Jill E. Moore

A data model for longitudinal multi-modal biomedical cohorts

The paper introduces a data model for longitudinal multimodal biomedical cohorts, demonstrating its ability to manage heterogeneous data across multiple modalities and study visits.

Inferring causal cell types of human diseases and risk variants from candidate regulatory elements

This paper introduces CT-FM and CT-FM-SNP methods to identify causal cell types and variants for diseases, finding most SNPs affect traits via a single cell type set.

Architectural chromatin interactions provide a framework for context-dependent gene regulation

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

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.

A consensus variant-to-function score to functionally prioritize variants for disease

This paper introduces a consensus variant-to-function score to prioritize disease-causing variants, showing improved performance in heritability enrichment and fine-mapping.

Single-cell genomics and regulatory networks for 388 human brains

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.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

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

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

Integrating gene annotation with orthology inference at scale

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

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

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

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

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

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

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 EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

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.

Multi-center integrated analysis of non-coding CRISPR screens

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome

FAVOR provides an online resource and tool for functional annotation of variants from whole genome sequencing studies to aid in disease gene prioritization.

A catalog of transcription start sites across 115 human tissue and cell types

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.

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites

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.

Genetic and Epigenetic Features of Promoters with Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription of Cell-essential Genes

The paper identifies ubiquitously open chromatin regions in human and mouse genomes that support the transcription of cell-essential genes.

Annotation of Chromatin States in 66 Complete Mouse Epigenomes During Development

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.

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

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

Transcriptome-wide interrogation of the functional intronome by spliceosome profiling

This study introduces spliceosome profiling to map intron excision sites with high resolution, revealing new introns and correcting misannotations in S. pombe.