Melissa Gymrek

This study improves gene expression prediction models by incorporating tandem repeats, showing significant performance gains and identifying nonlinear effects on gene expression.

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

This paper introduces a haplotype-based fine-mapping method called happler to identify causal variants for complex traits, showing improved performance over traditional methods in detecting haplotype effects.

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

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

Trex-QTL identifies trans-eQTLs with global effects on molecular phenotypes, showing improved power and replicating known loci in rat brain data.

This study identifies STRs associated with alternative splicing in human brain tissue and links some to disease-related GWAS signals.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

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

This paper identifies Mysm1 mutations as the cause of meander tail mouse cerebellum malformation and links them to hematological and neurological defects.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

This study uses admixture mapping in the All of Us Research Program to identify local ancestry associations with complex traits, finding distinct patterns between African and Native American ancestry.

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 PIPSORT, a method to detect shared and ancestry-specific genetic signals in complex traits, and applies it to GWAS data from diverse populations.

This study evaluates how promoter proximal short tandem repeats (STRs) affect gene expression using MPRA, identifying key factors like repeat unit sequence and copy number.

VADEr, a Vision Transformer-inspired framework, improves polygenic risk prediction for prostate cancer by capturing genetic interactions and revealing heterogeneity through DARTH scores.

The paper introduces scGeneHE, a method to estimate cis-heritability from scRNA-seq data, reducing false positives in eGene detection.

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 identifies 119 high-confidence STR-trait associations across 93 STRs for blood and serum traits using imputed genotypes from UK Biobank data.

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.

The paper identifies a quantitative trait locus on chromosome 13 associated with STR expansion propensity in mice, implicating Msh3 in genome-wide mutation patterns.

The paper presents a multi-omics cell line atlas for Ewing sarcoma, identifying new target genes and regulatory mechanisms of EWSR1-ETS fusion oncogenes.

The paper uses linked-read whole-genome sequencing to identify DNA variants in BXD mice and maps them to phenotypes, enabling systems genetics and precision medicine.

The paper identifies genetic variants responsible for gene expression differences between C57BL/6 and C57BL/10 mouse substrains.

The paper identifies how non-coding genetic variation affects macrophage responses to IL-4 by analyzing SNP and InDel effects across five inbred mouse strains.

The paper develops adVNTR-NN to genotype VNTRs efficiently and identifies eVNTR loci associated with gene expression in multiple tissues.