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

Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes

(2011) Kerrin S Small et al.   NATURE GENETICS

Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

(2011) Leopold Parts et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Correction for hidden confounders in the genetic analysis of gene expression

(2010) J. Listgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

(2010) Wei Zhang et al.   PLoS Computational Biology

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

puma: a Bioconductor package for propagating uncertainty in microarray analysis

(2009) Richard D Pearson et al.   BMC BIOINFORMATICS

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

(2008) Shameek Biswas et al.   BMC BIOINFORMATICS

Using genetic markers to orient the edges in quantitative trait networks: The NEO software

(2008) Jason E Aten et al.   BMC Systems Biology

Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots

(2008) H. M. Kang et al.   GENETICS

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Extreme Clonality in Lymphoblastoid Cell Lines with Implications for Allele Specific Expression Analyses

(2008) Vincent Plagnol et al.   PLoS One

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

Genetical Genomics: Spotlight on QTL Hotspots

(2008) Rainer Breitling et al.   PLoS Genetics