J Engreitz

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

The paper identifies a compact regulatory logic governing fibroblast plasticity in fibrosis by analyzing enhancer repression and gene perturbations across multiple tissues.

This paper introduces Swap-seq, a method to systematically delete and quantify the effects of enhancers, silencers, and topological elements on gene expression in human cells.

The paper maps and redesigns the MYBPC3 promoter to enhance expression and treat haploinsufficient hypertrophic cardiomyopathy.

A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

The paper tests enhancer-promoter compatibility using improved assays, finding that promoter responsiveness, not enhancer rank order, determines activation sensitivity.

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

PerturbPlan provides an analytical framework to design single-cell CRISPR screens by calculating statistical power and enabling interactive experiment planning.

The paper uses Perturb-seq in mice to identify genes that promote collateral artery formation by comparing gene expression between guinea pigs and mice.

The paper maps variant, enhancer, and gene function in primary human CD4+ T cells by combining Perturb-seq of regulatory elements and genes, identifying CRE-gene pairs and linking variants to disease-related programs.

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

The paper uses a single-cell multi-omic atlas and deep learning to identify cis-regulatory elements and genetic drivers of heart development and disease.

The paper identifies disease-linked regulatory DNA variants and their impact on epidermal homeostasis by analyzing SNVs, TF binding, and gene dysregulation in polygenic skin diseases.

This study identifies most distal element-gene interactions have small effect sizes (<10%) using DC-TAP-seq, revealing limitations in prior CRISPR screens and suggesting new model requirements.

The paper identifies causal genetic mechanisms at CAD GWAS loci using CRISPR screens and chromatin analysis, revealing enhancer-gene links and ancestry/sex-specific risk factors.

This study identifies RUNX1 as a key regulator of cardiac recovery by reprogramming macrophages, showing that its inhibition promotes heart function recovery in a chronic heart failure model.

The paper introduces Variant-FlowFISH to measure the effects of DNA sequence variants on gene expression, identifies regulatory mechanisms, and benchmarks predictive models.

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.

KGWAS improves GWAS power in small cohorts by integrating a functional knowledge graph, discovering more associations for rare diseases.

This study creates a gene regulation map of the human fetal heart to interpret genetic variants associated with congenital heart disease and cardiac traits, identifying valvular interstitial cells as key regulators.

This paper links CAD GWAS variants to causal genes in SMCs using single-cell chromatin accessibility and Hi-C data, creating a scV2E2G map for disease mechanism discovery.

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

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

The paper shows high shear stress induces endothelial-mesenchymal transition and pulmonary arterial hypertension by reducing ERG expression, which can be mitigated by ERG replenishment.

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 introduces a method to prioritize causal genes for complex traits by integrating GWAS data with gene expression and biological data, achieving high precision in gene-trait pair identification.

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.

This study uses single-cell chromatin accessibility analysis to identify developmental trajectories and non-coding mutations associated with congenital heart disease.

The paper maps coronary artery disease risk loci to endothelial cell gene programs, identifying convergence on the CCM pathway and a new CAD gene, TLNRD1.