An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

Dissecting the genetics of the human transcriptome identifies novel trait-relatedtrans-eQTLs and corroborates the regulatory relevance of non-protein coding loci

(2015) Holger Kirsten et al.   HUMAN MOLECULAR GENETICS

Characterization of Expression Quantitative Trait Loci in the Human Colon

(2015) Tarjinder Singh et al.   INFLAMMATORY BOWEL DISEASES

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus

(2015) Michael R. Johnson et al.   Nature Communications

The Genetic and Mechanistic Basis for Variation in Gene Regulation

(2015) Athma A. Pai et al.   PLoS Genetics

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Novel Insights into the Regulatory Architecture of CD4+ T Cells in Rheumatoid Arthritis

(2014) Adrià Aterido et al.   PLoS One

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

(2014) Anne Biton et al.   Cell Reports

A Systems Genetics Approach Identifies CXCL14, ITGAX, and LPCAT2 as Novel Aggressive Prostate Cancer Susceptibility Genes

(2014) Kendra A. Williams et al.   PLoS Genetics

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

(2014) Ville-Petteri Mäkinen et al.   PLoS Genetics

Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS

(2013) Xin He et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Beyond GWASs: Illuminating the Dark Road from Association to Function

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

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

(2013) Can Yang et al.   BIOINFORMATICS

Genetic and Nongenetic Variation Revealed for the Principal Components of Human Gene Expression

(2013) Anita Goldinger et al.   GENETICS

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

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

(2013) Sara Mostafavi et al.   PLoS One

Refining Susceptibility Loci of Chronic Obstructive Pulmonary Disease with Lung eqtls

(2013) Maxime Lamontagne et al.   PLoS One

Correcting for Population Structure and Kinship Using the Linear Mixed Model: Theory and Extensions

(2013) Gabriel E. Hoffman   PLoS One

Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

(2013) Vinod Kumar et al.   PLoS Genetics

Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus

(2013) Clint L. Miller et al.   PLoS Genetics

Impact of common regulatory single-nucleotide variants on gene expression profiles in whole blood

(2012) Divya Mehta et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

IRX4 at 5p15 suppresses prostate cancer growth through the interaction with vitamin D receptor, conferring prostate cancer susceptibility

(2012) Hai Ha Nguyen et al.   HUMAN MOLECULAR GENETICS

Bayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data

(2012) Jan Krumsiek et al.   JOURNAL OF PROTEOME RESEARCH

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

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

(2012) Oliver Stegle et al.   Nature Protocols

What Can Causal Networks Tell Us about Metabolic Pathways?

(2012) Rachael Hageman Blair et al.   PLoS Computational Biology

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

(2012) Nicoló Fusi et al.   PLoS Computational Biology

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

(2012) Fanggeng Zou et al.   PLoS Genetics

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes

(2011) Claus H Bang-Berthelsen et al.   BMC GENOMICS

Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain

(2011) A L Richards et al.   MOLECULAR PSYCHIATRY

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

(2011) Kerrin S Small et al.   NATURE GENETICS

From expression QTLs to personalized transcriptomics

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

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

(2011) Alkes L. Price et al.   PLoS Genetics

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans

(2011) Maxime Rotival et al.   PLoS Genetics

Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

(2011) Rudolf S. N. Fehrmann et al.   PLoS Genetics

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

(2010) Hua Zhong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Expression Quantitative Trait Loci: Replication, Tissue- and Sex-Specificity in Mice

(2010) A. van Nas et al.   GENETICS

Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease

(2010) Karin Fransen et al.   HUMAN MOLECULAR GENETICS

Independent component analysis: Mining microarray data for fundamental human gene expression modules

(2010) Jesse M. Engreitz et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk

(2010) Matthias Heinig et al.   NATURE

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois 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

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

Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations

(2010) Benjamin A. Logsdon 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

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

SCAN: SNP and copy number annotation

(2009) Eric R. Gamazon et al.   BIOINFORMATICS

Mapping complex disease traits with global gene expression

(2009) William Cookson 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

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

(2008) H. M. Kang et al.   GENETICS

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

From gene expression to disease risk

(2008) Emmanouil T Dermitzakis   NATURE GENETICS

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

(2008) Jun Zhu et al.   NATURE GENETICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

(2008) Erin L Heinzen et al.   PLOS BIOLOGY

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators

(2008) Chunlei Wu et al.   PLoS Genetics

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics