Helyaneh Ziaei Jam

The paper identifies non-SNP variants as significant regulators of gene expression and addiction-related traits in HS rats using joint cis-eQTL analysis.

This study shows that long-read genome sequencing improves detection of structural and repeat variants in autism and links them to functional consequences.

The paper extends SISTR to jointly estimate selection coefficients across STRs, showing variation in mutation and selection parameters and greater selective burden of de novo STR mutations compared to standing variation.

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

The paper introduces prancSTR, a method to detect somatic mosaicism at short tandem repeats (STRs) using whole genome sequencing data without requiring a matched control sample.

This paper introduces LongTR, a tool for accurately genotyping tandem repeats from long reads, and provides its code repository.

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

The paper creates a deep population reference panel of tandem repeat variation using whole genome sequencing and develops a method to genotype over 1.7 million TR loci, identifying novel eQTL signals and a phased haplotype panel for imputation.