Published in Mamm Genome on August 01, 2007
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet (2009) 2.24
Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity (2012) 2.16
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics (2009) 2.15
A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol (2009) 1.96
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol (2008) 1.93
Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia. Genome Res (2010) 1.83
The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74
High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet (2008) 1.72
Modulated modularity clustering as an exploratory tool for functional genomic inference. PLoS Genet (2009) 1.71
CHAC1/MGC4504 is a novel proapoptotic component of the unfolded protein response, downstream of the ATF4-ATF3-CHOP cascade. J Immunol (2009) 1.70
Gene networks and microRNAs implicated in aggressive prostate cancer. Cancer Res (2009) 1.68
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Syst Biol (2008) 1.64
Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics (2008) 1.56
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics (2010) 1.53
Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle. BMC Genomics (2015) 1.52
Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A (2011) 1.49
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
A statistical framework for differential network analysis from microarray data. BMC Bioinformatics (2010) 1.46
Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PLoS Pathog (2013) 1.43
When is hub gene selection better than standard meta-analysis? PLoS One (2013) 1.41
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics (2010) 1.38
Gene networks associated with conditional fear in mice identified using a systems genetics approach. BMC Syst Biol (2011) 1.30
Random generalized linear model: a highly accurate and interpretable ensemble predictor. BMC Bioinformatics (2013) 1.29
Beyond differential expression: the quest for causal mutations and effector molecules. BMC Genomics (2012) 1.29
Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics (2012) 1.28
Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics (2011) 1.19
Two gene co-expression modules differentiate psychotics and controls. Mol Psychiatry (2012) 1.15
Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol (2013) 1.14
Complex genetics of obesity in mouse models. Annu Rev Nutr (2008) 1.06
Identification of cyclin B1 and Sec62 as biomarkers for recurrence in patients with HBV-related hepatocellular carcinoma after surgical resection. Mol Cancer (2012) 1.03
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. BMC Med Genomics (2014) 1.02
Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PLoS One (2009) 1.01
DDN: a caBIG® analytical tool for differential network analysis. Bioinformatics (2011) 0.96
Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients. Lung Cancer (2013) 0.96
Gene networks and haloperidol-induced catalepsy. Genes Brain Behav (2011) 0.95
Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer. BMC Med Genomics (2011) 0.94
Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks. Sci Rep (2013) 0.94
Differential coexpression analysis of obesity-associated networks in human subcutaneous adipose tissue. Int J Obes (Lond) (2011) 0.94
Genome-wide co-expression analysis in multiple tissues. PLoS One (2008) 0.93
Systems genetic analysis of osteoblast-lineage cells. PLoS Genet (2012) 0.93
Differential C3NET reveals disease networks of direct physical interactions. BMC Bioinformatics (2011) 0.92
Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis. Plant Cell (2014) 0.92
Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control. BMC Bioinformatics (2012) 0.91
Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases. Curr Cardiovasc Risk Rep (2012) 0.89
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics (2014) 0.89
Protein expression based multimarker analysis of breast cancer samples. BMC Cancer (2011) 0.88
A differential network approach to exploring differences between biological states: an application to prediabetes. PLoS One (2011) 0.87
Network module detection: Affinity search technique with the multi-node topological overlap measure. BMC Res Notes (2009) 0.87
Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease. BMC Med Genomics (2013) 0.86
Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. Cancer Inform (2016) 0.86
An Integrative Genomic Study Implicates the Postsynaptic Density in the Pathogenesis of Bipolar Disorder. Neuropsychopharmacology (2015) 0.85
Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. Elife (2017) 0.85
Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data. Bioinformation (2012) 0.84
dna: An R package for differential network analysis. Bioinformation (2014) 0.84
An inferential framework for biological network hypothesis tests. BMC Bioinformatics (2013) 0.83
Acute response of peripheral blood cell to autologous hematopoietic stem cell transplantation in type 1 diabetic patient. PLoS One (2012) 0.83
Gene network exploration of crosstalk between apoptosis and autophagy in chronic myelogenous leukemia. Biomed Res Int (2015) 0.82
Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis. Int J Ophthalmol (2015) 0.80
Functional annotation of novel lineage-specific genes using co-expression and promoter analysis. BMC Genomics (2010) 0.80
Gene differential coexpression analysis based on biweight correlation and maximum clique. BMC Bioinformatics (2014) 0.79
Dual-trait selection for ethanol consumption and withdrawal: genetic and transcriptional network effects. Alcohol Clin Exp Res (2014) 0.78
Comparative network analysis via differential graphlet communities. Proteomics (2014) 0.78
Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages. Int J Biol Sci (2014) 0.77
Hippocampal gene expression analysis highlights Ly6a/Sca-1 as candidate gene for previously mapped novelty induced behaviors in mice. PLoS One (2011) 0.77
Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis. PLoS One (2016) 0.77
Construction of citrus gene coexpression networks from microarray data using random matrix theory. Hortic Res (2015) 0.77
The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits. Mamm Genome (2013) 0.77
Co-expression network analysis identifies transcriptional modules in the mouse liver. Mol Genet Genomics (2014) 0.77
Differential network analysis in human cancer research. Curr Pharm Des (2014) 0.77
Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows. Genes Brain Behav (2015) 0.76
Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia. Sci Rep (2015) 0.76
The Association Between Low Back Pain and Composition of IgG Glycome. Sci Rep (2016) 0.76
Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection. BMC Genomics (2015) 0.76
Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data. BMC Syst Biol (2014) 0.76
Systems genetics of environmental response in the mature wheat embryo. Genetics (2013) 0.76
Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle. Asian-Australas J Anim Sci (2013) 0.76
Cluster and propensity based approximation of a network. BMC Syst Biol (2013) 0.76
Analysis of time-resolved gene expression measurements across individuals. PLoS One (2013) 0.76
Different Statistical Approaches to Investigate Porcine Muscle Metabolome Profiles to Highlight New Biomarkers for Pork Quality Assessment. PLoS One (2016) 0.76
Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses. BMC Med Genomics (2016) 0.76
Module Based Differential Coexpression Analysis Method for Type 2 Diabetes. Biomed Res Int (2015) 0.76
Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One (2017) 0.76
Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits. Int J Mol Sci (2017) 0.75
The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus. BMC Pulm Med (2016) 0.75
Detection of statistically significant network changes in complex biological networks. BMC Syst Biol (2017) 0.75
Inference for High-dimensional Differential Correlation Matrices. J Multivar Anal (2016) 0.75
A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal. Front Genet (2017) 0.75
Preservation affinity in consensus modules among stages of HIV-1 progression. BMC Bioinformatics (2017) 0.75
Reversal of dendritic phenotypes in 16p11.2 microduplication mouse model neurons by pharmacological targeting of a network hub. Proc Natl Acad Sci U S A (2016) 0.75
Ethical and public policy challenges for pharmacogenomics. Dialogues Clin Neurosci (2014) 0.75
Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PLoS One (2017) 0.75
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet (2005) 10.03
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. Nucleic Acids Res (2005) 8.19
Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet (2005) 7.82
Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet (2005) 6.91
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A (2006) 6.33
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Functional analysis of genetic variation in catechol-O-methyltransferase (COMT): effects on mRNA, protein, and enzyme activity in postmortem human brain. Am J Hum Genet (2004) 5.70
Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A (2006) 5.69
Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet (2006) 3.51
A prospective study of risk factors for pulmonary embolism in women. JAMA (1997) 3.12
Genetic determinants of energy expenditure and insulin resistance in diet-induced obesity in mice. Diabetes (2004) 2.54
Comparative genomics and gene expression analysis identifies BBS9, a new Bardet-Biedl syndrome gene. Am J Hum Genet (2005) 2.25
A human-specific role of cell death-inducing DFFA (DNA fragmentation factor-alpha)-like effector A (CIDEA) in adipocyte lipolysis and obesity. Diabetes (2005) 1.94
Mutations within the protein Z-dependent protease inhibitor gene are associated with venous thromboembolic disease: a new form of thrombophilia. Br J Haematol (2004) 1.81
Obesity: risk of venous thrombosis and the interaction with coagulation factor levels and oral contraceptive use. Thromb Haemost (2003) 1.80
Genomic analysis of metabolic pathway gene expression in mice. Genome Biol (2005) 1.79
Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes. J Lipid Res (2006) 1.69
Cis- and trans-acting gene regulation is associated with osteoarthritis. Am J Hum Genet (2006) 1.55
Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice. Mamm Genome (2006) 1.33
From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm Genome (2006) 1.18
Genetic kininogen deficiency contributes to aortic aneurysm formation but not to atherosclerosis. Physiol Genomics (2004) 1.02
Links between inflammation and thrombogenicity in atherosclerosis. Curr Mol Med (2006) 0.96
Coagulation factor VII gene haplotypes, obesity-related traits, and cardiovascular risk in young women. J Thromb Haemost (2006) 0.94
Genome-wide analysis of gene transcription in the hypothalamus. Physiol Genomics (2005) 0.92
Involvement of epidermal growth factor in inducing obesity in ovariectomized mice. Am J Physiol (1993) 0.91
Glycosylphosphatidylinositol-specific phospholipase D influences triglyceride-rich lipoprotein metabolism. Am J Physiol Endocrinol Metab (2005) 0.89
Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17
Mapping the genetic architecture of gene expression in human liver. PLoS Biol (2008) 19.44
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med (2005) 15.42
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature (2011) 13.53
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet (2005) 11.40
Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature (2011) 10.16
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med (2013) 9.44
Gene expression profiling of gliomas strongly predicts survival. Cancer Res (2004) 7.79
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics (2007) 7.72
DNA methylation age of human tissues and cell types. Genome Biol (2013) 7.48
Role of the murine reprogramming factors in the induction of pluripotency. Cell (2009) 7.46
Global histone modification patterns predict risk of prostate cancer recurrence. Nature (2005) 7.03
Functional organization of the transcriptome in human brain. Nat Neurosci (2008) 7.02
Cis-acting expression quantitative trait loci in mice. Genome Res (2005) 6.66
Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res (2006) 6.45
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A (2006) 5.69
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
Synthetic LXR ligand inhibits the development of atherosclerosis in mice. Proc Natl Acad Sci U S A (2002) 4.23
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Arachidonate 5-lipoxygenase promoter genotype, dietary arachidonic acid, and atherosclerosis. N Engl J Med (2004) 4.06
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene (2003) 3.83
A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res (2010) 3.81
Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet (2005) 3.74
Relationship of paraoxonase 1 (PON1) gene polymorphisms and functional activity with systemic oxidative stress and cardiovascular risk. JAMA (2008) 3.64
Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet (2006) 3.51
Epigenetic predictor of age. PLoS One (2011) 3.46
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res (2003) 3.36
Understanding network concepts in modules. BMC Syst Biol (2007) 3.28
Ambient particulate pollutants in the ultrafine range promote early atherosclerosis and systemic oxidative stress. Circ Res (2008) 3.26
Carbonic anhydrase IX is an independent predictor of survival in advanced renal clear cell carcinoma: implications for prognosis and therapy. Clin Cancer Res (2003) 3.25
Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet (2011) 3.23
Myeloperoxidase, a leukocyte-derived vascular NO oxidase. Science (2002) 3.13
Gene expression profiling identifies molecular subtypes of gliomas. Oncogene (2003) 3.13
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 3.06
Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol (2012) 3.05
Thioredoxin-interacting protein: a critical link between glucose toxicity and beta-cell apoptosis. Diabetes (2008) 3.05
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A (2006) 3.03
Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metab (2013) 3.01
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet (2009) 2.97
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
The unfolded protein response is an important regulator of inflammatory genes in endothelial cells. Arterioscler Thromb Vasc Biol (2006) 2.90
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell (2013) 2.87
Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nat Genet (2004) 2.86
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A (2010) 2.85
Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A (2010) 2.81
The oxidation hypothesis of atherogenesis: the role of oxidized phospholipids and HDL. J Lipid Res (2004) 2.72
Retracted Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies. Nat Genet (2003) 2.70
Identification of 5-lipoxygenase as a major gene contributing to atherosclerosis susceptibility in mice. Circ Res (2002) 2.69
Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Genomics (2005) 2.61
Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov (2012) 2.61
Identification of macrophage liver X receptors as inhibitors of atherosclerosis. Proc Natl Acad Sci U S A (2002) 2.56
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
Neutrophils and NADPH oxidase mediate intrapancreatic trypsin activation in murine experimental acute pancreatitis. Gastroenterology (2002) 2.45
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genet (2010) 2.43
Mechanisms underlying adverse effects of HDL on eNOS-activating pathways in patients with coronary artery disease. J Clin Invest (2011) 2.37
Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics (2006) 2.35
Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am J Transplant (2004) 2.35
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics (2008) 2.29
Relationship between stearoyl-CoA desaturase activity and plasma triglycerides in human and mouse hypertriglyceridemia. J Lipid Res (2002) 2.28
Global levels of histone modifications predict prognosis in different cancers. Am J Pathol (2009) 2.28
Targeting distinct tumor-infiltrating myeloid cells by inhibiting CSF-1 receptor: combating tumor evasion of antiangiogenic therapy. Blood (2009) 2.26
A treasure trove for lipoprotein biology. Nat Genet (2008) 2.25
Ligand activation of LXR beta reverses atherosclerosis and cellular cholesterol overload in mice lacking LXR alpha and apoE. J Clin Invest (2007) 2.24
A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet (2009) 2.24
EGFR signaling through an Akt-SREBP-1-dependent, rapamycin-resistant pathway sensitizes glioblastomas to antilipogenic therapy. Sci Signal (2009) 2.23
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab (2013) 2.17
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics (2009) 2.15
Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. Proc Natl Acad Sci U S A (2007) 2.13
Neurosphere formation is an independent predictor of clinical outcome in malignant glioma. Stem Cells (2009) 2.10
Thioredoxin-interacting protein deficiency induces Akt/Bcl-xL signaling and pancreatic beta-cell mass and protects against diabetes. FASEB J (2008) 2.09