Publications
Reading the genome's regulatory code.
Peer-reviewed papers and preprints from the lab. Lab members are shown in bold; follow the chips for the paper, code, and data.
2026
An expanded registry of candidate cis-regulatory elements
Common Coronary Artery Disease Risk Variants in Endothelial Regulatory Elements Modulate Tetraspanin 14 Expression and Notch Signaling
Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells
Junction-targeting designs limit the application of CRISPR-Cas13d in circular RNA perturbation studies
PerturbPlan: An analytical framework for designing Perturb-seq experiments
The IGVF catalog—from genetic variation to function
2025
An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq
Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation
Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis
Endothelial cell-related genetic variants identify LDL cholesterol-sensitive individuals who derive greater benefit from aggressive lipid lowering
Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk
Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci
MorPhiC Consortium: towards functional characterization of all human genes
Rewriting regulatory DNA to dissect and reprogram gene expression
Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma
Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery
2024
Convergence of coronary artery disease genes onto endothelial cell programs
A consensus variant-to-function score to functionally prioritize variants for disease
Cohesin-mediated 3D contacts tune enhancer-promoter regulation
Deciphering the impact of genomic variation on function
Genetic and functional analysis of Raynaud's syndrome implicates loci in vasculature and immunity
High Shear Stress Reduces ERG Causing Endothelial-Mesenchymal Transition and Pulmonary Arterial Hypertension
Mapping enhancer-gene regulatory interactions from single-cell data
Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart
Multicenter integrated analysis of noncoding CRISPR screens
Reduced FOXF1 links unrepaired DNA damage to pulmonary arterial hypertension
Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma
Single cell variant to enhancer to gene map for coronary artery disease
Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph
2023
An encyclopedia of enhancer-gene regulatory interactions in the human genome
Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy
Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases
Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes
2022
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Compatibility rules of human enhancer and promoter sequences
Computational estimates of annular diameter reveal genetic determinants of mitral valve function and disease
Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease
KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress
SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease
2021
Genome-wide enhancer maps link risk variants to disease genes
Activity-dependent regulome of human GABAergic neurons reveals new patterns of gene regulation and neurological disease heritability
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease
2020
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
Inherited causes of clonal haematopoiesis in 97,691 whole genomes
Integrative approaches to improve the informativeness of deep learning models for human complex diseases
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
2019
Activity-by-Contact model of enhancer regulation from thousands of CRISPR perturbations
Discovering metabolic disease gene interactions by correlated effects on cellular morphology
Functional disease architectures reveal unique biological role of transposable elements
Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
2018
CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data
Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries
Deep-coverage whole genome sequences and blood lipids among 16,324 individuals
Positional specificity of different transcription factor classes within enhancers
Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability
2017
A genetic variant associated with five vascular diseases is a distal regulator of Endothelin-1 gene expression
Cohesin loss eliminates all loop domains
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood
Recurrent and functional regulatory mutations in breast cancer
Systematic dissection of genomic features determining transcription factor binding and enhancer function
2010–2016
Eradication of large established tumors by combination immunotherapy engaging innate and adaptive immunity
Local regulation of gene expression by lncRNA promoters, transcription, and splicing
Long non-coding RNAs (lncRNAs) as spatial amplifiers that control nuclear architecture and gene expression
Systematic mapping of functional enhancer-promoter connections with CRISPR interference
RNA Antisense Purification (RAP) for mapping RNA interactions with chromatin
RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridylation of ncRNA and mRNA
Neuregulin autocrine signaling promotes self-renewal of breast tumor-initiating cells by triggering HER2/HER3 activation
The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome
Three Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
The Lin28/let-7 Axis Regulates Glucose Metabolism
Content-based microarray search using differential expression profiles
Independent component analysis: Mining microarray data for fundamental human gene expression modules
For the complete, continuously updated list, see Google Scholar.