XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

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

(2016) Biola M. Javierre et al.   CELL

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

(2016) David Ellinghaus et al.   NATURE GENETICS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

(2016) Maria Gutierrez-Arcelus et al.   NATURE REVIEWS GENETICS

Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

(2016) Jennifer M. Whitehead Pavlides et al.   Genome Medicine

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

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

A promoter-level mammalian expression atlas

(2014)   NATURE

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

MHC-I expression renders catecholaminergic neurons susceptible to T-cell-mediated degeneration

(2014) Carolina Cebrián et al.   Nature Communications

Approaches for establishing the function of regulatory genetic variants involved in disease

(2014) Julian Charles Knight   Genome Medicine

RCircos: an R package for Circos 2D track plots

(2013) Hongen Zhang et al.   BMC BIOINFORMATICS

Innate immune mechanisms in vitiligo: danger from within

(2013) Jillian M Richmond et al.   CURRENT OPINION IN IMMUNOLOGY

The big challenges of big data

(2013) Vivien Marx   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

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

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Genetic insights into common pathways and complex relationships among immune-mediated diseases

(2013) Miles Parkes et al.   NATURE REVIEWS GENETICS

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Linking disease associations with regulatory information in the human genome

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

(2009) Cynthia L. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics