectral libraries, outperforming existing tools in speed and memory usage.

The paper uses epigenetic data to identify sequence patterns in enhancers that predict cell type-specific regulatory activity and finds that some patterns correspond to transcription factor footprints.

CRUP predicts condition-specific regulatory units by analyzing histone modification ChIP-seq data and linking enhancers to target genes in rheumatoid arthritis.

This study develops synSTARR-seq to analyze how DNA sequence and shape affect transcriptional activity and noise using synthetic GR binding sites.