Maryam Ghareghani

TandemTwister is a tool for tandem repeat genotyping and visualization, showing high accuracy and speed across sequencing technologies and datasets.

The paper introduces dicast, a machine-learning method that improves the detection of pathogenic structural variants from short-read sequencing by leveraging genomic context and alignment features.

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

This paper introduces scTRIP, a method to detect structural variations in single cells, revealing new SV classes and mutational processes in cancer samples.

GW-CALL improves variant calling by using all reads, including those mappable to multiple locations, to enhance accuracy in repeat regions.