Nina P. Farrell

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.

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 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 presents a computational framework to align and quantify ChIP-exo crosslinking patterns, enabling inference of spatial organization within protein-DNA complexes.

The paper introduces ChExMix, a method to detect and classify distinct protein-DNA binding subtypes in ChIP-exo data using probabilistic modeling of tag distributions and DNA motifs.