Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution

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Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

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Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription

(2018) Yong Hoon Kim et al.   SCIENCE

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry

(2018) Sara L Pulit et al.   HUMAN MOLECULAR GENETICS

Power, false discovery rate and Winner’s Curse in eQTL studies

(2018) Qin Qin Huang et al.   NUCLEIC ACIDS RESEARCH

Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits

(2018) Aldi T. Kraja et al.   AMERICAN JOURNAL OF HUMAN 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

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Global aetiology and epidemiology of type 2 diabetes mellitus and its complications

(2017) Yan Zheng et al.   Nature Reviews Endocrinology

The Role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-expression Networks

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

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Genome-Wide Association Study of the Modified Stumvoll Insulin Sensitivity Index Identifies BCL2 and FAM19A2 as Novel Insulin Sensitivity Loci

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Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance

(2016) Luca A Lotta et al.   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

NAD+ repletion improves muscle function in muscular dystrophy and counters global PARylation

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Genome-wide screen of DNA methylation identifies novel markers in childhood obesity

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The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

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Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Second-generation PLINK: rising to the challenge of larger and richer datasets

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Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

(2014) Yibo Wu et al.   CELL

Pharmacological Inhibition of Poly(ADP-Ribose) Polymerases Improves Fitness and Mitochondrial Function in Skeletal Muscle

(2014) Eija Pirinen et al.   Cell Metabolism

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

An Evolutionarily Conserved Role for the Aryl Hydrocarbon Receptor in the Regulation of Movement

(2014) Evan G. Williams et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity

(2013) Antigone S. Dimas et al.   DIABETES

Oleate prevents saturated-fatty-acid-induced ER stress, inflammation and insulin resistance in skeletal muscle cells through an AMPK-dependent mechanism

(2013) L. Salvadó et al.   DIABETOLOGIA

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

(2013) B. Zhang et al.   GENOME RESEARCH

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

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Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

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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

Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits

(2012) Pénélope A. Andreux et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

(2012) Robert A Scott et al.   NATURE GENETICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Camera: a competitive gene set test accounting for inter-gene correlation

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Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Characterization of the colorectal cancer–associated enhancer MYC-335 at 8q24: the role of rs67491583

(2012) Sari Tuupanen et al.   Cancer Genetics

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

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

(2011) Jason Ernst et al.   NATURE

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

(2010) Michael L. Stitzel et al.   Cell Metabolism

Palmitate-induced skeletal muscle insulin resistance does not require NF-κB activation

(2010) Pascal P. H. Hommelberg et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

(2010) Josée Dupuis et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Skeletal Muscle Insulin Resistance Is the Primary Defect in Type 2 Diabetes

(2009) R. A. DeFronzo et al.   DIABETES CARE

Saturated fatty acid-induced insulin resistance is associated with mitochondrial dysfunction in skeletal muscle cells

(2009) Sandro M. Hirabara et al.   JOURNAL OF CELLULAR PHYSIOLOGY

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Obesity and Free Fatty Acids

(2008) Guenther Boden   ENDOCRINOLOGY AND METABOLISM CLINICS OF NORTH AMERICA

Mutations in ligands and receptors of the leptin–melanocortin pathway that lead to obesity

(2008) I Sadaf Farooqi et al.   Nature clinical practice. Endocrinology & metabolism