Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules

(2017) Colin Ruprecht et al.   PLANT JOURNAL

Tools of the trade: studying molecular networks in plants

(2016) Sebastian Proost et al.   CURRENT OPINION IN PLANT BIOLOGY

Coexpression network analysis of the genes regulated by two types of resistance responses to powdery mildew in wheat

(2016) Juncheng Zhang et al.   Scientific Reports

Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome

(2015) Pierre Luisi et al.   Genome Biology and Evolution

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

(2013) Darren CJ Wong et al.   BMC GENOMICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Evolutionary Rate and Duplicability in the Arabidopsis thaliana Protein–Protein Interaction Network

(2012) David Alvarez-Ponce et al.   Genome Biology and Evolution

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Comparative Genomics of the Vertebrate Insulin/TOR Signal Transduction Pathway: A Network-Level Analysis of Selective Pressures

(2010) David Alvarez-Ponce et al.   Genome Biology and Evolution

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks

(2010) Stephen P. Ficklin et al.   PLANT PHYSIOLOGY

An Extended Synthesis for Evolutionary Biology

(2009) Massimo Pigliucci   Annals of the New York Academy of Sciences

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

(2009) Osnat Atias et al.   BMC Systems Biology

Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants

(2009) Kevin Livingstone et al.   JOURNAL OF HEREDITY

The Correlation of Evolutionary Rate with Pathway Position in Plant Terpenoid Biosynthesis

(2009) Heather Ramsay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice

(2009) Nicole K. MacLennan et al.   MOLECULAR GENETICS AND METABOLISM

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters

(2008) Yi Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Variation in Constraint Versus Positive Selection as an Explanation for Evolutionary Rate Variation Among Anthocyanin Genes

(2008) Mark D. Rausher et al.   JOURNAL OF MOLECULAR EVOLUTION

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE