Andrew J. Knights

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

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.

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

MultiMAP integrates multimodal data by reducing dimensionality and preserving structure, outperforming existing methods in various tasks.

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-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 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.