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

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

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 Transcriptome Atlas of Murine Endothelial Cells

(2020) Joanna Kalucka et al.   CELL

Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure

(2020) Marios Arvanitis et al.   Nature Communications

Heritable arrhythmia syndromes associated with abnormal cardiac sodium channel function: ionic and non-ionic mechanisms

(2020) Mathilde R Rivaud et al.   CARDIOVASCULAR RESEARCH

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia

(2020) Paul W. Hook et al.   GENOME RESEARCH

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

(2020) Wilson Lek Wen Tan et al.   CIRCULATION RESEARCH

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

(2020) Kazuyoshi Ishigaki et al.   NATURE GENETICS

Assigning Distal Genomic Enhancers to Cardiac Disease–Causing Genes

(2020) Chukwuemeka George Anene-Nzelu et al.   CIRCULATION

Cells of the adult human heart

(2020) Monika Litviňuková et al.   NATURE

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

Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data

(2019) Ioanna Tachmazidou et al.   NATURE GENETICS

Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

(2019) Yueli Cui et al.   Cell Reports

A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome

(2019) Akira Wiberg et al.   Nature Communications

Assessing the causal association of glycine with risk of cardio-metabolic diseases

(2019) Laura B. L. Wittemans et al.   Nature Communications

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways

(2019) Philip R. Jansen et al.   NATURE GENETICS

Varicose veins of lower extremities: Insights from the first large-scale genetic study

(2019) Alexandra S. Shadrina et al.   PLoS Genetics

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

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

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

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

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

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Reactivation of the Nkx2.5 cardiac enhancer after myocardial infarction does not presage myogenesis

(2018) Marcus-André Deutsch et al.   CARDIOVASCULAR RESEARCH

Genetic Fate Mapping Defines the Vascular Potential of Endocardial Cells in the Adult HeartNovelty and Significance

(2018) Juan Tang et al.   CIRCULATION RESEARCH

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes

(2018) Rainer Malik et al.   NATURE GENETICS

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels

(2018) Xia Jiang et al.   Nature Communications

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

(2018) Ralf Gilsbach et al.   Nature Communications

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

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

A molecular atlas of cell types and zonation in the brain vasculature

(2018) Michael Vanlandewijck et al.   NATURE

Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

(2018) Jonas B. Nielsen et al.   NATURE GENETICS

Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells

(2018) Jennifer Veevers et al.   Stem Cell Reports

Shared genetic risk contributes to type 1 and type 2 diabetes etiology

(2018) Anthony Aylward et al.   HUMAN MOLECULAR GENETICS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

(2018) Guangshuai Jia et al.   Nature Communications

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

Matrix-driven Myosin II Mediates the Pro-fibrotic Fibroblast Phenotype

(2016) Brian D. Southern et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide associations for birth weight and correlations with adult disease

(2016) Momoko Horikoshi et al.   NATURE

Genome-wide association study identifies 74 loci associated with educational attainment

(2016) Aysu Okbay et al.   NATURE

Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes

(2015) Alexander Teumer et al.   DIABETES

Functions of myosin light chain-2 (MYL2) in cardiac muscle and disease

(2015) Farah Sheikh et al.   GENE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

(2015) Felix R Day 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

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

Cardiogenic Genes Expressed in Cardiac Fibroblasts Contribute to Heart Development and Repair

(2014) Milena B. Furtado et al.   CIRCULATION RESEARCH

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

A common genetic variant within SCN10A modulates cardiac SCN5A expression

(2014) Malou van den Boogaard et al.   JOURNAL OF CLINICAL INVESTIGATION

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

(2014) John A Zuris et al.   NATURE BIOTECHNOLOGY

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

hERG 1b is critical for human cardiac repolarization

(2014) David K. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

(2014) Ralf Gilsbach et al.   Nature Communications

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Identification of heart rate–associated loci and their effects on cardiac conduction and rhythm disorders

(2013) Marcel den Hoed et al.   NATURE GENETICS

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Switched on with magnets

(2013) Sanjay Kumar   Nature Nanotechnology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

(2012) Scott Smemo et al.   HUMAN MOLECULAR GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

EGFL7: a unique angiogenic signaling factor in vascular development and disease

(2011) D. Nichol et al.   BLOOD

Fibroblasts and Myofibroblasts: What Are We Talking About?

(2011) Jennifer Baum et al.   JOURNAL OF CARDIOVASCULAR PHARMACOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Chemically defined conditions for human iPSC derivation and culture

(2011) Guokai Chen et al.   NATURE METHODS

Narrow scope for resolution-limit-free community detection

(2011) V. A. Traag et al.   PHYSICAL REVIEW E

Differential gene expressions in atrial and ventricular myocytes: insights into the road of applying embryonic stem cell-derived cardiomyocytes for future therapies

(2010) Sze Ying Ng et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Limited forward trafficking of connexin 43 reduces cell-cell coupling in stressed human and mouse myocardium

(2010) James W. Smyth et al.   JOURNAL OF CLINICAL INVESTIGATION

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Themis, a T cell–specific protein important for late thymocyte development

(2009) Renaud Lesourne et al.   NATURE IMMUNOLOGY

Bayes factors for genome-wide association studies: comparison withP-values

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

Cidea is associated with lipid droplets and insulin sensitivity in humans

(2008) V. Puri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY