Published in J Stat Softw on March 01, 2012
Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer. Nat Med (2016) 1.62
bacterial infection drives the expression dynamics of microRNAs and their isomiRs. PLoS Genet (2015) 1.50
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
When is hub gene selection better than standard meta-analysis? PLoS One (2013) 1.41
Temporal specification and bilaterality of human neocortical topographic gene expression. Neuron (2013) 1.26
Visualising associations between paired 'omics' data sets. BioData Min (2012) 1.14
Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. Am J Hum Genet (2014) 1.08
Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels. Aging (Albany NY) (2016) 1.00
Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus. Plant Cell (2015) 0.98
Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS One (2014) 0.97
Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data. BMC Genomics (2014) 0.92
A comprehensive transcriptional map of primate brain development. Nature (2016) 0.91
VoICE: A semi-automated pipeline for standardizing vocal analysis across models. Sci Rep (2015) 0.88
Significantly reduced function of T cells in patients with acute arterial thrombosis. J Geriatr Cardiol (2015) 0.87
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J (2016) 0.86
Changes in gene expression within the ventral tegmental area following repeated excessive binge-like alcohol drinking by alcohol-preferring (P) rats. Alcohol (2013) 0.86
Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. Elife (2017) 0.85
Gene expression within the extended amygdala of 5 pairs of rat lines selectively bred for high or low ethanol consumption. Alcohol (2013) 0.84
Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish. PLoS Genet (2015) 0.84
Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. RNA Biol (2014) 0.83
Discovering New Biology through Sequencing of RNA. Plant Physiol (2015) 0.83
Protein co-expression network analysis (ProCoNA). J Clin Bioinforma (2013) 0.82
Discovering study-specific gene regulatory networks. PLoS One (2014) 0.82
Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis. PLoS One (2015) 0.81
PIM1 kinase inhibition as a targeted therapy against triple-negative breast tumors with elevated MYC expression. Nat Med (2016) 0.80
RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias. BMC Plant Biol (2014) 0.80
Coexpression network analysis of the genes regulated by two types of resistance responses to powdery mildew in wheat. Sci Rep (2016) 0.80
PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links. Front Bioeng Biotechnol (2015) 0.80
Genetic modulation of diabetic nephropathy among mouse strains with Ins2 Akita mutation. Physiol Rep (2014) 0.79
Changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats. Pharmacol Biochem Behav (2013) 0.79
Genome-wide association study of aggressive behaviour in chicken. Sci Rep (2016) 0.78
Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas. Hum Genet (2016) 0.78
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. Front Oncol (2014) 0.78
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics (2014) 0.78
Dysregulated long intergenic non-coding RNA modules contribute to heart failure. Oncotarget (2016) 0.78
Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits. Am J Hum Genet (2017) 0.78
Multi-omic network signatures of disease. Front Genet (2014) 0.77
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host Microbe (2016) 0.77
Gene Expression Correlated to Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. Am J Respir Crit Care Med (2016) 0.77
Protection genes in nucleus accumbens shell affect vulnerability to nicotine self-administration across isogenic strains of adolescent rat. PLoS One (2014) 0.76
Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay. 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
The Association Between Low Back Pain and Composition of IgG Glycome. Sci Rep (2016) 0.76
Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity. Glia (2017) 0.75
Identifying a gene expression signature of cluster headache in blood. Sci Rep (2017) 0.75
Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus. Front Plant Sci (2016) 0.75
Identification of Differentially Expressed Gene after Femoral Fracture via Microarray Profiling. Int J Genomics (2014) 0.75
Altered expression of mRNA profiles in blood of early-onset schizophrenia. Sci Rep (2016) 0.75
GLITTER: a web-based application for gene link inspection through tissue-specific coexpression. Sci Rep (2016) 0.75
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. EURASIP J Bioinform Syst Biol (2017) 0.75
The E. coli molecular phenotype under different growth conditions. Sci Rep (2017) 0.75
Large-scale gene co-expression network as a source of functional annotation for cattle genes. BMC Genomics (2016) 0.75
Multiplex matrix network analysis of protein complexes in the human TCR signalosome. Sci Signal (2016) 0.75
The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets. BMC Genomics (2016) 0.75
A systems genetics approach identifies Trp53inp2 as a link between cardiomyocyte glucose utilization and hypertrophic response. Am J Physiol Heart Circ Physiol (2017) 0.75
Aberrant transcriptional networks in step-wise neurogenesis of paroxysmal kinesigenic dyskinesia-induced pluripotent stem cells. Oncotarget (2016) 0.75
Fibroblast growth factor receptor (FGFR) alterations in squamous differentiated bladder cancer: a putative therapeutic target for a small subgroup. Oncotarget (2016) 0.75
Antibiotic Resistance in Animal and Environmental Samples Associated with Small-Scale Poultry Farming in Northwestern Ecuador. mSphere (2016) 0.75
DTW-MIC Coexpression Networks from Time-Course Data. PLoS One (2016) 0.75
Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes. PLoS One (2016) 0.75
Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. Hum Mol Genet (2017) 0.75
Gene Co-Expression Analysis Predicts Genetic Variants Associated with Drug Responsiveness in Lung Cancer. AMIA Jt Summits Transl Sci Proc (2016) 0.75
Differential correlation for sequencing data. BMC Res Notes (2017) 0.75
Gene co-expression network reveals shared modules predictive of stage and grade in serous ovarian cancers. Oncotarget (2017) 0.75
Gene expression profile of subcutaneous adipose tissue in BMI-discordant monozygotic twin pairs unravels molecular and clinical changes associated with sub-types of obesity. Int J Obes (Lond) (2017) 0.75
Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations. Front Immunol (2017) 0.75
Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems (2017) 0.75
Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs. Sci Rep (2017) 0.75
Hierarchical organization of modularity in metabolic networks. Science (2002) 22.47
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
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics (2007) 7.72
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
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
A robust measure of correlation between two genes on a microarray. BMC Bioinformatics (2007) 1.25
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
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature (2011) 10.16
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
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
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 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
Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome (2007) 3.59
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
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
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
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
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell (2013) 2.87
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
Retracted Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies. Nat Genet (2003) 2.70
Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov (2012) 2.61
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
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
Global levels of histone modifications predict prognosis in different cancers. Am J Pathol (2009) 2.28
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
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics (2009) 2.15
Neurosphere formation is an independent predictor of clinical outcome in malignant glioma. Stem Cells (2009) 2.10
Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res (2008) 1.96
Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics (2011) 1.96
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol (2008) 1.93
Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation. Brain Res Mol Brain Res (2003) 1.93
Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma. Mod Pathol (2005) 1.89
The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74
Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics (2009) 1.72
Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics (2012) 1.70
Using tumor markers to predict the survival of patients with metastatic renal cell carcinoma. J Urol (2005) 1.60
Cellular histone modification patterns predict prognosis and treatment response in resectable pancreatic adenocarcinoma: results from RTOG 9704. J Clin Oncol (2010) 1.57
Using protein expressions to predict survival in clear cell renal carcinoma. Clin Cancer Res (2004) 1.51
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc Natl Acad Sci U S A (2003) 1.47
Prostate stem cell antigen expression is associated with gleason score, seminal vesicle invasion and capsular invasion in prostate cancer. J Urol (2004) 1.47
Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells. Genome Biol (2007) 1.46
Gene coexpression network topology of cardiac development, hypertrophy, and failure. Circ Cardiovasc Genet (2010) 1.46
A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes. PLoS One (2012) 1.45
Breast cancer molecular signatures as determined by SAGE: correlation with lymph node status. Mol Cancer Res (2007) 1.45
Presence of a putative tumor-initiating progenitor cell population predicts poor prognosis in smokers with non-small cell lung cancer. Cancer Res (2010) 1.44
Prostate stem cell antigen is overexpressed in prostate cancer metastases. Clin Cancer Res (2005) 1.43
Prognostic value of carbonic anhydrase IX and KI67 as predictors of survival for renal clear cell carcinoma. J Urol (2004) 1.42
When is hub gene selection better than standard meta-analysis? PLoS One (2013) 1.41
Expression of colony-stimulating factor 1 receptor during prostate development and prostate cancer progression. Proc Natl Acad Sci U S A (2002) 1.40
Network organization of the huntingtin proteomic interactome in mammalian brain. Neuron (2012) 1.38
Expression of transcription factor Yin Yang 1 in prostate cancer. Int J Oncol (2005) 1.37
Relationship between survival and edema in malignant gliomas: role of vascular endothelial growth factor and neuronal pentraxin 2. Clin Cancer Res (2007) 1.35
Multivariate variance-components analysis of longitudinal blood pressure measurements from the Framingham Heart Study. BMC Genet (2003) 1.34
An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association. J Bone Miner Res (2009) 1.33
Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome (2013) 1.32
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
Higher levels of GATA3 predict better survival in women with breast cancer. Hum Pathol (2010) 1.28
CLCN2 variants in idiopathic generalized epilepsy. Nat Genet (2009) 1.26
Development of a real-time RT-PCR assay for detecting EGFRvIII in glioblastoma samples. Clin Cancer Res (2008) 1.25
Expression of X-linked inhibitor of apoptosis protein is a strong predictor of human prostate cancer recurrence. Clin Cancer Res (2007) 1.23
Statistical methods for analyzing tissue microarray data. J Biopharm Stat (2004) 1.23
Is human blood a good surrogate for brain tissue in transcriptional studies? BMC Genomics (2010) 1.22
Antibody-based profiling of the phosphoinositide 3-kinase pathway in clinical prostate cancer. Clin Cancer Res (2004) 1.21
Differential expression of anterior gradient gene AGR2 in prostate cancer. BMC Cancer (2010) 1.16
Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells Dev (2011) 1.15
p53 is an independent predictor of tumor recurrence and progression after nephrectomy in patients with localized renal cell carcinoma. J Urol (2005) 1.15
Systems biology analysis of Sjögren's syndrome and mucosa-associated lymphoid tissue lymphoma in parotid glands. Arthritis Rheum (2009) 1.14
Molecular microcircuitry underlies functional specification in a basal ganglia circuit dedicated to vocal learning. Neuron (2012) 1.14
Loss of CD10 (neutral endopeptidase) is a frequent and early event in human prostate cancer. Prostate (2003) 1.13
"Good enough solutions" and the genetics of complex diseases. Circ Res (2012) 1.13
Repetitive sequence environment distinguishes housekeeping genes. Gene (2006) 1.12
Analysis of the Na,K-ATPase alpha- and beta-subunit expression profiles of bladder cancer using tissue microarrays. Cancer (2003) 1.10
Trefoil factor 3 is overexpressed in human prostate cancer. Prostate (2004) 1.09
Detecting network modules in fMRI time series: a weighted network analysis approach. Neuroimage (2010) 1.07
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One (2013) 1.06
Tissue microarray analysis of cytoskeletal actin-associated biomarkers gelsolin and E-cadherin in urothelial carcinoma. Cancer (2002) 1.06
Correlation of Ki-67 and gelsolin expression to clinical outcome in renal clear cell carcinoma. Urology (2003) 1.05
Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling. Eur J Hum Genet (2007) 1.03
A family-based test for correlation between gene expression and trait values. Am J Hum Genet (2003) 1.03
Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood. PLoS One (2009) 1.03
Clinicopathologic and molecular correlations of necrosis in the primary tumor of patients with renal cell carcinoma. Cancer (2005) 1.02
Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity. Hum Mol Genet (2005) 1.01