Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors

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(2015) Julie George et al.   NATURE

The alternative role of DNA methylation in splicing regulation

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Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

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Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types

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Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

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Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis

(2013) Xing Qiu et al.   BMC BIOINFORMATICS

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

(2013) Qiyuan Li et al.   CELL

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

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

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

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Linking disease associations with regulatory information in the human genome

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Detecting differential usage of exons from RNA-seq data

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GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

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A comparison of approaches to account for uncertainty in analysis of imputed genotypes

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

(2011) Matthew L Freedman et al.   NATURE GENETICS

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

(2011) Irina M. Shapiro et al.   PLoS Genetics

Leveraging Genetic Variability across Populations for the Identification of Causal Variants

(2010) Noah Zaitlen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor–negative breast cancer in the general population

(2010) Antonis C Antoniou et al.   NATURE GENETICS

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

(2010) Alexandra C. Nica et al.   PLoS Genetics

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Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

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Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers

(2009) Buhm Han 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

Shape-IT: new rapid and accurate algorithm for haplotype inference

(2008) Olivier Delaneau et al.   BMC BIOINFORMATICS

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS