Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

(2012) Nicoló Fusi et al.   PLoS Computational Biology

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

A fused lasso latent feature model for analyzing multi-sample aCGH data

(2011) G. Nowak et al.   BIOSTATISTICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

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

(2010) Hyun Min Kang et al.   NATURE GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS 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

Guaranteed Minimum-Rank Solutions of Linear Matrix Equations via Nuclear Norm Minimization

(2010) Benjamin Recht et al.   SIAM REVIEW

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

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

(2009) Da Wei Huang et al.   Nature Protocols

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

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

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

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

(2008) H. M. Kang et al.   GENETICS

Using gene expression to investigate the genetic basis of complex disorders

(2008) A. C. Nica et al.   HUMAN MOLECULAR GENETICS

Sure independence screening for ultrahigh dimensional feature space

(2008) Jianqing Fan et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY