The genetic regulatory signature of type 2 diabetes in human skeletal muscle

RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power

(2015) Chee Lee et al.   BIOINFORMATICS

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

mTOR signaling in cellular and organismal energetics

(2015) Verena Albert et al.   CURRENT OPINION IN CELL BIOLOGY

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

(2015) Alain Pacis et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

(2015) Daniel X Quang et al.   Epigenetics & Chromatin

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(2015) Fiona Allum et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

minimac2: faster genotype imputation

(2014) Christian Fuchsberger et al.   BIOINFORMATICS

Calcium signaling in insulin action on striated muscle

(2014) A. Contreras-Ferrat et al.   CELL CALCIUM

Increased Interaction With Insulin Receptor Substrate 1, a Novel Abnormality in Insulin Resistance and Type 2 Diabetes

(2014) Michael Caruso et al.   DIABETES

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing

(2014) Malene E. Lindholm et al.   FASEB JOURNAL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quality of life along the diabetes continuum: a cross-sectional view of health-related quality of life and general health status in middle-aged and older Finns

(2014) Saku Väätäinen et al.   QUALITY OF LIFE RESEARCH

Identification of a Regulatory Variant That Binds FOXA1 and FOXA2 at the CDC123/CAMK1D Type 2 Diabetes GWAS Locus

(2014) Marie P. Fogarty et al.   PLoS Genetics

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Expression of Phosphofructokinase in Skeletal Muscle Is Influenced by Genetic Variation and Associated With Insulin Sensitivity

(2013) S. Keildson et al.   DIABETES

Pathophysiology and treatment of type 2 diabetes: perspectives on the past, present, and future

(2013) Steven E Kahn et al.   LANCET

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen 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

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

A single-nucleotide polymorphism in ANK1 is associated with susceptibility to type 2 diabetes in Japanese populations

(2012) Minako Imamura et al.   HUMAN MOLECULAR GENETICS

Hydrophobic residues in small ankyrin 1 participate in binding to obscurin

(2012) Chris D. Willis et al.   MOLECULAR MEMBRANE BIOLOGY

Diabetes in numbers

(2012) Tony Scully   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Bryan Howie et al.   NATURE GENETICS

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

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

(2012) Oliver Stegle et al.   Nature Protocols

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Integrity of the network sarcoplasmic reticulum in skeletal muscle requires small ankyrin 1

(2011) M. A. Ackermann et al.   JOURNAL OF CELL SCIENCE

Nuclear Receptors TR2 and TR4 Recruit Multiple Epigenetic Transcriptional Corepressors That Associate Specifically with the Embryonic  -Type Globin Promoters in Differentiated Adult Erythroid Cells

(2011) S. Cui et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) Jason Ernst et al.   NATURE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Statistical Modeling of RNA-Seq Data

(2011) Julia Salzman et al.   STATISTICAL SCIENCE

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Diet, fitness and metabolic syndrome – The DR’s EXTRA Study

(2010) R. Kouki et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Association of 18 Confirmed Susceptibility Loci for Type 2 Diabetes With Indices of Insulin Release, Proinsulin Conversion, and Insulin Sensitivity in 5,327 Nondiabetic Finnish Men

(2009) A. Stancakova et al.   DIABETES

Long-Range LD Can Confound Genome Scans in Admixed Populations

(2008) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics