Henry Pratt

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 processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper constructs a cross-ancestry, cell-type-informed gene regulatory atlas of the developing human brain, identifying genetic regulation and linking it to neuropsychiatric disorders.

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 identifies interactions between MafB, WDR77, and β-catenin and shows they share similar genomic binding profiles near paused RNA polymerase at promoter-proximal regions.

The paper generates a catalog of experimentally validated transcription start sites (TSSs) across 115 human tissues and cell types, updating TSS annotations for 20% of GENCODE genes and identifying new GWAS candidate genes.

The paper updates Factorbook, a TF-centric database, by expanding its motif catalog and integrating it with ENCODE data to annotate candidate regulatory sites and provide tools for variant and disease analysis.

This study identifies YAP and TAZ as transcriptional co-activators of AP-1 and STAT3 in breast cancer, showing their role in gene regulation and poor patient survival.

The paper annotates 18 chromatin states in 66 mouse epigenomes across twelve tissues during development using ChromHMM, identifying bivalent states with evolutionary conservation and gene silencing functions.

The paper maps and characterizes RNA elements recognized by human RNA binding proteins in K562 and HepG2 cells, expanding the catalog of functional elements in the human genome.

GS-Preprocess simplifies GUIDE-seq analysis by converting standard Illumina sequencer output into compatible input for off-target profiling, enhancing accessibility and reducing costs.

The paper benchmarks enhancer-gene prediction methods using a curated dataset, finding TargetFinder performs best but has limited cross-cell-type effectiveness.

The paper introduces BEAPR, a computational method to detect allele-specific binding of RNA-binding proteins, showing it outperforms existing methods and identifies disease-relevant variants.