Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity

(2011) N. A. Furlotte et al.   BIOINFORMATICS

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

(2011) Qinghua Xu et al.   PLoS One

Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

(2011) Stephen B. Montgomery et al.   PLoS Genetics

Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

(2011) Leopold Parts et al.   PLoS Genetics

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

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 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

Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis

(2010) Barbara E. Engelhardt et al.   PLoS Genetics

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2008) H. M. Kang et al.   GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY