Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy et al.   NUCLEIC ACIDS RESEARCH

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

(2015) et al.   SCIENCE

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

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

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

(2014) James C. Chen et al.   CELL

A genome-wide association study of anorexia nervosa

(2014) V Boraska et al.   MOLECULAR PSYCHIATRY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

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

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

The multifactorial role of neutrophils in rheumatoid arthritis

(2014) Helen L. Wright et al.   Nature Reviews Rheumatology

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Identifying and mapping cell-type-specific chromatin programming of gene expression

(2014) Troels T. Marstrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

(2014) Konrad J. Karczewski et al.   PLoS Genetics

A Central Role for GRB10 in Regulation of Islet Function in Man

(2014) Inga Prokopenko et al.   PLoS Genetics

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

(2014) Ville-Petteri Mäkinen et al.   PLoS Genetics

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis

(2013)   LANCET

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Seven new loci associated with age-related macular degeneration

(2013) Lars G Fritsche et al.   NATURE GENETICS

Genome-wide association analysis identifies 13 new risk loci for schizophrenia

(2013) Stephan Ripke 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

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

(2013) P. Kheradpour 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

Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification

(2013) Laura L. Faye et al.   PLoS Genetics

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

(2012) D. Marbach et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Developing predictive molecular maps of human disease through community-based modeling

(2012) Jonathan M J Derry et al.   NATURE GENETICS

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

(2012) Karol Estrada et al.   NATURE GENETICS

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

(2012) Gosia Trynka et al.   NATURE GENETICS

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

(2012)   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

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

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

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

(2011) Georg B. Ehret et al.   NATURE

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

(2011) Stephen Sawcer et al.   NATURE

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

(2011) Heribert Schunkert et al.   NATURE GENETICS

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

Role of the endothelium in inflammatory bowel diseases

(2011) Walter E Cromer   WORLD JOURNAL OF GASTROENTEROLOGY

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

DA DA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

(2011) Sinan Erten et al.   BioData Mining

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Common Variants at 10 Genomic Loci Influence Hemoglobin A1C Levels via Glycemic and Nonglycemic Pathways

(2010) N. Soranzo et al.   DIABETES

Genetic Variation in IL28B Is Associated With Chronic Hepatitis C and Treatment Failure: A Genome-Wide Association Study

(2010) Andri Rauch et al.   GASTROENTEROLOGY

Basal ganglia pathology in schizophrenia: dopamine connections and anomalies

(2010) Emma Perez-Costas et al.   JOURNAL OF NEUROCHEMISTRY

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy

(2010) Hyun Hor et al.   NATURE GENETICS

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

(2010) Elizabeth K Speliotes et al.   NATURE GENETICS

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

(2010) Eli A Stahl et al.   NATURE GENETICS

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

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

(2010) Josée Dupuis et al.   NATURE GENETICS

Entrez Gene: gene-centered information at NCBI

(2010) D. Maglott et al.   NUCLEIC ACIDS RESEARCH

Role of Mast Cells in Inflammatory Bowel Disease and Inflammation-Associated Colorectal Neoplasia in IL-10-Deficient Mice

(2010) Maciej Chichlowski et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association study reveals genetic risk underlying Parkinson's disease

(2009) Javier Simón-Sánchez et al.   NATURE GENETICS

Identification of Splenic Reservoir Monocytes and Their Deployment to Inflammatory Sites

(2009) F. K. Swirski et al.   SCIENCE

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE