Steven K. Reilly

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

This study evaluates over 3,000 congenital heart disease-risk variants using SNP Bind-n-Seq and MPRA to identify variants with allelic TF binding and regulatory activity.

This study introduces MPAC, a machine learning model that predicts the cis-regulatory impact of non-coding variants, demonstrating its accuracy across diverse applications and datasets.

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

This paper designs synthetic cis-regulatory elements (CREs) that outperform natural ones in driving cell type-specific gene expression using deep learning and experimental validation.

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.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

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

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 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.

Fine-mapping 148 complex traits in three biobanks with combined n = 811,261 yields 4,518 causal variant-trait pairs, 285 of them repeating in more than one population.

The paper identifies causal 3'UTR variants linked to human disease and evolution using a new high-throughput assay and functional analysis.

The paper introduces DNA spike-ins to detect contamination in SARS-CoV-2 amplicon-based sequencing and demonstrates their utility in a real-world outbreak investigation.

The paper identifies human-specific substitutions affecting enhancer activity in neurodevelopmental regions by testing their impact in human neural stem cells.

HCR-FlowFISH identifies cis-regulatory elements and their target genes by quantifying gene expression changes after CRISPR perturbations, using >270,000 perturbations to detect CREs for multiple genes.

The paper identifies functional β cell transcriptional variants from T2D GWAS SNPs using MPRA, showing strong correlation with chromatin accessibility and revealing regulatory features under stress conditions.