Timothy Barry

Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations

The paper uses CRISPRi Perturb-seq to identify 238 enhancer-gene regulatory associations in colorectal cancer and integrates chromatin data to understand their spatial organization.

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.

Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection

This study benchmarks association testing methods for low MOI perturb-seq data, identifies analysis challenges, and introduces SCEPTRE low-MOI to improve calibration and power.

Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing

The paper identifies target genes and pathways of blood trait loci using CRISPR screens and single-cell RNA sequencing, revealing cis and trans regulatory effects of noncoding variants.

Conditional resampling improves calibration and sensitivity in single cell CRISPR screen analysis

The paper introduces SCEPTRE, a method for analyzing single-cell CRISPR screens that improves calibration and sensitivity by addressing technical confounders through conditional resampling.