Eugene Katsevich

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.

PerturbPlan provides an analytical framework to design single-cell CRISPR screens by calculating statistical power and enabling interactive experiment planning.

The paper integrates GWAS data with a CRISPRi screen in osteoblasts to identify genes affecting bone mineral density and reveals pleiotropy across non-bone tissues.

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.

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.

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.

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

KnockoffZoom identifies causal variants for complex traits at multiple resolutions using artificial genotypes and linkage disequilibrium models, outperforming mixed effects models in the UK Biobank.

The paper introduces interactive visualization tools for exploring Gene Ontology data, enabling better analysis of high-throughput genomic studies and simulation of single-cell RNA sequencing data.