Published in Nat Biotechnol on September 01, 2006
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics (2010) 7.78
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Antidepressant actions of histone deacetylase inhibitors. J Neurosci (2009) 3.17
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics (2008) 2.54
Filtering for increased power for microarray data analysis. BMC Bioinformatics (2009) 2.30
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol (2014) 2.19
Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology. Nucleic Acids Res (2008) 2.11
Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One (2009) 2.02
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics (2008) 1.99
The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics (2008) 1.93
Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics (2007) 1.92
Resistance exercise reverses aging in human skeletal muscle. PLoS One (2007) 1.90
Consistency of predictive signature genes and classifiers generated using different microarray platforms. Pharmacogenomics J (2010) 1.69
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
Characterization of the proneural gene regulatory network during mouse telencephalon development. BMC Biol (2008) 1.59
Fold change rank ordering statistics: a new method for detecting differentially expressed genes. BMC Bioinformatics (2014) 1.56
Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map. PLoS One (2011) 1.49
Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring. Genome Biol (2007) 1.43
Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station. PLoS One (2016) 1.40
Whole genome expression profiling associates activation of unfolded protein response with impaired production and release of epinephrine after recurrent hypoglycemia. PLoS One (2017) 1.39
Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS One (2014) 1.39
Technical variables in high-throughput miRNA expression profiling: much work remains to be done. Biochim Biophys Acta (2008) 1.36
Can subtle changes in gene expression be consistently detected with different microarray platforms? BMC Genomics (2008) 1.36
Characterization of primary human hepatocytes, HepG2 cells, and HepaRG cells at the mRNA level and CYP activity in response to inducers and their predictivity for the detection of human hepatotoxins. Cell Biol Toxicol (2012) 1.31
Depressive symptoms and cortisol rhythmicity predict survival in patients with renal cell carcinoma: role of inflammatory signaling. PLoS One (2012) 1.30
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics (2009) 1.29
Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biol (2008) 1.28
Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens. OMICS (2008) 1.26
Efficiency analysis of competing tests for finding differentially expressed genes in lung adenocarcinoma. Cancer Inform (2008) 1.21
Three methods for optimization of cross-laboratory and cross-platform microarray expression data. Nucleic Acids Res (2007) 1.21
Cross-platform analysis of global microRNA expression technologies. BMC Genomics (2010) 1.18
Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse. BMC Genomics (2008) 1.18
Role of nuclear factor kappaB in ovarian hormone-mediated stress hypersensitivity in female mice. Biol Psychiatry (2009) 1.17
Distinct roles of adenylyl cyclases 1 and 8 in opiate dependence: behavioral, electrophysiological, and molecular studies. Biol Psychiatry (2008) 1.14
Effect of various normalization methods on Applied Biosystems expression array system data. BMC Bioinformatics (2006) 1.14
Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen (2007) 1.14
Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics (2008) 1.14
Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements. BMC Genomics (2010) 1.14
Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res (2008) 1.12
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells. BMC Med Genomics (2009) 1.12
Microarray expression analysis and identification of serum biomarkers for Niemann-Pick disease, type C1. Hum Mol Genet (2012) 1.10
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biol (2015) 1.10
Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. BMC Bioinformatics (2008) 1.09
Perturbation of defense pathways by low-dose arsenic exposure in zebrafish embryos. Environ Health Perspect (2009) 1.09
A genome-wide expression analysis in blood identifies pre-elafin as a biomarker in ARDS. Am J Respir Cell Mol Biol (2008) 1.07
"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms Mol Biol (2008) 1.05
Methamphetamine preconditioning alters midbrain transcriptional responses to methamphetamine-induced injury in the rat striatum. PLoS One (2009) 1.02
Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics (2009) 1.01
Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools. BMC Genomics (2007) 1.01
Cognitive Behavioral Therapy and Tai Chi Reverse Cellular and Genomic Markers of Inflammation in Late-Life Insomnia: A Randomized Controlled Trial. Biol Psychiatry (2015) 0.99
Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy. Genomics (2009) 0.98
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinformatics (2009) 0.98
IL-32 is a molecular marker of a host defense network in human tuberculosis. Sci Transl Med (2014) 0.95
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinformatics (2010) 0.92
Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC Res Notes (2009) 0.92
Transcriptional profiling of the acute pulmonary inflammatory response induced by LPS: role of neutrophils. Respir Res (2010) 0.92
S-nitrosylation of HDAC2 regulates the expression of the chromatin-remodeling factor Brm during radial neuron migration. Proc Natl Acad Sci U S A (2013) 0.91
Abnormal gene expression in cerebellum of Npc1-/- mice during postnatal development. Brain Res (2010) 0.90
Comprehensive analysis of gene expression profiles of the beet armyworm Spodoptera exigua larvae challenged with Bacillus thuringiensis Vip3Aa toxin. PLoS One (2013) 0.89
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics (2007) 0.89
New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures. BMC Genomics (2007) 0.89
Genome-wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver. PLoS One (2013) 0.89
Toxicogenomic analysis of susceptibility to inhaled urban particulate matter in mice with chronic lung inflammation. Part Fibre Toxicol (2009) 0.89
Transcriptome analysis of a rotenone model of parkinsonism reveals complex I-tied and -untied toxicity mechanisms common to neurodegenerative diseases. PLoS One (2012) 0.89
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy. BMC Genomics (2008) 0.88
Intra- and inter-individual variance of gene expression in clinical studies. PLoS One (2012) 0.88
Global gene expression analysis reveals dynamic and developmental stage-dependent enrichment of lead-induced neurological gene alterations. Environ Health Perspect (2010) 0.88
An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era. Genome Biol (2014) 0.88
Extended analysis of benchmark datasets for Agilent two-color microarrays. BMC Bioinformatics (2007) 0.87
Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old. Mol Cancer (2010) 0.87
The vitamin D receptor and inducible nitric oxide synthase associated pathways in acquired resistance to Cooperia oncophora infection in cattle. Vet Res (2011) 0.86
Analysis of the toxicogenomic effects of exposure to persistent organic pollutants (POPs) in Slovakian girls: correlations between gene expression and disease risk. Environ Int (2011) 0.86
Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth. Funct Integr Genomics (2009) 0.86
Validation of differential gene expression algorithms: application comparing fold-change estimation to hypothesis testing. BMC Bioinformatics (2010) 0.85
Global expression of molecular transporters in the human vaginal tract: implications for HIV chemoprophylaxis. PLoS One (2013) 0.85
Lung fibroblasts from patients with idiopathic pulmonary fibrosis exhibit genome-wide differences in DNA methylation compared to fibroblasts from nonfibrotic lung. PLoS One (2014) 0.85
Transcriptome analysis reveals a major impact of JAK protein tyrosine kinase 2 (Tyk2) on the expression of interferon-responsive and metabolic genes. BMC Genomics (2010) 0.84
Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments. BMC Genomics (2011) 0.84
Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation. BMC Genomics (2010) 0.83
Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague-Dawley rats and C57BL/6 mice. Toxicol Appl Pharmacol (2012) 0.83
ACE inhibition with captopril retards the development of signs of neurodegeneration in an animal model of Alzheimer's disease. Int J Mol Sci (2013) 0.83
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PLoS Comput Biol (2016) 0.83
Does the F508-CFTR mutation induce a proinflammatory response in human airway epithelial cells? Am J Physiol Lung Cell Mol Physiol (2012) 0.82
A novel approach to analyze gene expression data demonstrates that the DeltaF508 mutation in CFTR downregulates the antigen presentation pathway. Am J Physiol Lung Cell Mol Physiol (2009) 0.82
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays. BMC Bioinformatics (2009) 0.82
Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Mol Biol Evol (2014) 0.82
Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation. BMC Proc (2009) 0.82
Evaluation of gene, protein and neurotrophin expression in the brain of mice exposed to space environment for 91 days. PLoS One (2012) 0.82
Transcriptomic profiling of human peritumoral neocortex tissues revealed genes possibly involved in tumor-induced epilepsy. PLoS One (2013) 0.82
Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica. J Microbiol Methods (2010) 0.82
Application of a correlation correction factor in a microarray cross-platform reproducibility study. BMC Bioinformatics (2007) 0.81
LTR: Linear Cross-Platform Integration of Microarray Data. Cancer Inform (2010) 0.81
Using the ratio of means as the effect size measure in combining results of microarray experiments. BMC Syst Biol (2009) 0.81
Transcriptome alterations following developmental atrazine exposure in zebrafish are associated with disruption of neuroendocrine and reproductive system function, cell cycle, and carcinogenesis. Toxicol Sci (2013) 0.81
Combination of meta-analysis and graph clustering to identify prognostic markers of ESCC. Genet Mol Biol (2012) 0.81
Developmental origins of neurotransmitter and transcriptome alterations in adult female zebrafish exposed to atrazine during embryogenesis. Toxicology (2015) 0.81
A novel method to quantify gene set functional association based on gene ontology. J R Soc Interface (2011) 0.81
Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats. BMC Bioinformatics (2007) 0.81
Toxicogenomic biomarkers for liver toxicity. J Toxicol Pathol (2009) 0.80
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35
Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol (2006) 8.87
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med (2011) 8.20
Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01
The adaptor protein MITA links virus-sensing receptors to IRF3 transcription factor activation. Immunity (2008) 7.60
A model of (often mixed) stereotype content: competence and warmth respectively follow from perceived status and competition. J Pers Soc Psychol (2002) 7.36
Activation of mGlu2/3 receptors as a new approach to treat schizophrenia: a randomized Phase 2 clinical trial. Nat Med (2007) 7.24
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res (2004) 6.98
DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell (2010) 6.72
Fatty acid-induced NLRP3-ASC inflammasome activation interferes with insulin signaling. Nat Immunol (2011) 6.53
Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods (2005) 6.23
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol (2006) 5.92
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science (2013) 4.94
Toward interoperable bioscience data. Nat Genet (2012) 4.72
The External RNA Controls Consortium: a progress report. Nat Methods (2005) 4.24
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS (2008) 4.15
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics (2005) 3.93
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature (2010) 3.90
Identification of a novel Ras-regulated proapoptotic pathway. Curr Biol (2002) 3.89
Simultaneous phase and size control of upconversion nanocrystals through lanthanide doping. Nature (2010) 3.53
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS (2006) 3.51
Aminotransferase elevations in healthy adults receiving 4 grams of acetaminophen daily: a randomized controlled trial. JAMA (2006) 3.49
Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol Cell (2006) 3.39
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect (2003) 3.39
Mutations in SLC20A2 link familial idiopathic basal ganglia calcification with phosphate homeostasis. Nat Genet (2012) 3.34
Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol (2006) 3.13
Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically stabilized nanoparticle. Nucleic Acids Res (2004) 3.03
Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics (2006) 2.96
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet (2012) 2.94
NOTCH reprograms mitochondrial metabolism for proinflammatory macrophage activation. J Clin Invest (2015) 2.93
Identification of a salmonellosis outbreak by means of molecular sequencing. N Engl J Med (2011) 2.81
Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet (2010) 2.74
QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn (2004) 2.73
Identification of an adenylyl cyclase inhibitor for treating neuropathic and inflammatory pain. Sci Transl Med (2011) 2.67
Monitoring avian influenza A(H7N9) virus through national influenza-like illness surveillance, China. Emerg Infect Dis (2013) 2.61
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Integrative genomic and functional analyses reveal neuronal subtype differentiation bias in human embryonic stem cell lines. Proc Natl Acad Sci U S A (2007) 2.60
Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol (2006) 2.59
Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque. Nat Med (2005) 2.55
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics (2008) 2.54
Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology. IEEE Trans Biomed Eng (2010) 2.52
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42
An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res (2002) 2.37
A multicenter, inpatient, phase 2, double-blind, placebo-controlled dose-ranging study of LY2140023 monohydrate in patients with DSM-IV schizophrenia. J Clin Psychopharmacol (2011) 2.31
Development of public toxicogenomics software for microarray data management and analysis. Mutat Res (2004) 2.29
Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast Cancer Res (2010) 2.26
Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet (2012) 2.26
Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One (2008) 2.22
Targeted synthesis of a porous aromatic framework with high stability and exceptionally high surface area. Angew Chem Int Ed Engl (2009) 2.22
The ubiquitin ligase RNF5 regulates antiviral responses by mediating degradation of the adaptor protein MITA. Immunity (2009) 2.21
Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference. Bioinformatics (2003) 2.21
Osteopontin deficiency does not prevent but promotes alcoholic neutrophilic hepatitis in mice. Hepatology (2014) 2.17
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One (2011) 2.16