Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

When Is Hub Gene Selection Better than Standard Meta-Analysis?

(2013) Peter Langfelder et al.   PLoS One

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

(2013) David Amar et al.   PLoS Computational Biology

An Evolutionary Perspective on Epistasis and the Missing Heritability

(2013) Gibran Hemani et al.   PLoS Genetics

Empirical Bayes conditional independence graphs for regulatory network recovery

(2012) R. Mahdi et al.   BIOINFORMATICS

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

(2012) Jason E Shoemaker et al.   BMC GENOMICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

Simultaneous Non-Negative Matrix Factorization for Multiple Large Scale Gene Expression Datasets in Toxicology

(2012) Clare M. Lee et al.   PLoS One

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

SNP-based pathway enrichment analysis for genome-wide association studies

(2011) Lingjie Weng et al.   BMC BIOINFORMATICS

Shrinkage-based regularization tests for high-dimensional data with application to gene set analysis

(2011) Yanfeng Shen et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Bayesian Detection of Expression Quantitative Trait Loci Hot Spots

(2011) Leonardo Bottolo et al.   GENETICS

Oxysterols direct immune cell migration via EBI2

(2011) Sébastien Hannedouche et al.   NATURE

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

(2011) Chris McDermott-Roe et al.   NATURE

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

(2011) K. Zhang et al.   NUCLEIC ACIDS RESEARCH

A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms

(2011) Sri Priya Ponnapalli et al.   PLoS One

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

(2011) Maxime Rotival et al.   PLoS Genetics

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

(2010) Bruno M Tesson et al.   BMC BIOINFORMATICS

A statistical framework for differential network analysis from microarray data

(2010) Ryan Gill et al.   BMC BIOINFORMATICS

Weighted Gene Coexpression Network Analysis: State of the Art

(2010) Wei Zhao et al.   Journal of Biopharmaceutical Statistics

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

(2010) Matthias Heinig et al.   NATURE

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Use of Genome-Wide Expression Data to Mine the “Gray Zone” of GWA Studies Leads to Novel Candidate Obesity Genes

(2010) Jussi Naukkarinen 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

A network view of disease and compound screening

(2009) Eric E. Schadt et al.   NATURE REVIEWS DRUG DISCOVERY

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

(2009) James A. Birchler et al.   NEW PHYTOLOGIST

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Differential dependency network analysis to identify condition-specific topological changes in biological networks

(2008) Bai Zhang et al.   BIOINFORMATICS

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS