Published in Nat Genet on December 01, 2002
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Obesity is associated with macrophage accumulation in adipose tissue. J Clin Invest (2003) 41.22
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A (2005) 8.65
Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol (2006) 3.52
Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer (2008) 3.43
Clustering cancer gene expression data: a comparative study. BMC Bioinformatics (2008) 2.00
Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci U S A (2006) 1.95
New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res (2004) 1.89
CoXpress: differential co-expression in gene expression data. BMC Bioinformatics (2006) 1.85
Entropy-based gene ranking without selection bias for the predictive classification of microarray data. BMC Bioinformatics (2003) 1.71
Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. Am J Respir Crit Care Med (2014) 1.69
Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res (2008) 1.69
ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res (2003) 1.68
Using GenePattern for gene expression analysis. Curr Protoc Bioinformatics (2008) 1.68
Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol (2008) 1.64
Genome-wide gene expression in response to parasitoid attack in Drosophila. Genome Biol (2005) 1.57
Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics (2015) 1.43
TiSGeD: a database for tissue-specific genes. Bioinformatics (2010) 1.41
Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Comput Biol (2006) 1.41
What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol (2009) 1.40
CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics (2009) 1.29
Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biol (2007) 1.29
Getting started in gene expression microarray analysis. PLoS Comput Biol (2009) 1.25
Transcriptional changes associated with breast cancer occur as normal human mammary epithelial cells overcome senescence barriers and become immortalized. Mol Cancer (2007) 1.24
Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes? Proc Am Thorac Soc (2006) 1.22
Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics (2004) 1.19
Optimization based tumor classification from microarray gene expression data. PLoS One (2011) 1.17
Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol (2004) 1.14
Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res Rev (2009) 1.12
Gene expression profiling of canine osteosarcoma reveals genes associated with short and long survival times. Mol Cancer (2009) 1.11
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data. Nucleic Acids Res (2005) 1.11
Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics (2006) 1.10
Complex diseases, complex genes: keeping pathways on the right track. Epidemiology (2009) 1.10
Inflammatory priming predisposes mice to age-related retinal degeneration. J Clin Invest (2012) 1.07
The application of transcriptional blood signatures to enhance our understanding of the host response to infection: the example of tuberculosis. Philos Trans R Soc Lond B Biol Sci (2014) 1.06
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. BMC Bioinformatics (2008) 1.06
A perspective on microarrays: current applications, pitfalls, and potential uses. Microb Cell Fact (2007) 1.05
Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer. BMC Med Genomics (2008) 1.04
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
Quantitative analysis of highly parallel transfection in cell microarrays. Nucleic Acids Res (2004) 1.01
Network biology methods integrating biological data for translational science. Brief Bioinform (2012) 0.99
Including probe-level uncertainty in model-based gene expression clustering. BMC Bioinformatics (2007) 0.98
Interactome data and databases: different types of protein interaction. Comp Funct Genomics (2004) 0.98
Overexpression of FABP7 in Down syndrome fetal brains is associated with PKNOX1 gene-dosage imbalance. Nucleic Acids Res (2003) 0.96
Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments. Funct Integr Genomics (2005) 0.96
Epigenome: biosensor of cumulative exposure to chemical and nonchemical stressors related to environmental justice. Am J Public Health (2014) 0.95
Motif-directed network component analysis for regulatory network inference. BMC Bioinformatics (2008) 0.95
Microarrays in ecological research: a case study of a cDNA microarray for plant-herbivore interactions. BMC Ecol (2004) 0.94
Patterns of human gene expression variance show strong associations with signaling network hierarchy. BMC Syst Biol (2010) 0.93
Mining gene expression data by interpreting principal components. BMC Bioinformatics (2006) 0.93
Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data. BMC Bioinformatics (2006) 0.92
