Published in Nat Protoc on January 01, 2009
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell (2009) 20.29
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron (2011) 10.61
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
Transcript length bias in RNA-seq data confounds systems biology. Biol Direct (2009) 8.53
Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson's disease. Nature (2011) 7.90
An anatomically comprehensive atlas of the adult human brain transcriptome. Nature (2012) 7.46
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell (2011) 6.83
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
A unifying model for mTORC1-mediated regulation of mRNA translation. Nature (2012) 6.44
Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring. Nature (2010) 6.23
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res (2013) 6.17
HIF1alpha-dependent glycolytic pathway orchestrates a metabolic checkpoint for the differentiation of TH17 and Treg cells. J Exp Med (2011) 5.99
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Depletion of carcinoma-associated fibroblasts and fibrosis induces immunosuppression and accelerates pancreas cancer with reduced survival. Cancer Cell (2014) 5.87
miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res (2010) 5.72
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature (2014) 5.47
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell (2014) 5.43
Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16
Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS One (2012) 5.03
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet (2012) 4.82
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature (2012) 4.53
Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science (2012) 4.52
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res (2011) 4.44
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science (2014) 4.34
Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet (2010) 4.27
Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature (2009) 4.21
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci (2011) 4.15
Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. J Clin Oncol (2012) 4.14
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol (2013) 4.04
Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature (2012) 3.96
g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res (2011) 3.94
ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death. Nat Cell Biol (2013) 3.84
Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nat Med (2011) 3.82
Highly multiplexed subcellular RNA sequencing in situ. Science (2014) 3.77
Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science (2011) 3.77
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature (2013) 3.57
R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell (2012) 3.56
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature (2011) 3.56
Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet (2010) 3.55
The expanding universe of p53 targets. Nat Rev Cancer (2009) 3.49
Differentiation and persistence of memory CD8(+) T cells depend on T cell factor 1. Immunity (2010) 3.49
De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat Genet (2012) 3.49
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Wnt5a potentiates TGF-β signaling to promote colonic crypt regeneration after tissue injury. Science (2012) 3.45
JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms (2010) 3.42
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet (2013) 3.41
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood (2011) 3.37
Retracted Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease. Nature (2013) 3.35
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Res (2012) 3.29
Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet (2010) 3.28
A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell (2009) 3.27
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol (2010) 3.23
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One (2010) 3.15
Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet (2012) 3.14
Global identification of modular cullin-RING ligase substrates. Cell (2011) 3.13
Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature (2012) 3.08
Therapy-induced tumour secretomes promote resistance and tumour progression. Nature (2015) 3.07
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 3.06
Transcriptional landscape of the prenatal human brain. Nature (2014) 3.05
The tumor suppressor Tsc1 enforces quiescence of naive T cells to promote immune homeostasis and function. Nat Immunol (2011) 3.03
Making sense of cancer genomic data. Genes Dev (2011) 3.01
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. Nat Struct Mol Biol (2011) 3.00
TRIM24 links a non-canonical histone signature to breast cancer. Nature (2010) 2.99
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet (2010) 2.99
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature (2012) 2.96
Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol (2011) 2.94
Xist RNA is a potent suppressor of hematologic cancer in mice. Cell (2013) 2.93
Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet (2012) 2.92
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat Genet (2014) 2.91
TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res (2012) 2.90
Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A (2012) 2.90
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat Immunol (2013) 2.87
Clinical role of microRNAs in cytogenetically normal acute myeloid leukemia: miR-155 upregulation independently identifies high-risk patients. J Clin Oncol (2013) 2.86
Epigenetic and immune function profiles associated with posttraumatic stress disorder. Proc Natl Acad Sci U S A (2010) 2.85
GOBO: gene expression-based outcome for breast cancer online. PLoS One (2011) 2.81
Inactivation of conserved C. elegans genes engages pathogen- and xenobiotic-associated defenses. Cell (2012) 2.81
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. Nucleic Acids Res (2010) 2.80
An enteric virus can replace the beneficial function of commensal bacteria. Nature (2014) 2.80
RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell (2012) 2.77
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol (2011) 2.73
The microglial sensome revealed by direct RNA sequencing. Nat Neurosci (2013) 2.73
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A (2015) 2.72
Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nat Genet (2012) 2.71
Platelets direct monocyte differentiation into epithelioid-like multinucleated giant foam cells with suppressive capacity upon mycobacterial stimulation. J Infect Dis (2014) 2.69
Obesity accelerates epigenetic aging of human liver. Proc Natl Acad Sci U S A (2014) 2.68
The DNA methylation landscape of human early embryos. Nature (2014) 2.67
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics (2005) 22.22
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci U S A (2002) 17.22
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol (2004) 15.61
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics (2007) 12.76
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res (2004) 12.19
GObar: a gene ontology based analysis and visualization tool for gene sets. BMC Bioinformatics (2005) 10.55
DAVID gene ID conversion tool. Bioinformation (2008) 9.16
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res (2005) 9.05
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci U S A (2002) 17.22
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics (2007) 12.76
DAVID gene ID conversion tool. Bioinformation (2008) 9.16
Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08
HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nat Immunol (2008) 5.01
Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A (2003) 3.47
PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics (2003) 3.11
Extracting biological meaning from large gene lists with DAVID. Curr Protoc Bioinformatics (2009) 2.88
DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics (2012) 2.14
Induction of prolonged survival of CD4+ T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J Clin Invest (2005) 1.82
Safety, tolerability, and mechanisms of antiretroviral activity of pegylated interferon Alfa-2a in HIV-1-monoinfected participants: a phase II clinical trial. J Infect Dis (2010) 1.51
Telomere length and heavy-chain mutation status in familial chronic lymphocytic leukemia. Leuk Res (2002) 1.44
Cutting edge: L-selectin (CD62L) expression distinguishes small resting memory CD4+ T cells that preferentially respond to recall antigen. J Immunol (2003) 1.42
Cutting edge: Ku70 is a novel cytosolic DNA sensor that induces type III rather than type I IFN. J Immunol (2011) 1.41
Human immunodeficiency virus viremia induces plasmacytoid dendritic cell activation in vivo and diminished alpha interferon production in vitro. J Virol (2008) 1.36
IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages. AIDS (2008) 1.33
Diminished production of monocyte proinflammatory cytokines during human immunodeficiency virus viremia is mediated by type I interferons. J Virol (2006) 1.24
A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS. J Data Mining Genomics Proteomics (2013) 1.23
Noninfectious papilloma virus-like particles inhibit HIV-1 replication: implications for immune control of HIV-1 infection by IL-27. Blood (2006) 1.21
Identification and functional clustering of global gene expression differences between human age-related cataract and clear lenses. Mol Vis (2003) 1.21
