Published in BMC Bioinformatics on June 08, 2005
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Resveratrol improves health and survival of mice on a high-calorie diet. Nature (2006) 20.91
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Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol (2012) 6.38
Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending life span. Cell Metab (2008) 6.22
Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoS One (2008) 5.86
A general modular framework for gene set enrichment analysis. BMC Bioinformatics (2009) 3.92
GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics (2009) 3.86
Growth hormone receptor deficiency is associated with a major reduction in pro-aging signaling, cancer, and diabetes in humans. Sci Transl Med (2011) 3.84
Nicotinamide mononucleotide, a key NAD(+) intermediate, treats the pathophysiology of diet- and age-induced diabetes in mice. Cell Metab (2011) 3.38
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
Metformin improves healthspan and lifespan in mice. Nat Commun (2013) 2.68
Fasting cycles retard growth of tumors and sensitize a range of cancer cell types to chemotherapy. Sci Transl Med (2012) 2.58
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Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res (2012) 2.54
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res (2010) 2.32
GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics (2013) 2.29
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood (2008) 2.26
Fasting-Mimicking Diet Reduces HO-1 to Promote T Cell-Mediated Tumor Cytotoxicity. Cancer Cell (2016) 2.24
Prolonged fasting reduces IGF-1/PKA to promote hematopoietic-stem-cell-based regeneration and reverse immunosuppression. Cell Stem Cell (2014) 2.24
Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics (2008) 2.14
Modeling cancer progression via pathway dependencies. PLoS Comput Biol (2008) 2.12
GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res (2010) 2.09
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res (2013) 2.05
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst Biol (2008) 2.02
Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet (2008) 1.99
microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discov (2012) 1.94
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. Cell Metab (2015) 1.89
A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res (2011) 1.89
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Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Gene set enrichment analysis made simple. Stat Methods Med Res (2009) 1.79
Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics (2006) 1.76
Gene set enrichment analysis using linear models and diagnostics. Bioinformatics (2008) 1.75
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res (2006) 1.69
A molecular function map of Ewing's sarcoma. PLoS One (2009) 1.69
Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics (2010) 1.59
DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One (2010) 1.59
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol (2012) 1.58
Mitochondrial DNA mutations induce mitochondrial dysfunction, apoptosis and sarcopenia in skeletal muscle of mitochondrial DNA mutator mice. PLoS One (2010) 1.57
Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information. BMC Med Genomics (2010) 1.57
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res (2016) 1.52
Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol (2011) 1.52
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics (2009) 1.50
Calorie restriction in humans inhibits the PI3K/AKT pathway and induces a younger transcription profile. Aging Cell (2013) 1.48
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics (2009) 1.48
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics (2008) 1.45
Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants. Aging Cell (2009) 1.44
Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res (2006) 1.43
The SIRT1 activator SRT1720 extends lifespan and improves health of mice fed a standard diet. Cell Rep (2014) 1.42
Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics (2007) 1.41
An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet (2008) 1.40
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics (2007) 1.35
The E2F3-Oncomir-1 axis is activated in Wilms' tumor. Cancer Res (2008) 1.33
Gene set analysis methods: statistical models and methodological differences. Brief Bioinform (2014) 1.30
Gene module level analysis: identification to networks and dynamics. Curr Opin Biotechnol (2008) 1.29
Getting started in gene expression microarray analysis. PLoS Comput Biol (2009) 1.25
Longevity in mice is promoted by probiotic-induced suppression of colonic senescence dependent on upregulation of gut bacterial polyamine production. PLoS One (2011) 1.22
Multidimensional gene set analysis of genomic data. PLoS One (2010) 1.21
Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res (2011) 1.20
Direct and indirect roles of RECQL4 in modulating base excision repair capacity. Hum Mol Genet (2009) 1.18
Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model. J Bacteriol (2012) 1.17
Metabolically normal obese people are protected from adverse effects following weight gain. J Clin Invest (2015) 1.17
Target of rapamycin signaling regulates metabolism, growth, and life span in Arabidopsis. Plant Cell (2012) 1.16
Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders. PLoS Pathog (2011) 1.14
Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure. Genome Biol (2009) 1.13
Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci Rep (2011) 1.11
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. BMC Bioinformatics (2008) 1.11
Differential expression analysis for pathways. PLoS Comput Biol (2013) 1.11
Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell (2011) 1.11
Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach. Cancer Res (2008) 1.11
Whole genome transcriptome polymorphisms in Arabidopsis thaliana. Genome Biol (2008) 1.09
Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet (2016) 1.08
Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep (2013) 1.08
Time-dependent c-Myc transactomes mapped by Array-based nuclear run-on reveal transcriptional modules in human B cells. PLoS One (2010) 1.08
Patterns of positive selection in seven ant genomes. Mol Biol Evol (2014) 1.08
Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics (2010) 1.08
Intercohort gene expression co-analysis reveals chemokine receptors as prognostic indicators in Ewing's sarcoma. Clin Cancer Res (2010) 1.07
Conserved and differential effects of dietary energy intake on the hippocampal transcriptomes of females and males. PLoS One (2008) 1.07
A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol (2009) 1.05
Hypoxia modulates EWS-FLI1 transcriptional signature and enhances the malignant properties of Ewing's sarcoma cells in vitro. Cancer Res (2010) 1.05
Gene set internal coherence in the context of functional profiling. BMC Genomics (2009) 1.04
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Proc Natl Acad Sci U S A (2013) 1.04
Knowledge-based analysis of proteomics data. BMC Bioinformatics (2012) 1.03
Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics (2008) 1.03
Amplified genes may be overexpressed, unchanged, or downregulated in cervical cancer cell lines. PLoS One (2012) 1.03
Identification of transcription factors for lineage-specific ESC differentiation. Stem Cell Reports (2013) 1.02
Growth factor signals in neural cells: coherent patterns of interaction control multiple levels of molecular and phenotypic responses. J Biol Chem (2008) 1.02
Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts. BMC Genomics (2014) 1.02
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
The leukemia-specific fusion gene ETV6/RUNX1 perturbs distinct key biological functions primarily by gene repression. PLoS One (2011) 1.01
Gonadal transcriptome alterations in response to dietary energy intake: sensing the reproductive environment. PLoS One (2009) 1.00
Genome-wide pathway analysis of memory impairment in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort implicates gene candidates, canonical pathways, and networks. Brain Imaging Behav (2012) 1.00
Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics (2007) 1.00
Disease and phenotype gene set analysis of disease-based gene expression in mouse and human. Physiol Genomics (2010) 1.00
Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. Nat Commun (2014) 1.00
The limitations of simple gene set enrichment analysis assuming gene independence. Stat Methods Med Res (2012) 0.99
Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae. BMC Genomics (2009) 0.99
Overexpression of HGF Promotes HBV-Induced Hepatocellular Carcinoma Progression and Is an Effective Indicator for Met-Targeting Therapy. Genes Cancer (2013) 0.98
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Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A (1999) 39.79
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
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GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol (2003) 20.83
Microarray data normalization and transformation. Nat Genet (2002) 15.04
An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet (2004) 10.92
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42
Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08
Fundamentals of experimental design for cDNA microarrays. Nat Genet (2002) 7.49
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res (2002) 7.29
Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (2002) 7.07
Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci U S A (2002) 5.18
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res (2004) 4.43
A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res (2004) 3.20
Are data from different gene expression microarray platforms comparable? Genomics (2004) 3.13
HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages. Nat Med (2003) 2.62
Genomic approaches to hematologic malignancies. Blood (2004) 2.03
Skeletal muscle gene expression profiles in 20-29 year old and 65-71 year old women. Exp Gerontol (2004) 2.00
Statistical concerns about the GSEA procedure. Nat Genet (2004) 1.91
Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics (2004) 1.75
Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann N Y Acad Sci (2004) 1.73
Senescence-related changes in gene expression in muscle: similarities and differences between mice and men. Physiol Genomics (2001) 1.35
Microarray analysis of changes in cellular gene expression induced by productive infection of primary human astrocytes: implications for HAD. J Neuroimmunol (2004) 1.18
Use of high-throughput DNA microarrays to identify biomarkers for bladder cancer. Clin Chem (2003) 1.05
Cloning and characterization of HIV-1-inducible astrocyte elevated gene-1, AEG-1. Gene (2005) 2.58
Mechanism of ceftriaxone induction of excitatory amino acid transporter-2 expression and glutamate uptake in primary human astrocytes. J Biol Chem (2008) 2.08
GAzer: gene set analyzer. Bioinformatics (2007) 2.04
Astrocyte elevated gene-1: recent insights into a novel gene involved in tumor progression, metastasis and neurodegeneration. Pharmacol Ther (2007) 1.80
Insights into glutamate transport regulation in human astrocytes: cloning of the promoter for excitatory amino acid transporter 2 (EAAT2). Proc Natl Acad Sci U S A (2003) 1.61
Reduced expression of glutamate transporter EAAT2 and impaired glutamate transport in human primary astrocytes exposed to HIV-1 or gp120. Virology (2003) 1.39
Effects of human immunodeficiency virus type 1 on astrocyte gene expression and function: potential role in neuropathogenesis. J Neurovirol (2004) 1.38
A mouse model for study of systemic HIV-1 infection, antiviral immune responses, and neuroinvasiveness. Proc Natl Acad Sci U S A (2005) 1.32
HIV-1 neuropathogenesis: glial mechanisms revealed through substance abuse. J Neurochem (2006) 1.31
Protective efficacy of serially up-ranked subdominant CD8+ T cell epitopes against virus challenges. PLoS Pathog (2011) 1.27
HIV-1 Tat activates neuronal ryanodine receptors with rapid induction of the unfolded protein response and mitochondrial hyperpolarization. PLoS One (2008) 1.23
Microarray analysis of changes in cellular gene expression induced by productive infection of primary human astrocytes: implications for HAD. J Neuroimmunol (2004) 1.18
Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders. PLoS Pathog (2011) 1.14
Functional domains of APOBEC3G required for antiviral activity. J Cell Biochem (2004) 1.12
Human immunodeficiency virus type 1 efficiently binds to human fetal astrocytes and induces neuroinflammatory responses independent of infection. BMC Neurosci (2007) 1.08
Copolymer-1 induces adaptive immune anti-inflammatory glial and neuroprotective responses in a murine model of HIV-1 encephalitis. J Immunol (2007) 1.07
Transcriptional regulation of human excitatory amino acid transporter 1 (EAAT1): cloning of the EAAT1 promoter and characterization of its basal and inducible activity in human astrocytes. J Neurochem (2003) 1.01
Proteomic modeling for HIV-1 infected microglia-astrocyte crosstalk. PLoS One (2008) 0.99
Monocyte chemotactic protein-1 regulates voltage-gated K+ channels and macrophage transmigration. J Neuroimmune Pharmacol (2008) 0.98
Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders. J Neuroimmune Pharmacol (2009) 0.97
The common insecticides cyfluthrin and chlorpyrifos alter the expression of a subset of genes with diverse functions in primary human astrocytes. Toxicol Sci (2006) 0.97
Neuropathologic and neuroinflammatory activities of HIV-1-infected human astrocytes in murine brain. Glia (2006) 0.97
Testing antiretroviral drug efficacy in conventional mice infected with chimeric HIV-1. AIDS (2007) 0.96
Common transcriptional signatures in brain tissue from patients with HIV-associated neurocognitive disorders, Alzheimer's disease, and Multiple Sclerosis. J Neuroimmune Pharmacol (2012) 0.96
Transmission of chimeric HIV by mating in conventional mice: prevention by pre-exposure antiretroviral therapy and reduced susceptibility during estrus. Dis Model Mech (2013) 0.94
Identification of gene products suppressed by human immunodeficiency virus type 1 infection or gp120 exposure of primary human astrocytes by rapid subtraction hybridization. J Neurovirol (2003) 0.94
Induction of secreted human immunodeficiency virus type 1 (HIV-1) resistance factors in CD4-positive T lymphocytes by attenuated HIV-1 infection. Virology (2002) 0.93
HIV-1-infected astrocytes and the microglial proteome. J Neuroimmune Pharmacol (2008) 0.92
HIV type 1-specific IgE in serum of long-term surviving children inhibits HIV type 1 production in vitro. AIDS Res Hum Retroviruses (2002) 0.90
Activation of NF-kappaB by R5 and X4 human immunodeficiency virus type 1 induces macrophage inflammatory protein 1alpha and tumor necrosis factor alpha in macrophages. J Virol (2002) 0.90
T cells induced by recombinant chimpanzee adenovirus alone and in prime-boost regimens decrease chimeric EcoHIV/NDK challenge virus load. Eur J Immunol (2012) 0.88
Novel HIV-1 clade B candidate vaccines designed for HLA-B*5101(+) patients protected mice against chimaeric ecotropic HIV-1 challenge. Eur J Immunol (2009) 0.88
Mice chronically infected with chimeric HIV resist peripheral and brain superinfection: a model of protective immunity to HIV. J Neuroimmune Pharmacol (2011) 0.87
Vaccine-induced protection from infection of mice by chimeric human immunodeficiency virus type 1, EcoHIV/NL4-3. Vaccine (2007) 0.87
Productive infection of primary murine astrocytes, lymphocytes, and macrophages by human immunodeficiency virus type 1 in culture. J Neurovirol (2004) 0.86
Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution. Biol Direct (2006) 0.86
A novel role for the viral Rev protein in promoting resistance to superinfection by human immunodeficiency virus type 1. J Gen Virol (2010) 0.85
Gene expression profiling of human primary astrocytes exposed to manganese chloride indicates selective effects on several functions of the cells. Neurotoxicology (2006) 0.84
Novel regulation of HIV-1 replication and pathogenicity: Rev inhibition of integration. Protein Eng Des Sel (2009) 0.84
Role of the macrophage in HIV-associated neurocognitive disorders and other comorbidities in patients on effective antiretroviral treatment. J Neurovirol (2015) 0.83
Cloning and characterization of the 3'-untranslated region of the human excitatory amino acid transporter 2 transcript. J Neurochem (2003) 0.83
Enhanced human immunodeficiency virus Type 1 expression and neuropathogenesis in knockout mice lacking Type I interferon responses. J Neuropathol Exp Neurol (2014) 0.82
Mechanism of action of the HIV-1 integrase inhibitory peptide LEDGF 361-370. Biochem Biophys Res Commun (2010) 0.81
An infectious murine model for studying the systemic effects of opioids on early HIV pathogenesis in the gut. J Neuroimmune Pharmacol (2014) 0.81
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HIV-associated neurocognitive disorder - pathogenesis and prospects for treatment. Nat Rev Neurol (2016) 0.80
Response to 'Remarks on the article of Hadas et al.: Transmission of chimeric HIV by mating in conventional mice: prevention by pre-exposure antiretroviral therapy and reduced susceptibility during estrus'. Dis Model Mech (2014) 0.77