Published in Bioinformatics on November 16, 2006
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
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell (2015) 4.42
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
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Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol (2012) 3.05
A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci (2008) 2.97
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics (2009) 2.15
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Plankton networks driving carbon export in the oligotrophic ocean. Nature (2016) 1.72
Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics (2009) 1.72
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
RNA-Seq Reveals the Angiogenesis Diversity between the Fetal and Adults Bone Mesenchyme Stem Cell. PLoS One (2016) 1.40
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Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells Dev (2011) 1.15
CCDC22: a novel candidate gene for syndromic X-linked intellectual disability. Mol Psychiatry (2011) 1.07
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics (2012) 1.05
Linking proteins to signaling pathways for experiment design and evaluation. PLoS One (2012) 0.98
A developmental transcriptional network for maize defines coexpression modules. Plant Physiol (2013) 0.97
Convergent Functional Genomics of bipolar disorder: from animal model pharmacogenomics to human genetics and biomarkers. Neurosci Biobehav Rev (2007) 0.95
Spectral affinity in protein networks. BMC Syst Biol (2009) 0.94
A systems level, functional genomics analysis of chronic epilepsy. PLoS One (2011) 0.94
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. Cancer Inform (2014) 0.88
Protein expression based multimarker analysis of breast cancer samples. BMC Cancer (2011) 0.88
Using semantic and structural properties of the Unified Medical Language System to discover potential terminological relationships. J Am Med Inform Assoc (2009) 0.87
Network module detection: Affinity search technique with the multi-node topological overlap measure. BMC Res Notes (2009) 0.87
Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer. BMC Genomics (2014) 0.86
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An inferential framework for biological network hypothesis tests. BMC Bioinformatics (2013) 0.83
Regulation of the ESC transcriptome by nuclear long noncoding RNAs. Genome Res (2015) 0.81
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. BMC Genomics (2009) 0.80
Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background. BMC Genomics (2010) 0.80
Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One (2012) 0.78
Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations. J Anat (2014) 0.78
Systematic identification of core transcription factors mediating dysregulated links bridging inflammatory bowel diseases and colorectal cancer. PLoS One (2013) 0.76
Preservation affinity in consensus modules among stages of HIV-1 progression. BMC Bioinformatics (2017) 0.75
Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways. Front Microbiol (2016) 0.75
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
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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
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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
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
Fast R Functions for Robust Correlations and Hierarchical Clustering. J Stat Softw (2012) 1.72
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
Prostate stem cell antigen expression is associated with gleason score, seminal vesicle invasion and capsular invasion in prostate cancer. J Urol (2004) 1.47
High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc Natl Acad Sci U S A (2003) 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
Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood. PLoS One (2009) 1.03
A family-based test for correlation between gene expression and trait values. Am J Hum Genet (2003) 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