Published in BMC Genomics on June 02, 2010
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Serum microRNA signatures identified by Solexa sequencing predict sepsis patients' mortality: a prospective observational study. PLoS One (2012) 1.52
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet (2013) 1.48
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. PLoS One (2012) 1.31
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The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis. BMC Bioinformatics (2013) 0.96
Inflammatory transcriptome profiling of human monocytes exposed acutely to cigarette smoke. PLoS One (2012) 0.92
Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments. OMICS (2013) 0.91
No DNA damage response and negligible genome-wide transcriptional changes in human embryonic stem cells exposed to terahertz radiation. Sci Rep (2015) 0.88
Preprocessing and Quality Control Strategies for Illumina DASL Assay-Based Brain Gene Expression Studies with Semi-Degraded Samples. Front Genet (2012) 0.87
Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†. Hum Mol Genet (2015) 0.86
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Endothelial inflammatory transcriptional responses to an altered plasma exposome following inhalation of diesel emissions. Inhal Toxicol (2015) 0.82
Functional genomics annotation of a statistical epistasis network associated with bladder cancer susceptibility. BioData Min (2014) 0.81
Niche-dependent gene expression profile of intratumoral heterogeneous ovarian cancer stem cell populations. PLoS One (2013) 0.81
The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney. PLoS Genet (2015) 0.80
Pontin is a critical regulator for AML1-ETO-induced leukemia. Leukemia (2013) 0.80
Phenocopy--a strategy to qualify chemical compounds during hit-to-lead and/or lead optimization. PLoS One (2010) 0.79
Divergent effects of muscarinic receptor subtype gene ablation on murine colon tumorigenesis reveals association of M3R and zinc finger protein 277 expression in colon neoplasia. Mol Cancer (2014) 0.79
Blunted HPA axis activity prior to suicide attempt and increased inflammation in attempters. Psychoneuroendocrinology (2017) 0.78
Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes. Microarrays (Basel) (2013) 0.78
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines. PLoS One (2014) 0.77
Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood. PLoS Genet (2015) 0.76
Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. Br J Cancer (2017) 0.76
Robust Expansion of Human Pluripotent Stem Cells: Integration of Bioprocess Design With Transcriptomic and Metabolomic Characterization. Stem Cells Transl Med (2015) 0.76
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Hybrid-controlled neurofuzzy networks analysis resulting in genetic regulatory networks reconstruction. ISRN Bioinform (2012) 0.75
Whole Blood Gene Expression Differentiates between Atrial Fibrillation and Sinus Rhythm after Cardioversion. PLoS One (2016) 0.75
Comparison of pre-processing methods for multiplex bead-based immunoassays. BMC Genomics (2016) 0.75
Evaluation of bias-variance trade-off for commonly used post-summarizing normalization procedures in large-scale gene expression studies. PLoS One (2014) 0.75
Alteration of Multiple Leukocyte Gene Expression Networks is Linked with Magnetic Resonance Markers of Prognosis After Acute ST-Elevation Myocardial Infarction. Sci Rep (2017) 0.75
Blood Transcriptional Profiling Reveals Immunological Signatures of Distinct States of Infection of Humans with Leishmania infantum. PLoS Negl Trop Dis (2016) 0.75
Distinct carbon sources affect structural and functional maturation of cardiomyocytes derived from human pluripotent stem cells. Sci Rep (2017) 0.75
Genome-wide expression and response to exposure-based psychological therapy for anxiety disorders. Transl Psychiatry (2017) 0.75
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Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
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Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
lumi: a pipeline for processing Illumina microarray. Bioinformatics (2008) 17.19
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Statistical tests for differential expression in cDNA microarray experiments. Genome Biol (2003) 7.65
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41
A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32
Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63
Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology. Nucleic Acids Res (2008) 2.11
Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res (2008) 2.04
Statistical methods of background correction for Illumina BeadArray data. Bioinformatics (2009) 1.99
Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes (2008) 1.28
Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes. BMC Genomics (2009) 0.96
Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics (2008) 0.94
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Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Signatures of mutational processes in human cancer. Nature (2013) 21.63
International network of cancer genome projects. Nature (2010) 20.35
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
Variation in transcription factor binding among humans. Science (2010) 9.33
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
Software for computing and annotating genomic ranges. PLoS Comput Biol (2013) 8.20
Systemic spread is an early step in breast cancer. Cancer Cell (2008) 7.91
Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. PLoS One (2010) 7.48
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
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature (2008) 6.10
Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell (2012) 6.07
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics (2008) 5.95
A global map of human gene expression. Nat Biotechnol (2010) 5.32
Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A (2010) 5.21
From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression. Proc Natl Acad Sci U S A (2003) 4.79
Dissecting the genomic complexity underlying medulloblastoma. Nature (2012) 4.77
Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol (2006) 4.35
Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol (2005) 4.33
Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J Exp Med (2005) 4.06
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc (2013) 4.00
Analysis of cell-based RNAi screens. Genome Biol (2006) 3.99
The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) (2013) 3.82
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc (2009) 3.77
Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol (2006) 3.66
Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina. Cell (2002) 3.64
Global chromosome positions are transmitted through mitosis in mammalian cells. Cell (2003) 3.27
Automatic identification of subcellular phenotypes on human cell arrays. Genome Res (2004) 3.25
Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics (2010) 3.10
Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell (2013) 3.08
Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles. Proc Natl Acad Sci U S A (2002) 3.05
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (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
Expression profiling of epithelial plasticity in tumor progression. Oncogene (2003) 2.67
Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics (2007) 2.50
Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods (2011) 2.47
A contractile nuclear actin network drives chromosome congression in oocytes. Nature (2005) 2.45
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet (2013) 2.42
EBImage--an R package for image processing with applications to cellular phenotypes. Bioinformatics (2010) 2.42
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol (2010) 2.41
Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics (2006) 2.37
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics (2005) 2.36
Argonaute--a database for gene regulation by mammalian microRNAs. Nucleic Acids Res (2006) 2.26
Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters. J Exp Med (2004) 2.23
Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics (2009) 2.17
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
Directional tissue migration through a self-generated chemokine gradient. Nature (2013) 2.06
Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol (2012) 2.06
Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer. Cancer Cell (2005) 2.03
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol (2010) 2.03
arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics (2004) 2.02
Visualizing telomere dynamics in living mammalian cells using PNA probes. EMBO J (2003) 1.99
CD95-ligand on peripheral myeloid cells activates Syk kinase to trigger their recruitment to the inflammatory site. Immunity (2010) 1.91
Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol (2010) 1.85
Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Rep (2012) 1.84
Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol (2011) 1.83
CCM2 mediates death signaling by the TrkA receptor tyrosine kinase. Neuron (2009) 1.79
GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics (2006) 1.75
Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping. Nat Methods (2013) 1.72
Dynamics of HIV-1 assembly and release. PLoS Pathog (2009) 1.67
Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biol (2008) 1.64
A constitutively active dioxin/aryl hydrocarbon receptor promotes hepatocarcinogenesis in mice. Cancer Res (2004) 1.64
Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma. Cancer Res (2002) 1.64
Argatroban therapy for heparin-induced thrombocytopenia in ICU patients with multiple organ dysfunction syndrome: a retrospective study. Crit Care (2010) 1.63
Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Oncogene (2005) 1.62
Etiology-dependent molecular mechanisms in human hepatocarcinogenesis. Hepatology (2008) 1.62
Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat Cell Biol (2002) 1.60
An Optogenetic Method to Modulate Cell Contractility during Tissue Morphogenesis. Dev Cell (2015) 1.59
Dynamics within the CD95 death-inducing signaling complex decide life and death of cells. Mol Syst Biol (2010) 1.57
Integration of activating and inhibitory receptor signaling by regulated phosphorylation of Vav1 in immune cells. Sci Signal (2011) 1.57
Analysis of CD95 threshold signaling: triggering of CD95 (FAS/APO-1) at low concentrations primarily results in survival signaling. J Biol Chem (2007) 1.55
Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e sigmaB regulon. BMC Microbiol (2008) 1.54
Auditory evoked potentials compared with bispectral index for monitoring of midazolam and propofol sedation during colonoscopy. Am J Gastroenterol (2009) 1.53
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
Incidence of acute pancreatitis does not increase during Oktoberfest, but is higher than previously described in Germany. Clin Gastroenterol Hepatol (2011) 1.52