Christopher D. Brown

The paper integrates chromatin accessibility data with GWAS to identify regulatory mechanisms underlying blood lipid traits, finding 20% of signals lack proposed mechanisms.

The paper improves sQTL modeling by incorporating alternative splicing representation and introduces MAJIQTL, finding new sQTLs linked to Alzheimer's disease.

The paper identifies 693 SNPs associated with transcription factor binding in liver ATAC-seq data by analyzing footprint quantitative trait loci (fpQTLs).

The paper performs genotype inference from aggregated chromatin accessibility data to identify caQTLs and their links to gene expression and complex traits.

The paper maps GWAS variants associated with late-onset Alzheimer's disease to functional effects in microglial cells, identifying RTFDC1 as a novel effector gene at the CASS4 locus.

The paper identifies cell-type specific splicing quantitative trait loci (sQTLs) in iPSCs and HLCs and shows they contribute to lipid level variation beyond what is captured by gene expression alone.

This study maps expression and splicing QTLs in East Africans and finds population-specific genetic variation related to immunity, metabolism, and pigmentation.

This study conducts a trans-ancestry GWAS using chronic ALT elevation as a proxy for NAFLD, identifies 77 significant loci, and validates 17 SNPs with histology and imaging data, revealing genetic links to metabolic and inflammatory traits.

The paper identifies differential regulatory control of APOEε4 on African versus European haplotypes through enhancer activity and promoter interactions analyses.

The paper maps genetic variants to cell types in the kidney to identify disease mechanisms and drug targets.

The paper maps regulatory effects of human disease variants in pluripotent cells, identifying cis- and trans-QTL across 18,556 genes and linking them to GWAS traits.

The paper uses GTEx data to analyze GWAS loci, showing dose-dependent RNA effects and proposing target genes for 47% of loci using combined methods.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper assesses the impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx, finding that local ancestry adjustment improves power but has limited effect on colocalization probabilities.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper uses matrix factorization to analyze eQTLs across 49 human tissues, identifying tissue-specific and shared genetic regulation patterns and their potential transcription factor drivers.

The paper identifies distinct regulatory patterns and trait associations of lncRNA genes compared to protein-coding genes across human tissues.

GTEx v8 maps expression and splicing QTLs in 49 tissues from 838 donors: cis-eQTLs cover 94.7% of protein-coding genes, and cross-tissue QTL sharing mirrors cell-type composition.

The paper identifies enhancer dysregulation and target genes for noncoding Alzheimer's disease-associated variants using GWAS and eQTL data.

The paper fine-maps 77 GWAS loci in the human liver by integrating epigenetic and gene expression data to understand genetic and epigenetic regulation of gene expression.

The paper identifies Shh responsive genes and regulatory sequences involved in cochlear morphogenesis using genomic approaches.

The paper develops a high-throughput assay to identify allele-specific effects on DNA:protein binding and gene transcription, finding significant associations with complex trait variants.

This study identifies genetic pleiotropy between bipolar disorder and metabolic/endocrine traits in a multigenerational Amish pedigree using imputed WGS and polygenic risk scores.

INFERNO integrates GWAS data with functional genomics to identify causal noncoding variants and their molecular mechanisms in schizophrenia.

The paper uses targeted resequencing to identify rare coding and noncoding variants associated with extreme HDL-C levels in humans.

The paper analyzes transposable elements (TEs) in human tissues to show their tissue-specific contribution to gene regulation through active and repressed chromatin associations.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

The paper identifies a causal variant near TMEM106B that alters chromatin architecture and gene expression, linking it to frontotemporal lobar degeneration and neurodegenerative disease risk.

The paper identifies transposable elements as the main source of novelty in primate gene regulation by analyzing conserved and newly evolved cis-regulatory elements across six primate species.