Charles B. Epstein

This study identifies 12 enhancers in the 9p21.3 CAD risk locus that regulate MTAP, modulating vascular cell-state transitions and CAD risk through stress-responsive mechanisms.

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 paper develops a CRISPRi approach using truncated guides to screen multiple transcription factor binding sites, showing they can disrupt enhancer activity and repress transcription factor binding.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

This paper develops a platform to model and manipulate human microglial states in vitro using single-cell RNA sequencing and genetic tools, identifying disease-associated transcriptional signatures.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

The paper introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

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.

Crosscheck detects mislabeled samples in NGS data by analyzing linkage disequilibrium, correcting errors in 1% of ENCODE datasets.

This study compares monoclonal and polyclonal antibodies for ChIP-seq of histone modifications, finding monoclonals perform similarly in most cases but show differences for H3K27ac.