Published in Nucleic Acids Res on November 21, 2010
Cancer genome landscapes. Science (2013) 25.33
NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res (2012) 15.84
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res (2011) 7.93
Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res (2011) 6.69
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun (2011) 4.57
The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res (2011) 4.34
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res (2011) 3.61
Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science (2016) 3.45
Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37
Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. Nat Genet (2011) 3.20
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics (2011) 3.12
The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res (2011) 3.05
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Res (2011) 3.05
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res (2013) 2.97
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PLoS One (2012) 2.85
Reuse of public genome-wide gene expression data. Nat Rev Genet (2012) 2.79
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68
BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res (2012) 2.57
Human cancer long non-coding RNA transcriptomes. PLoS One (2011) 2.38
Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc (2011) 2.36
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics (2011) 2.31
The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22
modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res (2012) 2.11
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat Biotechnol (2013) 1.91
PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res (2011) 1.86
Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. Proc Natl Acad Sci U S A (2012) 1.82
MOPED: Model Organism Protein Expression Database. Nucleic Acids Res (2011) 1.79
A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics (2012) 1.55
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res (2011) 1.54
Viral perturbations of host networks reflect disease etiology. PLoS Comput Biol (2012) 1.54
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PLoS Genet (2012) 1.52
An Osteopontin/CD44 Axis in RhoGDI2-Mediated Metastasis Suppression. Cancer Cell (2016) 1.48
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
IL-10-producing NKT10 cells are a distinct regulatory invariant NKT cell subset. J Clin Invest (2014) 1.48
Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PLoS One (2012) 1.47
Selective gene-expression profiling of migratory tumor cells in vivo predicts clinical outcome in breast cancer patients. Breast Cancer Res (2012) 1.43
The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res (2011) 1.43
Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients. Bioessays (2012) 1.42
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol (2012) 1.41
When is hub gene selection better than standard meta-analysis? PLoS One (2013) 1.41
MERTK receptor tyrosine kinase is a therapeutic target in melanoma. J Clin Invest (2013) 1.34
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Res (2012) 1.33
Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol (2012) 1.30
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet (2012) 1.28
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol (2012) 1.26
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol (2012) 1.24
Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production- and development-correlated expression and new small RNA classes. Plant Physiol (2011) 1.23
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biol (2012) 1.23
Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. Philos Trans R Soc Lond B Biol Sci (2012) 1.22
MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res (2012) 1.21
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol Cell Proteomics (2013) 1.20
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res (2012) 1.17
A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. PLoS Biol (2013) 1.16
Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. Arthritis Res Ther (2014) 1.15
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. J Bacteriol (2011) 1.15
Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci U S A (2012) 1.14
A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet (2013) 1.13
Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. BMC Genomics (2013) 1.12
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res (2012) 1.12
Generation of mouse ES cell lines engineered for the forced induction of transcription factors. Sci Rep (2011) 1.11
Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. BMC Bioinformatics (2012) 1.10
Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in Senescing Barley leaves. PLoS One (2015) 1.10
Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets. Biol Direct (2013) 1.10
Application of genomic tools in plant breeding. Curr Genomics (2012) 1.09
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics (2011) 1.09
Probabilistic error correction for RNA sequencing. Nucleic Acids Res (2013) 1.08
bioNerDS: exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics (2013) 1.08
Analytical methods in untargeted metabolomics: state of the art in 2015. Front Bioeng Biotechnol (2015) 1.08
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells. Oncotarget (2011) 1.08
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics (2012) 1.07
Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PLoS One (2013) 1.07
Loss of caveolin-1 in prostate cancer stroma correlates with reduced relapse-free survival and is functionally relevant to tumour progression. J Pathol (2013) 1.07
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res (2012) 1.07
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc (2012) 1.07
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell (2014) 1.07
The transcription factor Th-POK negatively regulates Th17 differentiation in Vα14i NKT cells. Blood (2012) 1.07
AXL is a key regulator of inherent and chemotherapy-induced invasion and predicts a poor clinical outcome in early-stage colon cancer. Clin Cancer Res (2013) 1.06
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol (2011) 1.06
Systematic review of genome-wide gene expression studies of bipolar disorder. BMC Psychiatry (2013) 1.06
Mapping yeast transcriptional networks. Genetics (2013) 1.06
DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information. Cell Death Dis (2014) 1.05
Chapter 15: disease gene prioritization. PLoS Comput Biol (2013) 1.05
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PLoS One (2012) 1.05
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol (2013) 1.04
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res (2012) 1.04
The latent membrane protein 1 (LMP1) oncogene of Epstein-Barr virus can simultaneously induce and inhibit apoptosis in B cells. J Virol (2012) 1.04
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. Aging (Albany NY) (2015) 1.04
The integrated web service and genome database for agricultural plants with biotechnology information. Bioinformation (2011) 1.03
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res (2011) 1.03
RiceFREND: a platform for retrieving coexpressed gene networks in rice. Nucleic Acids Res (2012) 1.03
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A (2007) 11.46
Archiving next generation sequencing data. Nucleic Acids Res (2009) 6.98
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics (2007) 6.67
Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One (2010) 3.96
NCBI Epigenomics: a new public resource for exploring epigenomic data sets. Nucleic Acids Res (2010) 3.27
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol (2010) 3.23
Microarray standards at last. Nature (2002) 2.96
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A (2010) 1.84
Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach. BMC Genomics (2009) 1.68
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PLoS One (2010) 1.64
TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One (2008) 1.60
Predicting environmental chemical factors associated with disease-related gene expression data. BMC Med Genomics (2010) 1.55
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res (2010) 1.45
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics (2009) 1.35
An 8-gene qRT-PCR-based gene expression score that has prognostic value in early breast cancer. BMC Cancer (2010) 1.34
Reducing the algorithmic variability in transcriptome-based inference. Bioinformatics (2010) 1.33
Detection of gene orthology from gene co-expression and protein interaction networks. BMC Bioinformatics (2010) 1.32
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res (2005) 17.61
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res (2012) 15.84
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
Activation of the interferon system by short-interfering RNAs. Nat Cell Biol (2003) 8.63
Annotating the human genome with Disease Ontology. BMC Genomics (2009) 4.71
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (2009) 2.37
Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity. Proc Natl Acad Sci U S A (2004) 2.04
NCBI Peptidome: a new repository for mass spectrometry proteomics data. Nucleic Acids Res (2009) 1.38
Promyelocytic leukemia zinc finger protein regulates interferon-mediated innate immunity. Immunity (2009) 1.22
One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors. Genetics (2004) 0.96
Cytogenetic characterization and gene expression profiling in the rat reflux-induced esophageal tumor model. J Thorac Cardiovasc Surg (2007) 0.96
Expression of IFITM1 in chronic myeloid leukemia patients. Leuk Res (2005) 0.89
Lipid metabolism genes in contralateral unaffected breast and estrogen receptor status of breast cancer. Cancer Prev Res (Phila) (2013) 0.78