Drew T. Bergman

This paper develops an RNA sequencing-based radiosensitivity index (RSI-seq) that preserves the clinical utility of the genomic-adjusted radiation dose (GARD) model, enabling personalized radiotherapy across diverse cancer types.

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

The paper maps coronary artery disease risk loci to endothelial cell gene programs, identifying convergence on the CCM pathway and a new CAD gene, TLNRD1.

The paper measures enhancer-promoter compatibility in human cells using a high-throughput assay, finding a multiplicative model with some class-specific preferences.

HyPR-seq sensitively quantifies up to 100 chosen genes in single cells, achieving high sensitivity for individual transcripts and reducing costs compared to whole-transcriptome scRNA-seq.

The paper uses the ABC Model to map enhancer-gene regulation across 131 cell types and tissues, linking GWAS variants to disease genes, particularly in IBD.

The paper introduces CRISPRi-FlowFISH to perturb enhancers and an Activity-by-Contact model to predict enhancer-gene regulatory connections.