Overcoming heterogeneity in pediatric asthma: tobacco smoke and asthma characteristics within phenotypic clusters in an African American cohort. J Asthma (2010) 0.92
Dynamic changes in protein functional linkage networks revealed by integration with gene expression data. PLoS Comput Biol (2008) 0.91
Finding unexpected patterns in microarray data. Plant Physiol (2003) 0.89
Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence. Environ Health Perspect (2004) 0.89
Algorithmic and analytical methods in network biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.87
Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation. Plant Cell Rep (2009) 0.87
Gene profiling in experimental models of eye growth: clues to myopia pathogenesis. Vision Res (2010) 0.87
Activation of the epidermal growth factor signalling pathway by tissue plasminogen activator in pancreas cancer cells. Gut (2007) 0.86
Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences. BMC Syst Biol (2012) 0.86
The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level. Mol Genet Genomics (2006) 0.86
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. BMC Bioinformatics (2012) 0.86
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. BMC Bioinformatics (2010) 0.86
Statistical methods for comparative phenomics using high-throughput phenotype microarrays. Int J Biostat (2010) 0.85
Signal and sensitivity enhancement through optical interference coating for DNA and protein microarray applications. J Biomol Tech (2006) 0.84
A novel approach to the clustering of microarray data via nonparametric density estimation. BMC Bioinformatics (2011) 0.84
Computational approaches for translational clinical research in disease progression. J Investig Med (2011) 0.84
New tools for functional genomic analysis. Drug Discov Today (2009) 0.84
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. BMC Bioinformatics (2015) 0.81
Introducing knowledge into differential expression analysis. J Comput Biol (2010) 0.81
MADNet: microarray database network web server. Nucleic Acids Res (2008) 0.80
Concise review: new paradigms for Down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. Stem Cells Transl Med (2013) 0.80
biDCG: a new method for discovering global features of DNA microarray data via an iterative re-clustering procedure. PLoS One (2014) 0.80
Estimating differential expression from multiple indicators. Nucleic Acids Res (2014) 0.80
Standards affecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev (2010) 0.80
Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency. BMC Genomics (2008) 0.79
Hierarchical Bayesian neural network for gene expression temporal patterns. Stat Appl Genet Mol Biol (2004) 0.79
Genetic factors involved in risk for methamphetamine intake and sensitization. Mamm Genome (2013) 0.79
A toolbox for spatiotemporal analysis of voltage-sensitive dye imaging data in brain slices. PLoS One (2014) 0.78
A genomic approach to investigate expression profiles in Slovenian patients with gastric cancer. Oncol Lett (2011) 0.78
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. BMC Bioinformatics (2016) 0.78
Dynamic covariation between gene expression and proteome characteristics. BMC Bioinformatics (2005) 0.78
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. Adv Microb Physiol (2012) 0.78
Analyzing kernel matrices for the identification of differentially expressed genes. PLoS One (2013) 0.77
Quality determination and the repair of poor quality spots in array experiments. BMC Bioinformatics (2005) 0.77
Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model. EURASIP J Bioinform Syst Biol (2007) 0.76
Balancing false discovery and false negative rates in selection of differentially expressed genes in microarrays. Open Access Bioinformatics (2010) 0.76
Transcriptomic analysis of (group I) Clostridium botulinum ATCC 3502 cold shock response. PLoS One (2014) 0.76
A ratiometric-based measure of gene co-expression. BMC Bioinformatics (2014) 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
Impact of Male and Female Weight, Smoking, and Intercourse Frequency on Live Birth in Women With Polycystic Ovary Syndrome. J Clin Endocrinol Metab (2015) 0.75
CSAX: Characterizing Systematic Anomalies in eXpression Data. J Comput Biol (2015) 0.75
Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays. Sci Rep (2015) 0.75
Progress of science from microscopy to microarrays (part 1): diagnosis of parasitic diseases. J Lab Physicians (2009) 0.75
Progeny Clustering: A Method to Identify Biological Phenotypes. Sci Rep (2015) 0.75
MicroCore: mapping genome expression to cell pathways and networks. Comp Funct Genomics (2004) 0.75
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology. BMC Genomics (2015) 0.75
AgingDB: A database for oxidative stress and calorie restriction in the study of aging. J Am Aging Assoc (2003) 0.75