Daniel J. Gaffney

The paper benchmarks genetic prevalence estimates of autosomal recessive diseases against newborn screening data, finding concordance influenced by population databases and ancestry matching.

The paper maps eQTLs in stimulated iPSC-derived macrophages and identifies condition-specific reQTLs that colocalize with disease-associated variants.

This study identifies genetic determinants of blood gene expression and splicing, linking them to molecular phenotypes and health outcomes through QTL analysis and colocalization.

The paper identifies low-usage splice junctions as contributors to immune-mediated disease risk by linking sQTLs to disease loci and showing their impact on gene expression in inflammation.

This study creates a single-cell atlas of human liver development, identifying pathways and factors that guide hepatic cell fates and improving hepatocyte-like cell functionality.

The paper analyzes genomic variation in hiPSCs derived from skin and blood, finding high mutation rates in fibroblast-derived lines and frequent BCOR mutations in blood-derived lines.

The paper generates a molecular map of human in vitro myelopoiesis from iPSC to macrophages, revealing conserved regulatory networks and new myeloid progenitors.

The paper shows enzymatic dissociation causes gene expression changes in microglia and proposes a protocol to reduce these artifacts in scRNA-seq.

The paper identifies TSPAN8 variants associated with metabolomic regulation and metabolic diseases using CNV analysis and functional characterization in human induced pluripotent stem cells.

The paper profiles gene expression in human microglia from 141 patients, identifies population shifts in acute brain injury, maps eQTLs, and fine-maps Alzheimer's risk variants using hIPSC-derived macrophages.

The paper uses single-cell RNA sequencing to study genetic variant effects on dopaminergic neuron differentiation from iPSCs, identifying eQTL and cell fate markers.

Meta-analysing UK Biobank family-history GWAS with diagnosed-AD GWAS yields 37 loci, four novel (NCK2, TSPAN14, SPRED2, CCDC6); fine-mapping, colocalisation and network scoring prioritize causal genes.

The paper introduces CELLO-seq, a long-read RNA sequencing method for single cells, to study TE expression in mouse and human cells, finding locus-specific expression and regulatory heterogeneity.

The paper characterizes proteome variation across 202 human iPSC lines, identifies 700 pQTLs, and links pQTLs to disease-associated GWAS variants.

The paper uses single-cell RNA-seq of differentiating iPS cells from 125 donors to identify expression quantitative trait loci influencing gene expression during endoderm differentiation.

Souporcell clusters single-cell RNAseq data using genetic variants to accurately assign genotypes, detect doublets, and estimate ambient RNA without reference genotypes.

The paper identifies context-specific genetic effects on promoter usage and shows they contribute to complex traits more than canonical splicing QTLs.

Cardelino integrates whole exomes and single-cell transcriptomes to identify clone-of-origin and reveal phenotypic impacts of somatic variants in human fibroblasts.

The paper identifies genetic effects on chromatin and gene expression in immune response conditions, revealing enhancer priming in naive cells.

The paper maps regulatory variants in iPSC-derived sensory neurons, identifying genetic influences on gene expression, chromatin accessibility, and RNA splicing, with overlaps to disease associations.

This study develops a statistical model to infer causal regulatory interactions using ATAC-seq data and applies it to fine-map eQTL data, reducing credible set size by half.