Arman Simonyan

Overcoming the accuracy-generalization tradeoff in docking and scoring for prospective virtual screening

This paper introduces DODock and DOScore, hybrid ML/physics frameworks for docking and scoring that improve accuracy while generalizing better to novel molecules, showing significant improvements in hit rates for virtual screening.

Benchmarking full-length transcript single cell mRNA sequencing protocols

This study benchmarks three plate-based scRNA-seq protocols for high gene detection sensitivity, reproducibility, and cost efficiency in clinical applications.

A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

The paper benchmarks CNV detection tools on WGS and WES data using clinical standards and reference samples, finding that combining multiple tools improves recall but precision remains a challenge.

Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences

The paper analyzes telomere maintenance pathway activities in human tissues to identify gene-level and tissue-specific patterns of telomerase and ALT pathway activation.