R5 and X4 HIV envelopes induce distinct gene expression profiles in primary peripheral blood mononuclear cells. Proc Natl Acad Sci U S A (2006) 1.13
Increased peripheral expansion of naive CD4+ T cells in vivo after IL-2 treatment of patients with HIV infection. Proc Natl Acad Sci U S A (2002) 1.12
The HIV-1 envelope protein gp120 impairs B cell proliferation by inducing TGF-β1 production and FcRL4 expression. Nat Immunol (2013) 1.04
Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region. Nucleic Acids Res (2006) 1.03
Lifespan of effector memory CD4+ T cells determined by replication-incompetent integrated HIV-1 provirus. AIDS (2014) 1.03
Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics (2010) 1.01
Differential effects of HIV viral load and CD4 count on proliferation of naive and memory CD4 and CD8 T lymphocytes. Blood (2011) 1.00
HIV-1 gp120 induces NFAT nuclear translocation in resting CD4+ T-cells. Virology (2005) 0.99
CD4 T cell survival after intermittent interleukin-2 therapy is predictive of an increase in the CD4 T cell count of HIV-infected patients. J Infect Dis (2008) 0.99
Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies. Hum Biol (2013) 0.98
IL-27 inhibits HIV-1 infection in human macrophages by down-regulating host factor SPTBN1 during monocyte to macrophage differentiation. J Exp Med (2013) 0.98
Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. FASEB J (2013) 0.97
Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. J Immunol (2009) 0.93
HIV infection and antiretroviral therapy have divergent effects on mitochondria in adipose tissue. J Infect Dis (2012) 0.92
Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway. PLoS One (2013) 0.92
CCL5: a double-edged sword in host defense against the hepatitis C virus. Int Rev Immunol (2011) 0.91
Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties. Biochem Biophys Res Commun (2013) 0.88
Association of interleukin-15-induced peripheral immune activation with hepatic stellate cell activation in persons coinfected with hepatitis C virus and HIV. J Infect Dis (2009) 0.88
Differential gene and microRNA expression between etoposide resistant and etoposide sensitive MCF7 breast cancer cell lines. PLoS One (2012) 0.86
High interferon-stimulated gene ISG-15 expression affects HCV treatment outcome in patients co-infected with HIV and HCV. J Med Virol (2013) 0.86
Host gene expression changes correlating with anti-HIV-1 effects in human subjects after treatment with peginterferon Alfa-2a. J Infect Dis (2012) 0.85
Actinomycin D induces high-level resistance to thymidine analogs in replication of human immunodeficiency virus type 1 by interfering with host cell thymidine kinase expression. J Virol (2003) 0.85
Gene expression profiles predict emergence of psychiatric adverse events in HIV/HCV-coinfected patients on interferon-based HCV therapy. J Acquir Immune Defic Syndr (2012) 0.82
Pre-gastrula expression of zebrafish extraembryonic genes. BMC Dev Biol (2010) 0.82
LIM kinase 1 - dependent cofilin 1 pathway and actin dynamics mediate nuclear retinoid receptor function in T lymphocytes. BMC Mol Biol (2011) 0.81
Retinoic acid-induced downmodulation of telomerase activity in human cancer cells. Exp Mol Pathol (2005) 0.80
Zap70 signaling pathway mediates glucocorticoid receptor-dependent transcriptional activation: role in the regulation of annexin 1 expression in T cells. J Immunol (2007) 0.80
Interleukin-2 inhibits HIV-1 replication in some human T cell lymphotrophic virus-1-infected cell lines via the induction and incorporation of APOBEC3G into the virion. J Biol Chem (2013) 0.80
Cytokine/chemokine patterns connect host and viral characteristics with clinics during chronic hepatitis C. Eur J Med Res (2012) 0.80
Altered regulation of extrinsic apoptosis pathway in HCV-infected HCC cells enhances susceptibility to mapatumumab-induced apoptosis. Hepatol Res (2009) 0.80
Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach. AIDS (2008) 0.79
Interferon stimulated exonuclease gene 20 kDa links psychiatric events to distinct hepatitis C virus responses in human immunodeficiency virus positive patients. J Med Virol (2014) 0.79
The CD8+ HLA-DR+ T cells expanded in HIV-1 infection are qualitatively identical to those from healthy controls. Eur J Immunol (2012) 0.79
Interleukin-27 induces interferon-inducible genes: analysis of gene expression profiles using Affymetrix microarray and DAVID. Methods Mol Biol (2012) 0.79
Altered expression of SHIP, a Toll-like receptor pathway inhibitor, is associated with the severity of liver fibrosis in chronic hepatitis C virus infection. J Infect Dis (2011) 0.75
Immunodeficiency and intrinsic IFN resistance are associated with viral breakthrough to HCV therapy in HIV-coinfected patients. AIDS Res Hum Retroviruses (2007) 0.75