Association analysis identifies 65 new breast cancer risk loci

The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

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Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns

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Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

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Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

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Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

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

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

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

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An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1

(2014) Qiuyin Cai et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

Global view of enhancer-promoter interactome in human cells

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Genome-wide pathway analysis of breast cancer

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Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

(2014) Maya Ghoussaini et al.   Nature Communications

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

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Super-Enhancers in the Control of Cell Identity and Disease

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Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

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Targeting the PDGF signaling pathway in tumor treatment

(2013) Carl-Henrik Heldin   Cell Communication and Signaling

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

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A Common Deletion in the APOBEC3 Genes and Breast Cancer Risk

(2013) Jirong Long et al.   JNCI-Journal of the National Cancer Institute

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Fast and accurate inference of local ancestry in Latino populations

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GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

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Comprehensive molecular portraits of human breast tumours

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

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Bayesian refinement of association signals for 14 loci in 3 common diseases

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

(2012) Bryan Howie et al.   NATURE GENETICS

Predicting the Functional Effect of Amino Acid Substitutions and Indels

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Genome-Wide Association Study in East Asians Identifies Novel Susceptibility Loci for Breast Cancer

(2012) Jirong Long et al.   PLoS Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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Gene set analysis of genome-wide association studies: Methodological issues and perspectives

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Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

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GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Peilin Jia et al.   BIOINFORMATICS

METAL: fast and efficient meta-analysis of genomewide association scans

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ProbABEL package for genome-wide association analysis of imputed data

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Evaluating the power to discriminate between highly correlated SNPs in genetic association studies

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MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

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A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Analysing biological pathways in genome-wide association studies

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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

PH Domain-Only Protein PHLDA3 Is a p53-Regulated Repressor of Akt

(2009) Tatsuya Kawase et al.   CELL

Identification of deleterious mutations within three human genomes

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Genome-wide association studies identify loci associated with age at menarche and age at natural menopause

(2009) Chunyan He et al.   NATURE GENETICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

(2009) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

(2009) François-Olivier Desmet et al.   NUCLEIC ACIDS RESEARCH

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

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

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH