Published in PLoS One on July 08, 2011
Reuse of public genome-wide gene expression data. Nat Rev Genet (2012) 2.79
A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer. PLoS One (2013) 0.80
A pathway-based classification of breast cancer integrating data on differentially expressed genes, copy number variations and microRNA target genes. Mol Cells (2012) 0.76
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Molecular portraits of human breast tumours. Nature (2000) 94.14
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 71.36
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45
Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol (2009) 22.22
Genes that mediate breast cancer metastasis to lung. Nature (2005) 19.85
Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet (2005) 17.75
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell (2006) 16.05
Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst (2006) 14.60
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res (2005) 8.73
Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol (2007) 8.65
Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res (2007) 8.41
Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol (2010) 6.88
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2005) 6.73
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics (2008) 5.95
Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res (2008) 5.88
The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res (2008) 5.69
Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature (2008) 4.24
Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics (2006) 3.86
The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade. J Pathol (2010) 2.23
A protocol for building and evaluating predictors of disease state based on microarray data. Bioinformatics (2005) 2.08
Discovery and validation of breast cancer subtypes. BMC Genomics (2006) 1.83
Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer (2007) 1.75
Clinical implementation of the intrinsic subtypes of breast cancer. Lancet Oncol (2010) 1.47
Molecular classification of breast cancer: limitations and potential. Oncologist (2006) 1.46
Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability. BMC Genomics (2008) 1.45
Class prediction for high-dimensional class-imbalanced data. BMC Bioinformatics (2010) 1.34
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature. BMC Bioinformatics (2009) 1.18
A fuzzy gene expression-based computational approach improves breast cancer prognostication. Genome Biol (2010) 1.16
Stratification bias in low signal microarray studies. BMC Bioinformatics (2007) 1.16
Can survival prediction be improved by merging gene expression data sets? PLoS One (2009) 1.04
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. BMC Bioinformatics (2009) 0.84
MiR423-5p as a circulating biomarker for heart failure. Circ Res (2010) 3.83
An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas. Nat Genet (2005) 3.04
New insights on human T cell development by quantitative T cell receptor gene rearrangement studies and gene expression profiling. J Exp Med (2005) 2.44
A protocol for building and evaluating predictors of disease state based on microarray data. Bioinformatics (2005) 2.08
An algorithm-based topographical biomaterials library to instruct cell fate. Proc Natl Acad Sci U S A (2011) 1.99
Fewer permutations, more accurate P-values. Bioinformatics (2009) 1.91
Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiol (2006) 1.76
Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res (2002) 1.64
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact (2012) 1.62
Ig gene rearrangement steps are initiated in early human precursor B cell subsets and correlate with specific transcription factor expression. J Immunol (2005) 1.61
A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. BMC Bioinformatics (2006) 1.57
Molecular profiling of cytomegalovirus-induced human CD8+ T cell differentiation. J Clin Invest (2010) 1.50
Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability. BMC Genomics (2008) 1.45
The Selective Sirtuin 1 Activator SRT2104 Reduces Endotoxin-Induced Cytokine Release and Coagulation Activation in Humans. Crit Care Med (2015) 1.41
Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis. Genome Res (2014) 1.40
Interferon-beta signaling is enhanced in patients with insufficient coronary collateral artery development and inhibits arteriogenesis in mice. Circ Res (2008) 1.32
WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme. Nucleic Acids Res (2013) 1.28
Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res (2007) 1.19
Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology (2007) 1.18
Gene therapy: is IL2RG oncogenic in T-cell development? Nature (2006) 1.18
Microarray analysis reveals expression regulation of Wnt antagonists in differentiating osteoblasts. Bone (2005) 1.17
Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens. Plant Cell Environ (2007) 1.17
Involvement of the TGF-beta and beta-catenin pathways in pelvic lymph node metastasis in early-stage cervical cancer. Clin Cancer Res (2011) 1.13
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Syst Biol (2011) 1.10
Modulation of glycosphingolipid metabolism significantly improves hepatic insulin sensitivity and reverses hepatic steatosis in mice. Hepatology (2009) 1.09
Gene expression in early stage cervical cancer. Gynecol Oncol (2008) 1.08
Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data. BMC Genomics (2009) 1.07
Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients. Clin Cancer Res (2010) 1.05
Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina. Science (2013) 1.04
Predicting metabolic fluxes using gene expression differences as constraints. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.03
Distinctive expression of chemokines and transforming growth factor-beta signaling in human arterial endothelium during atherosclerosis. Am J Pathol (2007) 1.03
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics (2012) 1.00
Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics (2007) 1.00
Notch controls the magnitude of T helper cell responses by promoting cellular longevity. Proc Natl Acad Sci U S A (2012) 0.99
De novo detection of copy number variation by co-assembly. Bioinformatics (2012) 0.99
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages. Bioinformatics (2011) 0.98
Suppression of inflammatory signaling in monocytes from patients with coronary artery disease. J Mol Cell Cardiol (2008) 0.98
Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol (2007) 0.98
Differentially expressed genes in the pre-eclamptic placenta: a systematic review and meta-analysis. PLoS One (2013) 0.97
Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging. Aging Cell (2013) 0.93
Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340* and miRNA624*. PLoS One (2011) 0.93
Integration of clinical and gene expression data has a synergetic effect on predicting breast cancer outcome. PLoS One (2012) 0.93
Interorgan coordination of the murine adaptive response to fasting. J Biol Chem (2011) 0.93
Dissection of a quantitative trait locus for PR interval duration identifies Tnni3k as a novel modulator of cardiac conduction. PLoS Genet (2012) 0.93
Module-based outcome prediction using breast cancer compendia. PLoS One (2007) 0.92
Using a priori knowledge to align sequencing reads to their exact genomic position. Nucleic Acids Res (2012) 0.91
Sign language recognition by combining statistical DTW and independent classification. IEEE Trans Pattern Anal Mach Intell (2008) 0.89
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. BMC Bioinformatics (2006) 0.89
A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control. Nucleic Acids Res (2013) 0.89
Improving the description of metabolic networks: the TCA cycle as example. FASEB J (2012) 0.88
Predicting the therapeutic efficacy of MSC in bone tissue engineering using the molecular marker CADM1. Biomaterials (2013) 0.88
Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One (2011) 0.88
Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors. PLoS One (2013) 0.88
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (2013) 0.88
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Syst Biol (2008) 0.87
Local cytokine concentrations and oxygen pressure are related to maturation of the collateral circulation in humans. J Am Coll Cardiol (2009) 0.87
Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One (2011) 0.87
Introducing WISECONDOR for noninvasive prenatal diagnostics. Expert Rev Mol Diagn (2014) 0.86
Proteomic analysis of HIV-T cell interaction: an update. Front Microbiol (2012) 0.86
Equivalence testing in microarray analysis: similarities in the transcriptome of human atherosclerotic and nonatherosclerotic macrophages. Physiol Genomics (2010) 0.85
Knowledge representation in metabolic pathway databases. Brief Bioinform (2012) 0.85
Pattern recognition in bioinformatics. Brief Bioinform (2013) 0.85
Edge-based image restoration. IEEE Trans Image Process (2005) 0.85
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. BMC Bioinformatics (2009) 0.84
Consensus and conflict cards for metabolic pathway databases. BMC Syst Biol (2013) 0.84
Integrating protein-protein interaction networks with gene-gene co-expression networks improves gene signatures for classifying breast cancer metastasis. J Integr Bioinform (2011) 0.82
A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass. Proteome Sci (2012) 0.81
HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics (2010) 0.81
Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation. Genomics Proteomics Bioinformatics (2007) 0.80
SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets. BMC Bioinformatics (2007) 0.80
Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger. PLoS One (2012) 0.80
Muramyl dipeptide-induced differential gene expression in NOD2 mutant and wild-type Crohn's disease patient-derived dendritic cells. Inflamm Bowel Dis (2008) 0.80
Analysis of mass spectrometry data using sub-spectra. BMC Bioinformatics (2009) 0.80
Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages. Virology (2011) 0.80
The nearest subclass classifier: a compromise between the nearest mean and nearest neighbor classifier. IEEE Trans Pattern Anal Mach Intell (2005) 0.80
Maximum significance clustering of oligonucleotide microarrays. Bioinformatics (2005) 0.78
Proteomic profiling of plasma and serum in elderly patients with delirium. J Neuropsychiatry Clin Neurosci (2009) 0.78
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. Int J Bioinform Res Appl (2013) 0.77
Knowledge driven decomposition of tumor expression profiles. BMC Bioinformatics (2009) 0.77
Understanding regulation of metabolism through feasibility analysis. PLoS One (2012) 0.76
An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in acute myeloid leukemia. BMC Bioinformatics (2015) 0.76
Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients. BMC Genomics (2010) 0.76
SPiCE: a web-based tool for sequence-based protein classification and exploration. BMC Bioinformatics (2014) 0.75
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. Bioinformatics (2013) 0.75
Authors's reply. J Emerg Trauma Shock (2010) 0.75
Erratum: Programs for the persistence, vigilance and control of human CD8(+) lung-resident memory T cells. Nat Immunol (2017) 0.75
Protein complex prediction using an integrative bioinformatics approach. J Bioinform Comput Biol (2007) 0.75
Evolutionary optimization of kernel weights improves protein complex comembership prediction. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.75