Published in Nucleic Acids Res on May 28, 2008
MetaboAnalyst 3.0--making metabolomics more meaningful. Nucleic Acids Res (2015) 4.67
ETE: a python Environment for Tree Exploration. BMC Bioinformatics (2010) 4.17
Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell (2010) 3.40
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Mayday--integrative analytics for expression data. BMC Bioinformatics (2010) 1.91
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics (2009) 1.50
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
Retracted Reanalysis of the gene expression profile in chronic pancreatitis via bioinformatics methods. Eur J Med Res (2014) 1.39
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics (2009) 1.35
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res (2014) 1.29
WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics (2009) 1.27
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nat Protoc (2015) 1.17
Transcriptome changes in grapevine (Vitis vinifera L.) cv. Malbec leaves induced by ultraviolet-B radiation. BMC Plant Biol (2010) 1.10
Workflows for microarray data processing in the Kepler environment. BMC Bioinformatics (2012) 1.08
Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic Acids Res (2015) 1.07
Pomelo II: finding differentially expressed genes. Nucleic Acids Res (2009) 1.05
Functional assessment of time course microarray data. BMC Bioinformatics (2009) 0.97
A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One (2012) 0.94
PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. BMC Bioinformatics (2009) 0.92
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. Trends Biotechnol (2009) 0.90
PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PLoS One (2013) 0.88
Meta-Analysis of Global Transcriptomics Suggests that Conserved Genetic Pathways are Responsible for Quercetin and Tannic Acid Mediated Longevity in C. elegans. Front Genet (2012) 0.88
Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. BMC Bioinformatics (2009) 0.88
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data. BMC Bioinformatics (2009) 0.87
Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res (2010) 0.87
Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism. BMC Genomics (2013) 0.85
Analysis of a gene co-expression network establishes robust association between Col5a2 and ischemic heart disease. BMC Med Genomics (2013) 0.82
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. Physiol Genomics (2014) 0.82
Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis. Source Code Biol Med (2008) 0.79
Emergent Transcriptomic Technologies and Their Role in the Discovery of Biomarkers of Liver Transplant Tolerance. Front Immunol (2015) 0.75
Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics (2016) 0.75
Lmx1b is required for the glutamatergic fates of a subset of spinal cord neurons. Neural Dev (2016) 0.75
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82
Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 71.36
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A (2002) 30.32
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med (2002) 21.28
Ensembl 2008. Nucleic Acids Res (2007) 20.67
Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet (2006) 16.12
Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics (2007) 9.87
Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci U S A (2002) 9.83
GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res (2003) 4.82
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res (2005) 4.72
Gene-set approach for expression pattern analysis. Brief Bioinform (2008) 4.58
Computational cluster validation in post-genomic data analysis. Bioinformatics (2005) 4.46
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med (2003) 4.44
Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol (2005) 3.82
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res (2007) 3.68
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res (2006) 3.62
A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics (2001) 3.56
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics (2006) 2.59
Functional interpretation of microarray experiments. OMICS (2006) 2.56
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics (2006) 2.18
Next station in microarray data analysis: GEPAS. Nucleic Acids Res (2006) 2.05
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res (2005) 1.97
New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res (2004) 1.89
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics (2005) 1.82
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res (2007) 1.29
Prophet, a web-based tool for class prediction using microarray data. Bioinformatics (2006) 1.23
A cluster validity framework for genome expression data. Bioinformatics (2002) 1.21
Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics (2007) 1.11
Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol (2005) 1.09
Data-adaptive test statistics for microarray data. Bioinformatics (2005) 0.97
CLEAR-test: combining inference for differential expression and variability in microarray data analysis. J Biomed Inform (2007) 0.83
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res (2008) 13.51
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
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
GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res (2003) 4.82
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res (2005) 4.72
ETE: a python Environment for Tree Exploration. BMC Bioinformatics (2010) 4.17
The human phylome. Genome Biol (2007) 3.81
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res (2007) 3.68
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res (2006) 3.62
Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics (2012) 3.62
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res (2010) 3.36
PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res (2007) 3.30
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res (2007) 3.09
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res (2006) 3.04
SNP and haplotype mapping for genetic analysis in the rat. Nat Genet (2008) 2.96
Inhibition of cancer growth by resveratrol is related to its low bioavailability. Free Radic Biol Med (2002) 2.07
Next station in microarray data analysis: GEPAS. Nucleic Acids Res (2006) 2.05
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res (2005) 1.97
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol (2006) 1.95
Differential lipid partitioning between adipocytes and tissue macrophages modulates macrophage lipotoxicity and M2/M1 polarization in obese mice. Diabetes (2011) 1.91
New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res (2004) 1.89
Data integration in the era of omics: current and future challenges. BMC Syst Biol (2014) 1.82
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics (2005) 1.82
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol (2002) 1.77
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics (2007) 1.77
Atrial fibrillation in incident dialysis patients. Kidney Int (2009) 1.75
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res (2004) 1.74
Initial genomics of the human nucleolus. PLoS Genet (2010) 1.71
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res (2009) 1.69
Clustering of risk factors and social class in childhood and adulthood in British women's heart and health study: cross sectional analysis. BMJ (2004) 1.66
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res (2010) 1.59
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res (2009) 1.58
Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups. Leuk Lymphoma (2009) 1.58
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res (2002) 1.55
OGEE: an online gene essentiality database. Nucleic Acids Res (2011) 1.54
B2G-FAR, a species-centered GO annotation repository. Bioinformatics (2011) 1.53
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res (2011) 1.53
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res (2008) 1.53
Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. Bioinformatics (2007) 1.50
Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res Treat (2005) 1.45
DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics (2004) 1.45
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res (2009) 1.44
DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res (2010) 1.44
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res (2007) 1.43
Genome-scale evidence of the nematode-arthropod clade. Genome Biol (2005) 1.41
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics (2010) 1.41
Genome Maps, a new generation genome browser. Nucleic Acids Res (2013) 1.33