John A. Stamatoyannopoulos

The paper identifies a Runx1 enhancer that distinguishes hematopoietic stem cells (HSCs) from progenitor cells (HPCs) in the mouse dorsal aorta using enhancer-reporter models and single-cell multiome analysis.

The paper constructs a genome-scale transcriptional regulatory network of the human placenta using genomic and transcriptomic data, identifying key regulators of preterm birth.

FORGEdb integrates genomic annotations to prioritize functional variants and target genes for complex diseases.

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 paper identifies potent, compact, and lineage-specific enhancers for gene therapy vectors using epigenomic data and validates their efficacy in correcting a thalassemia phenotype.

This paper uses pleiotropy to discover new genetic loci for OSA and provide biological hypotheses by combining colocalization tests with pleiotropy analysis.

The paper investigates the link between genetic associations and regulatory function, finding limited evidence that baseline gene expression explains GWAS associations.

This study identifies two novel genetic loci associated with Tourette Syndrome through a genome-wide meta-analysis and integrates functional data to implicate specific genes.

The paper quantifies how tissue context influences the effect of regulatory DNA variants on transcription factor activity using allelic accessibility maps in mice.

The paper creates high-precision maps of DNase I hypersensitive sites across 733 human biosamples and develops a regulatory vocabulary to annotate regulatory DNA, concentrating disease-associated signals.

The paper maps transcription factor footprints across 243 human cell and tissue types, revealing their structure, function, and relationship to genetic variation and disease.

The paper creates a mouse regulatory DNA atlas by mapping DNase I hypersensitive sites across development and shows dynamic changes in regulatory elements and transcription factor activity.

This study maps chromatin dynamics and gene expression during human erythropoiesis, revealing regulatory modules that guide lineage commitment and maturation.

This study demonstrates precise control of gene expression levels by targeting the KRAB repressor domain in human cells.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

This study develops a method to quantify nuclear protein dynamics by isolating chromatin compartments and using mass spectrometry, revealing chromatin remodeling during BET protein degradation.