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

Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

(2021) Ilakya Selvarajan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Macrophage subsets in atherosclerosis as defined by single‐cell technologies

(2020) Lisa Willemsen et al.   JOURNAL OF PATHOLOGY

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture

(2020) Mark F Sabbagh et al.   eLife

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 Environment-Sensing Aryl-Hydrocarbon Receptor Inhibits the Chondrogenic Fate of Modulated Smooth Muscle Cells in Atherosclerotic Lesions

(2020) Juyong Brian Kim et al.   CIRCULATION

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

Cholesterol-Induced Phenotypic Modulation of Smooth Muscle Cells to Macrophage/Fibroblast–like Cells Is Driven by an Unfolded Protein Response

(2020) Abhijnan Chattopadhyay et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

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

Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells

(2020) Rédouane Aherrahrou et al.   CIRCULATION RESEARCH

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

(2019) Gregory J. Fonseca et al.   Nature Communications

Linear models enable powerful differential activity analysis in massively parallel reporter assays

(2019) Leslie Myint et al.   BMC GENOMICS

TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression

(2019) Quanyi Zhao et al.   Genome Medicine

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

(2019) Irene Miguel-Escalada et al.   NATURE GENETICS

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

Single-cell immune landscape of human atherosclerotic plaques

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

Transcriptional and epigenetic regulation of macrophages in atherosclerosis

(2019) Tatyana Kuznetsova et al.   Nature Reviews Cardiology

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

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

The matrix proteins aggrecan and fibulin-1 play a key role in determining aortic stiffness

(2018) Yasmin et al.   Scientific Reports

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

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

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Smooth muscle cell-driven vascular diseases and molecular mechanisms of VSMC plasticity

(2018) Agne Frismantiene et al.   CELLULAR SIGNALLING

High throughput characterization of genetic effects on DNA:protein binding and gene transcription

(2018) Cynthia A Kalita et al.   GENOME RESEARCH

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

TBX2 and TBX3 act downstream of canonical WNT signaling in patterning and differentiation of the mouse ureteric mesenchyme

(2018) Nurullah Aydoğdu et al.   DEVELOPMENT

SEdb: a comprehensive human super-enhancer database

(2018) Yong Jiang et al.   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels

(2018) Lina Dobnikar et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

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

(2017) Alicia N Schep et al.   NATURE METHODS

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells

(2017) Nicholas T Hogan et al.   eLife

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

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci

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

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

PDGFRβ signalling regulates local inflammation and synergizes with hypercholesterolaemia to promote atherosclerosis

(2015) Chaoyong He et al.   Nature Communications

Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap

(2015) Sylvia T. Nurnberg et al.   PLoS Genetics

Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease

(2015) Hong-Hee Won et al.   PLoS Genetics

Modulation of vascular smooth muscle cell phenotype by STAT-1 and STAT-3

(2014) Mayumi Namekata Kirchmer et al.   ATHEROSCLEROSIS

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Inactivation of Nuclear Factor-Y Inhibits Vascular Smooth Muscle Cell Proliferation and Neointima Formation

(2013) Carlos Silvestre-Roig et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

Nuclear Factor of Activated T Cells 5 Regulates Vascular Smooth Muscle Cell Phenotypic Modulation

(2011) Julia A. Halterman et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Transforming growth factor-β and atherosclerosis: interwoven atherogenic and atheroprotective aspects

(2011) Ian Toma et al.   CELL AND TISSUE RESEARCH

Genetic inactivation of IL-1 signaling enhances atherosclerotic plaque instability and reduces outward vessel remodeling in advanced atherosclerosis in mice

(2011) Matthew R. Alexander et al.   JOURNAL OF CLINICAL INVESTIGATION

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

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

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA