An integrative functional genomics framework for effective identification of novel regulatory variants in genome–phenome studies

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

(2017) Lauren A Peters et al.   NATURE GENETICS

Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants

(2017) Jason H. Karnes et al.   Science Translational Medicine

Phenome-Wide Association Studies as a Tool to Advance Precision Medicine

(2016) Joshua C. Denny et al.   Annual Review of Genomics and Human Genetics

Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci

(2016) Brett M. Reid et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

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

(2016) Daniel Marbach et al.   NATURE METHODS

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

Unravelling the human genome–phenome relationship using phenome-wide association studies

(2016) William S. Bush et al.   NATURE REVIEWS GENETICS

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

Tissue Specificity of Human Disease Module

(2016) Maksim Kitsak et al.   Scientific Reports

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles

(2015) Quan Wang et al.   BIOINFORMATICS

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

(2015) Jung Hoon Woo et al.   CELL

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

(2015) Junfei Zhao et al.   MOLECULAR & CELLULAR PROTEOMICS

SKA2 methylation is associated with decreased prefrontal cortical thickness and greater PTSD severity among trauma-exposed veterans

(2015) N Sadeh et al.   MOLECULAR PSYCHIATRY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

(2015) Feixiong Cheng et al.   PLoS Computational Biology

Epigenetic and genetic variation at SKA2 predict suicidal behavior and post-traumatic stress disorder

(2015) Z Kaminsky et al.   Translational Psychiatry

Genome-wide Interrogation of Longitudinal FEV1in Children with Asthma

(2014) Kehua Wu et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A promoter-level mammalian expression atlas

(2014)   NATURE

A Role for Noncoding Variation in Schizophrenia

(2014) Panos Roussos et al.   Cell Reports

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

(2014) Huy Vuong et al.   Genome Medicine

DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies

(2013) Xing Hua et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A PheWAS approach in studying HLA-DRB1*1501

(2013) S J Hebbring et al.   GENES AND IMMUNITY

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Functional Properties of Rare Missense Variants of Human CDH13 Found in Adult Attention Deficit/Hyperactivity Disorder (ADHD) Patients

(2013) Thegna Mavroconstanti et al.   PLoS One

Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

(2013) Sarah A. Pendergrass et al.   PLoS Genetics

Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls

(2012) Katherine P. Liao et al.   ARTHRITIS AND RHEUMATISM

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Genome-wide association study identifies multiple loci influencing human serum metabolite levels

(2012) Johannes Kettunen et al.   NATURE GENETICS

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

(2012) Cheng-Tsung Lu et al.   NUCLEIC ACIDS RESEARCH

Integrated cross-species transcriptional network analysis of metastatic susceptibility

(2012) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response

(2011) T Kuparinen et al.   GENES AND IMMUNITY

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

(2011) I. Lee et al.   GENOME RESEARCH

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

(2011) Jason Ernst et al.   NATURE

Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy

(2011) Günter U Höglinger et al.   NATURE GENETICS

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma

(2011) John C Chambers et al.   NATURE GENETICS

Principles for the post-GWAS functional characterization of cancer risk loci

(2011) Matthew L Freedman et al.   NATURE GENETICS

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

LITAF and TNFSF15, two downstream targets of AMPK, exert inhibitory effects on tumor growth

(2011) J Zhou et al.   ONCOGENE

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

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

A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease

(2011) 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 power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations

(2010) J. C. Denny et al.   BIOINFORMATICS

dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks

(2010) Peilin Jia et al.   BIOINFORMATICS

Breast cancer, cytomegalovirus and Epstein–Barr virus: a nested case–control study

(2010) B Cox et al.   BRITISH JOURNAL OF CANCER

Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain

(2010) AnhThu Nguyen et al.   FASEB JOURNAL

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction

(2009) Daniel F Gudbjartsson et al.   NATURE GENETICS

Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus

(2009) Jian-Wen Han et al.   NATURE GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose

(2009) Fumihiko Takeuchi et al.   PLoS Genetics

Association of genetic variations in the CSF2 and CSF3 genes with lung function in smoking-induced COPD

(2008) J-Q. He et al.   EUROPEAN RESPIRATORY JOURNAL

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS