Disease variants alter transcription factor levels and methylation of their binding sites

The Genetic Architecture of the Human Immune System: A Bioresource for Autoimmunity and Disease Pathogenesis

(2015) Mario Roederer et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci

(2015) Mathieu Lemire et al.   Nature Communications

Biological interpretation of genome-wide association studies using predicted gene functions

(2015) Tune H. Pers et al.   Nature Communications

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics

(2015) Ettje F Tigchelaar et al.   BMJ Open

A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension

(2015) Tianxiao Huan et al.   PLoS Genetics

Genetic and epigenetic regulation of gene expression in fetal and adult human livers

(2014) Marc Bonder et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’

(2014) Patrick Deelen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age

(2014) Joris Deelen et al.   HUMAN MOLECULAR GENETICS

Cohort Profile: LifeLines, a three-generation cohort study and biobank

(2014) Salome Scholtens et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Functional Interactions between NURF and Ctcf Regulate Gene Expression

(2014) Zhijun Qiu et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Breast Cancer Subtype Specific Classifiers of Response to Neoadjuvant Chemotherapy Do Not Outperform Classifiers Trained on All Subtypes

(2014) Jorma J. de Ronde et al.   PLoS One

A data-driven approach to preprocessing Illumina 450K methylation array data

(2013) Ruth Pidsley et al.   BMC GENOMICS

Genetic Variants Regulating Immune Cell Levels in Health and Disease

(2013) Valeria Orrù et al.   CELL

The Rotterdam Study: 2014 objectives and design update

(2013) Albert Hofman et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

From promises to practical strategies in epigenetic epidemiology

(2013) Jonathan Mill et al.   NATURE REVIEWS GENETICS

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

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

The Adult Netherlands Twin Register: Twenty-Five Years of Survey and Biological Data Collection

(2013) Gonneke Willemsen et al.   Twin Research and Human Genetics

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome-Wide Screen for Metabolic Syndrome Susceptibility Loci Reveals Strong Lipid Gene Contribution But No Evidence for Common Genetic Basis for Clustering of Metabolic Syndrome Traits

(2012) Kati Kristiansson et al.   Circulation-Cardiovascular Genetics

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

A genome-wide association study identifies two new susceptibility loci for lung adenocarcinoma in the Japanese population

(2012) Kouya Shiraishi et al.   NATURE GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation

(2012) Nizar Touleimat et al.   Epigenomics

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

(2011) Harm-Jan Westra et al.   BIOINFORMATICS

Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project

(2011) Guillaume Lettre et al.   PLoS Genetics

Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

(2011) Rudolf S. N. Fehrmann et al.   PLoS Genetics

The cross-sectional association between insulin resistance and circulating complement C3 is partly explained by plasma alanine aminotransferase, independent of central obesity and general inflammation (the CODAM study)

(2010) Marleen M. J. van Greevenbroek et al.   EUROPEAN 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

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes

(2009) Nobuhiro Sasai et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size

(2009) Nicole Soranzo et al.   PLoS Genetics

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Genome-wide association of major depression: description of samples for the GAIN Major Depressive Disorder Study: NTR and NESDA biobank projects

(2008) Dorret I Boomsma et al.   EUROPEAN JOURNAL OF HUMAN GENETICS