Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Prdm16 Supports Arterial Flow Recovery by Maintaining Endothelial Function

(2021) Sander Craps et al.   CIRCULATION RESEARCH

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

(2021) Joshua Chiou et al.   NATURE

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk

(2021) Joshua Chiou et al.   NATURE GENETICS

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

(2021) Yoshiharu Muto et al.   Nature Communications

Cardiac cell type–specific gene regulatory programs and disease risk association

(2021) James D. Hocker et al.   Science Advances

Genetic effects on liver chromatin accessibility identify disease regulatory variants

(2021) Kevin W. Currin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

(2021) Tiit Örd et al.   CIRCULATION RESEARCH

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

(2021) Samuel Morabito et al.   NATURE GENETICS

Single-cell epigenomics reveals mechanisms of human cortical development

(2021) Ryan S. Ziffra et al.   NATURE

Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits

(2020) Lindsey K. Stolze et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis

(2020) Gabriel F. Alencar et al.   CIRCULATION

Clonally expanding smooth muscle cells promote atherosclerosis by escaping efferocytosis and activating the complement cascade

(2020) Ying Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity

(2020) Lu Cui et al.   Nature Communications

PRDM16 Upregulation Induced by MicroRNA-448 Inhibition Alleviates Atherosclerosis via the TGF-β Signaling Pathway Inactivation

(2020) Dongxing Liu et al.   Frontiers in Physiology

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human

(2020) Huize Pan et al.   CIRCULATION

Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics

(2020) Marie AC Depuydt et al.   CIRCULATION RESEARCH

CDC42EP5/BORG3 modulates SEPT9 to promote actomyosin function, migration, and invasion

(2020) Aaron J. Farrugia et al.   JOURNAL OF CELL BIOLOGY

Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease

(2020) Satoshi Koyama et al.   NATURE GENETICS

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

Qtlizer: comprehensive QTL annotation of GWAS results

(2020) Matthias Munz et al.   Scientific Reports

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Abundant associations with gene expression complicate GWAS follow-up

(2019) Boxiang Liu et al.   NATURE GENETICS

GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs

(2019) Avanti Shrikumar et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The novel coronary artery disease risk gene JCAD/KIAA1462 promotes endothelial dysfunction and atherosclerosis

(2019) Suowen Xu et al.   EUROPEAN HEART JOURNAL

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

(2019) Robert C. Wirka et al.   NATURE MEDICINE

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Single-cell immune landscape of human atherosclerotic plaques

(2019) Dawn M. Fernandez et al.   NATURE MEDICINE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway

(2019) Manabu Nagao et al.   CIRCULATION RESEARCH

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Arid5a Regulation and the Roles of Arid5a in the Inflammatory Response and Disease

(2019) Kishan Kumar Nyati et al.   Frontiers in Immunology

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

(2019) Vivek Rai et al.   Molecular Metabolism

Endothelial–mesenchymal transition in atherosclerosis

(2018) Celine Souilhol et al.   CARDIOVASCULAR RESEARCH

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass CytometryNovelty and Significance

(2018) Holger Winkels et al.   CIRCULATION RESEARCH

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

(2018) Rachel E. Gate et al.   NATURE GENETICS

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci

(2018) Boxiang Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Type 2 Diabetes Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets

(2018) Shubham Khetan et al.   DIABETES

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

(2018) Julien Bryois et al.   Nature Communications

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

(2018) Ayush Giri et al.   NATURE GENETICS

GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes

(2018) Nora Franceschini et al.   Nature Communications

Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus

(2018) Vivek Nanda et al.   PLoS Genetics

Monocyte-Macrophages and T Cells in Atherosclerosis

(2017) Ira Tabas et al.   IMMUNITY

Association analyses based on false discovery rate implicate new loci for coronary artery disease

(2017) Christopher P Nelson et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease

(2017) Pim van der Harst et al.   CIRCULATION RESEARCH

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems

(2016) Le Shu et al.   BMC GENOMICS

Runx2 deletion in smooth muscle cells inhibits vascular osteochondrogenesis and calcification but not atherosclerotic lesion formation

(2016) Mu-En Lin et al.   CARDIOVASCULAR RESEARCH

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci

(2016) Clint L. Miller et al.   Nature Communications

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

(2016) Husain A. Talukdar et al.   Cell Systems

Runx2 Expression in Smooth Muscle Cells Is Required for Arterial Medial Calcification in Mice

(2015) Mu-En Lin et al.   AMERICAN JOURNAL OF PATHOLOGY

Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries

(2015) M. Beaudoin et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Natural progression of atherosclerosis from pathologic intimal thickening to late fibroatheroma in human coronary arteries: A pathology study

(2015) Fumiyuki Otsuka et al.   ATHEROSCLEROSIS

9p21.3 Coronary Artery Disease Risk Variants Disrupt TEAD Transcription Factor–Dependent Transforming Growth Factor β Regulation of p16 Expression in Human Aortic Smooth Muscle CellsCLINICAL PERSPECTIVE

(2015) Naif A. M. Almontashiri et al.   CIRCULATION

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

(2015) Majid Nikpay et al.   NATURE GENETICS

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Vasa Vasorum in Normal and Diseased Arteries

(2014) Mary Jo Mulligan-Kehoe et al.   CIRCULATION

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Regulation of endothelial cell development by ETS transcription factors

(2011) Stryder M. Meadows et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Indispensable Role of the Runx1-Cbfβ Transcription Complex for In Vivo-Suppressive Function of FoxP3+ Regulatory T Cells

(2009) Akihiko Kitoh et al.   IMMUNITY

Initiation of myoblast to brown fat switch by a PRDM16–C/EBP-β transcriptional complex

(2009) Shingo Kajimura et al.   NATURE

T-box 2, a mediator of Bmp-Smad signaling, induced hyaluronan synthase 2 and Tgf 2 expression and endocardial cushion formation

(2009) M. Shirai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

SKI and MEL1 Cooperate to Inhibit Transforming Growth Factor-β Signal in Gastric Cancer Cells

(2008) Mami Takahata et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PRDM16 controls a brown fat/skeletal muscle switch

(2008) Patrick Seale et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY