Ahmed Ibrahim Samir Khalil

DiffInvex identifies chemotherapy resistance genes by analyzing 10,000 cancer genomes, finding known and novel genes under conditional selection for specific therapies.

AStra is a framework for aneuploidy profiling of cancer data that assesses suitability for copy number analysis, showing high accuracy in identifying aneuploidy spectra and ploidy levels.

The paper develops HiCNAtra to correct Hi-C contact maps by integrating copy number variation information, improving accuracy over existing methods.

CNAtra detects and distinguishes large-scale and focal copy number alterations in low-coverage cancer genomes with high precision and recall.