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NAFLD and cardiovascular diseases: a clinical review

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The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

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Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

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Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis

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Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver

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Comprehensive Integration of Single-Cell Data

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

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

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

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Dissecting super-enhancer hierarchy based on chromatin interactions

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Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

(2018) David Z. Pan et al.   Nature Communications

A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver

(2018) Tobias Strunz et al.   Scientific Reports

A promoter interaction map for cardiovascular disease genetics

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

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

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Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

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

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

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

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Genetics of coronary artery disease: discovery, biology and clinical translation

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The Encyclopedia of DNA elements (ENCODE): data portal update

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Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

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Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells

(2017) Hiroki Ikeda et al.   Nature Communications

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin

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Identification of 15 novel risk loci for coronary artery disease and genetic risk of recurrent events, atrial fibrillation and heart failure

(2017) Niek Verweij et al.   Scientific Reports

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells

(2017) Maykel López Rodríguez et al.   Genome Medicine

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

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Functional Analysis of a Novel Genome-Wide Association Study Signal inSMAD3That Confers Protection From Coronary Artery DiseaseSignificance

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DGCA: A comprehensive R package for Differential Gene Correlation Analysis

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Correlation analysis between ApoM gene-promoter polymorphisms and coronary heart disease

(2016) Y Zhang et al.   Cardiovascular Journal of Africa

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

(2016) Biola M. Javierre et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits

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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

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Consensus Genome-Wide Expression Quantitative Trait Loci and Their Relationship with Human Complex Trait Disease

(2016) Chen-Hsin Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

(2016) O. Franzen et al.   SCIENCE

Correction: Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains

(2016) Brian J. Bennett et al.   PLoS Genetics

Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus

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

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Genetic determinants of quantitative traits associated with cardiovascular disease risk

(2015) Božena Smolková et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

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

(2015) Majid Nikpay et al.   NATURE GENETICS

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Predicting effects of noncoding variants with deep learning–based sequence model

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

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

Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains

(2015) Brian J. Bennett et al.   PLoS Genetics

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(2014) Zuguang Gu et al.   BIOINFORMATICS

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem Cell

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization

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svaseq: removing batch effects and other unwanted noise from sequencing data

(2014) Jeffrey T. Leek   NUCLEIC ACIDS RESEARCH

A Preliminary Study of the Relationship between Promoter Methylation of the ABCG1, GALNT2 and HMGCR Genes and Coronary Heart Disease

(2014) Ping Peng et al.   PLoS One

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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(2013) Marko Simonen et al.   HEPATOLOGY

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale 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

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Effect of 9p21.3 Coronary Artery Disease Locus Neighboring Genes on Atherosclerosis in Mice

(2012) Juyong Brian Kim et al.   CIRCULATION

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(2012)   NATURE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Association of LIPA Gene Polymorphisms With Obesity-Related Metabolic Complications Among Severely Obese Patients

(2012) Frédéric Guénard et al.   Obesity

The variant call format and VCFtools

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Synthetic Associations Are Unlikely to Account for Many Common Disease Genome-Wide Association Signals

(2011) Carl A. Anderson et al.   PLOS BIOLOGY

Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue

(2011) Federico Innocenti et al.   PLoS Genetics

Systems Genetics Analysis of Gene-by-Environment Interactions in Human Cells

(2010) Casey E. Romanoski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

(2010) Kiran Musunuru et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY