Ralf Herwig

scKNIFE integrates gene expression with functional annotations to identify tumor programs and treatment-related functional variation in breast cancer.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper introduces IsoTools, a Python package for analyzing long-read transcriptome data, showing it improves alternative and differential splicing analysis compared to short-read RNA-Seq.

The paper analyzes mutation phase in diploid human genomes and finds that protein-altering mutations are significantly more common in cis than trans configurations across diverse populations.