A single-cell atlas of chromatin accessibility in the human genome

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Systematic analysis of binding of transcription factors to noncoding variants

(2021) Jian Yan et al.   NATURE

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

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

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

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

(2021) Alexandro E. Trevino et al.   CELL

An atlas of gene regulatory elements in adult mouse cerebrum

(2021) Yang Eric Li et al.   NATURE

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Role of IRF8 in immune cells functions, protection against infections, and susceptibility to inflammatory diseases

(2020) Sandra Salem et al.   HUMAN GENETICS

Index and biological spectrum of human DNase I hypersensitive sites

(2020) Wouter Meuleman et al.   NATURE

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

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

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

The epigenetic basis of cellular heterogeneity

(2020) Benjamin Carter et al.   NATURE REVIEWS GENETICS

Genome-wide association analysis of diverticular disease points towards neuromuscular, connective tissue and epithelial pathomechanisms

(2019) Clemens Schafmayer et al.   GUT

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

(2019) Iris E. Jansen 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

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development

(2019) Kai Zhang et al.   Science Advances

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

(2019) Akira Wiberg et al.   Nature Communications

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

(2019) Nick Shrine et al.   NATURE GENETICS

Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations

(2019) Phuwanat Sakornsakolpat et al.   NATURE GENETICS

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

(2019) John R. Sinnamon et al.   GENOME RESEARCH

Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors

(2019) Nicole M. Warrington 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

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

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

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

A catalog of genetic loci associated with kidney function from analyses of a million individuals

(2019) Matthias Wuttke et al.   NATURE GENETICS

Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies

(2019) Milton Pividori et al.   Lancet Respiratory Medicine

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

A compendium of promoter-centered long-range chromatin interactions in the human genome

(2019) Inkyung Jung et al.   NATURE GENETICS

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

(2019)   SCIENCE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels

(2019) Adrienne Tin et al.   NATURE GENETICS

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

A large electronic-health-record-based genome-wide study of serum lipids

(2018) Thomas J. Hoffmann 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

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

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

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

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

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

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish 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

Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation

(2018) Alexander Teumer et al.   Nature Communications

Association analysis identifies 65 new breast cancer risk loci

(2017) Kyriaki Michailidou et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7

(2017) Yang Luo et al.   NATURE GENETICS

Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

(2017) John P Kemp et al.   NATURE GENETICS

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Myosin content of individual human muscle fibers isolated by laser capture microdissection

(2016) Charles A. Stuart et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Cutting Edge: Expression of IRF8 in Gastric Epithelial Cells Confers Protective Innate Immunity againstHelicobacter pyloriInfection

(2016) Ming Yan et al.   JOURNAL OF IMMUNOLOGY

Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease

(2016) Sun-Gou Ji et al.   NATURE GENETICS

Common variants at PVT1, ATG13–AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency

(2016) Paola G Bronson et al.   NATURE GENETICS

Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants

(2016) Ying Jin et al.   NATURE GENETICS

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels

(2016) Tuomas O. Kilpeläinen et al.   Nature Communications

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   BIOPRESERVATION AND BIOBANKING

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

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

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

(2015) Majid Nikpay et al.   NATURE GENETICS

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

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis

(2015) Lavinia Paternoster et al.   NATURE GENETICS

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

(2015) Hilary K Finucane 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

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

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

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

(2015) Heather J. Cordell et al.   Nature Communications

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   Biopreservation and Biobanking

Developmental myosins: expression patterns and functional significance

(2015) Stefano Schiaffino et al.   Skeletal Muscle

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

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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

(2012) Alisa K Manning et al.   NATURE GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genome-Wide Association Identifies Nine Common Variants Associated With Fasting Proinsulin Levels and Provides New Insights Into the Pathophysiology of Type 2 Diabetes

(2011) R. J. Strawbridge et al.   DIABETES

Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function

(2011) Tao Shen et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Narrow scope for resolution-limit-free community detection

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

Fiber Types in Mammalian Skeletal Muscles

(2011) Stefano Schiaffino et al.   PHYSIOLOGICAL REVIEWS

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

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge

(2010) Richa Saxena et al.   NATURE GENETICS

Ets Transcription Factors Control Epithelial Maturation and Transit and Crypt-Villus Morphogenesis in the Mammalian Intestine

(2009) Paul Jedlicka et al.   AMERICAN JOURNAL OF PATHOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

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

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY