Shahab Sarmashghi

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

This study shows that BRD4 gene deletions reduce toxicity from overexpression in ovarian and breast cancers, providing evidence for a novel mechanism in cancer progression.

This paper identifies how PVT1 rearrangements in MYC+ cancers generate oncogenic peptides that synergistically activate MYC, AKT, and RAS-MAPK pathways, enhancing tumor aggressiveness.

RESPECT estimates genome length and repeat spectra from low-coverage genome skims with <1.5% error, outperforming previous methods.

APPLES is a distance-based phylogenetic placement method that is faster, more memory efficient, and handles large trees and unassembled reads better than maximum likelihood methods.

The paper develops methods to compute statistical significance of interval overlaps and introduces a tool, iStat, to analyze simulated and real datasets.