eQTL / molecular QTL mapping

The paper identifies chr22q as a regulatory hub where genetic risk for neuropsychiatric conditions is associated with coordinated gene expression downregulation in brain tissue.

This study identifies novel and known genetic contributors to hypertension using RNA-seq and eQTL analyses, highlighting potential drug targets and pathways.

The paper identifies disease-specific genetic regulation of gene expression in immune cells during COVID-19 infection using single-cell eQTL mapping.

The paper constructs a cattle cell-type-specific regulatory variant atlas by integrating bulk and single-cell RNA-seq data, identifying eQTL and linking them to GWAS loci for breeding insights.

The paper identifies novel genetic loci for circulating fatty acids and reveals their molecular mechanisms through GWAS and multi-omics integration.

This study identifies genetic variants influencing brain geometry using GWAS on Laplace-Beltrami spectrum eigenvalues from UK Biobank data.

The paper uses a stacked chromatin state model to identify global patterns of histone modifications across individuals and applies them to predict transregulators and identify trans-QTL in disease contexts.

CACTI improves cQTL mapping by using correlations between regulatory elements, identifying more signals and colocalizing with GWAS loci better than traditional methods.

The paper identifies candidate causal cis-regulatory variants at electrocardiographic QT interval GWAS loci by integrating open chromatin data and expression quantitative trait loci.

The paper evaluates the contribution of expression, splicing, and protein QTL in blood to SNP-based heritability and polygenic prediction across 27 traits, finding they capture significant portions of genetic variation.

The paper identifies eQTLs associated with circadian clock gene expression variation in Drosophila melanogaster using GWAS and the DGRP dataset.

The paper investigates QTL regions associated with spontaneous sex-reversal in XX rainbow trout using genome-based approaches and statistical methods to identify potential sex-modifier genes.

The paper develops a statistical model to identify allelic imbalance quantitative trait loci (aiQTLs) and examines their relationship with cis-acting eQTLs and gene expression distance from the TSS.

The paper identifies STR variations associated with gene expression and DNA methylation across three cancer types and finds shared regulatory mechanisms.

The paper identifies new QTLs associated with stigma position in tomato and validates previously reported QTLs, supporting the role of multiple genes in controlling herkogamy.

This paper expands methylome analysis and detects quantitative trait loci by long-read sequencing of personal DNA, revealing tens of thousands of methylation QTLs associated with structural variants.

This study shows that analyzing genetic variants at the isoform level reveals significant associations with human phenotypes and rare variants, highlighting the importance of isoform-resolved analysis in genetics.

This study identifies molecular mechanisms underlying flowering time variation in Camelina sativa using transcriptomic and genetic analyses.

The paper maps eQTLs in yeast using single-cell RNA sequencing, revealing tradeoffs between growth and reproduction through allele-specific effects on gene expression and cell-cycle progression.

This study identifies 287 depression risk loci, 140 new, through cross-ancestry GWAS and integrates functional and pathway analyses to highlight potential therapeutic targets.

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

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

The paper examines gene expression variation in rice under salinity stress, finding trans-eQTLs dominate and cis-trans reinforcement is more common than compensation.

The paper identifies genetic variants associated with protein abundance and altered protein-protein correlations in the Gyrus Temporalis Medius in Alzheimer's Disease patients.

tadar reduces eQTL noise in bulk RNA-sequencing by accounting for differential allelic representation during differential expression analysis.

This study identifies pQTLs of sVEGFR1 levels during sepsis and links them to ARDS susceptibility and mortality using GWAS, colocalisation, and Mendelian randomisation.

The paper identifies eQTL in mouse neural progenitor cells and shows their effects on gene regulation across developmental stages.

The paper identifies meQTLs in African American hepatocytes, finds colocalization with eQTLs, and shows genetic differences in methylation regulation between African and European ancestry.

jaxQTL improves sc-eQTL mapping by using count-based models, identifying more eGenes and explaining more SNP-heritability than bulk-eQTLs.

This paper introduces IBSEP, a statistical framework that integrates bulk and scRNA-seq data to prioritize cell-type-specific eQTLs, showing improved performance over existing methods.