Evelyn Jagoda

Mapping enhancer-gene regulatory interactions from single-cell data

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

A systematic survey of distal element-gene regulatory interactions with Direct-Capture Targeted Perturb-seq

This study identifies most distal element-gene interactions have small effect sizes (<10%) using DC-TAP-seq, revealing limitations in prior CRISPR screens and suggesting new model requirements.

Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk

The paper identifies causal genetic mechanisms at CAD GWAS loci using CRISPR screens and chromatin analysis, revealing enhancer-gene links and ancestry/sex-specific risk factors.

Complex regulatory interactions at GDF5 shape joint morphology and osteoarthritis disease risk

The paper investigates regulatory interactions at the GDF5 locus, showing that epistasis between variants, rather than individual variants, influences disease risk and joint morphology.

Cohesin-mediated 3D contacts tune enhancer-promoter regulation

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

The paper identifies four Neanderthal introgressed alleles on chromosome 3 that may modulate the regulation of CCR1 and CCR5, contributing to severe COVID-19 risk.

Impact of non-LTR retrotransposons in the differentiation and evolution of Anatomically Modern Humans

This study identifies human-specific non-LTR retrotransposon insertions and shows their association with gene expression changes and phenotypic evolution in humans.