Published in Nat Methods on October 01, 2005
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature (2014) 5.47
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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol (2014) 3.99
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Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods (2013) 3.52
Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature (2015) 2.85
Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol (2014) 2.67
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Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res (2008) 2.04
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Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol (2015) 1.66
Data quality in genomics and microarrays. Nat Biotechnol (2006) 1.56
Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens. BMC Cancer (2014) 1.48
Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS One (2014) 1.39
Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics (2011) 1.36
Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Proc Natl Acad Sci U S A (2014) 1.26
Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers. J Transl Med (2008) 1.15
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Biased allelic expression in human primary fibroblast single cells. Am J Hum Genet (2014) 1.13
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The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech (2006) 1.11
A perspective on DNA microarrays in pathology research and practice. Am J Pathol (2007) 1.11
Genome-wide discovery of human splicing branchpoints. Genome Res (2015) 1.08
Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways. Mol Genet Genomics (2009) 1.08
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature (2016) 1.06
cGAS surveillance of micronuclei links genome instability to innate immunity. Nature (2017) 1.04
The mid-developmental transition and the evolution of animal body plans. Nature (2016) 1.04
Technical variations in low-input RNA-seq methodologies. Sci Rep (2014) 1.03
Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS One (2014) 1.01
How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif (2015) 1.01
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science (2016) 1.00
MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res (2006) 1.00
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Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature (2014) 0.98
The incredible shrinking world of DNA microarrays. Mol Biosyst (2008) 0.98
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol (2016) 0.97
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A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Evodevo (2013) 0.94
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. BMC Genomics (2015) 0.93
Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. Nat Biotechnol (2015) 0.93
Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae. BMC Microbiol (2010) 0.90
Development and verification of the PAM50-based Prosigna breast cancer gene signature assay. BMC Med Genomics (2015) 0.88
Molecular convergence of neurodevelopmental disorders. Am J Hum Genet (2014) 0.88
Exploring the use of internal and externalcontrols for assessing microarray technical performance. BMC Res Notes (2010) 0.88
Extended analysis of benchmark datasets for Agilent two-color microarrays. BMC Bioinformatics (2007) 0.87
Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design. BMC Biotechnol (2016) 0.84
Calling sample mix-ups in cancer population studies. PLoS One (2012) 0.83
Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq. Sci Data (2014) 0.82
Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model. PLoS One (2010) 0.82
Quality control methods for optimal BCR-ABL1 clinical testing in human whole blood samples. J Mol Diagn (2013) 0.82
Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq. Sci Data (2014) 0.82
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. Comput Struct Biotechnol J (2015) 0.82
The impact of amplification on differential expression analyses by RNA-seq. Sci Rep (2016) 0.81
Standards affecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev (2010) 0.80
Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays. J Mol Diagn (2016) 0.78
Stability of Reference Genes for Messenger RNA Quantification by Real-Time PCR in Mouse Dextran Sodium Sulfate Experimental Colitis. PLoS One (2016) 0.78
A Transcriptional Lineage of the Early C. elegans Embryo. Dev Cell (2016) 0.78
Challenges and emerging directions in single-cell analysis. Genome Biol (2017) 0.77
Standardization and quality management in next-generation sequencing. Appl Transl Genom (2016) 0.77
Reference standards for next-generation sequencing. Nat Rev Genet (2017) 0.77
SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics (2006) 0.77
Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis. BMC Genomics (2015) 0.77
The ABRF MARG microarray survey 2005: taking the pulse of the microarray field. J Biomol Tech (2006) 0.77
High standards for high dimensional investigations. Cytometry A (2016) 0.77
Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics (2016) 0.76
Using mixtures of biological samples as process controls for RNA-sequencing experiments. BMC Genomics (2015) 0.76
Evaluation of bias associated with high-multiplex, target-specific pre-amplification. Biomol Detect Quantif (2015) 0.75
Multiplex cDNA quantification method that facilitates the standardization of gene expression data. Nucleic Acids Res (2011) 0.75
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PLoS One (2016) 0.75
Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nat Methods (2016) 0.75
Hypertranscription in Development, Stem Cells, and Regeneration. Dev Cell (2016) 0.75
An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1. Biomol Detect Quantif (2016) 0.75
Genomic-Wide Analysis with Microarrays in Human Oncology. Microarrays (Basel) (2015) 0.75
External RNA Controls Consortium Beta Version Update. J Genomics (2016) 0.75
Improved definition of the mouse transcriptome via targeted RNA sequencing. Genome Res (2016) 0.75
Clinical implementation of RNA signatures for pharmacogenomic decision-making. Pharmgenomics Pers Med (2011) 0.75
Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls. IEEE EMBS Int Conf Biomed Health Inform (2016) 0.75
Arkas: Rapid reproducible RNAseq analysis. F1000Res (2017) 0.75
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell (2006) 21.66
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47
Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat Med (2008) 12.68
Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82
Diverse somatic mutation patterns and pathway alterations in human cancers. Nature (2010) 10.83
The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04
The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res (2007) 9.32
Cytochrome p-450 polymorphisms and response to clopidogrel. N Engl J Med (2008) 9.25
miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res (2008) 8.97
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol (2006) 8.87
Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc Natl Acad Sci U S A (2003) 8.20
Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet (2005) 7.82
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature (2013) 7.42
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
Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods (2005) 6.23
Intra-individual change over time in DNA methylation with familial clustering. JAMA (2008) 6.17
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (2014) 5.93
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol (2006) 5.92
Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med (2012) 5.69
Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med (2009) 5.63
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res (2004) 5.59
Frozen robust multiarray analysis (fRMA). Biostatistics (2010) 5.57
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet (2009) 5.52
Rethinking ovarian cancer: recommendations for improving outcomes. Nat Rev Cancer (2011) 5.28
Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary. J Pathol (2010) 5.23
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (2006) 5.20
Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol (2006) 5.14
IL-13 signaling through the IL-13alpha2 receptor is involved in induction of TGF-beta1 production and fibrosis. Nat Med (2005) 5.13
Recurrent R-spondin fusions in colon cancer. Nature (2012) 5.10
Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature (2004) 5.05
Epithelial versus mesenchymal phenotype determines in vitro sensitivity and predicts clinical activity of erlotinib in lung cancer patients. Clin Cancer Res (2005) 4.94
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70
Preprocessing of oligonucleotide array data. Nat Biotechnol (2004) 4.70
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet (2012) 4.70
Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation. Cancer Cell (2009) 4.47
Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A (2009) 4.40
A gene expression bar code for microarray data. Nat Methods (2007) 4.20
Accurate multiplex gene synthesis from programmable DNA microchips. Nature (2004) 4.16
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS (2008) 4.15
A framework for oligonucleotide microarray preprocessing. Bioinformatics (2010) 3.97
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics (2005) 3.93
Regulators of mitotic arrest and ceramide metabolism are determinants of sensitivity to paclitaxel and other chemotherapeutic drugs. Cancer Cell (2007) 3.89
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol (2014) 3.89
Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther (2007) 3.84
Submission of microarray data to public repositories. PLoS Biol (2004) 3.83
Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med (2010) 3.81
Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (2012) 3.74
Gene expression in human embryonic stem cell lines: unique molecular signature. Blood (2003) 3.73
Antitumor efficacy of the novel RAF inhibitor GDC-0879 is predicted by BRAFV600E mutational status and sustained extracellular signal-regulated kinase/mitogen-activated protein kinase pathway suppression. Cancer Res (2009) 3.72
PDGF-C mediates the angiogenic and tumorigenic properties of fibroblasts associated with tumors refractory to anti-VEGF treatment. Cancer Cell (2009) 3.71
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol (2012) 3.62
Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet (2013) 3.42
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet (2013) 3.41
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect (2003) 3.39
Thermoregulatory and metabolic defects in Huntington's disease transgenic mice implicate PGC-1alpha in Huntington's disease neurodegeneration. Cell Metab (2006) 3.38
A hierarchy of self-renewing tumor-initiating cell types in glioblastoma. Cancer Cell (2010) 3.34
Evidence for sequenced molecular evolution of IDH1 mutant glioblastoma from a distinct cell of origin. J Clin Oncol (2011) 3.23
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell (2006) 3.22
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Standards for microarray data: an open letter. Environ Health Perspect (2004) 3.15
Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol (2006) 3.13
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol (2012) 3.13
The effects of IL-20 subfamily cytokines on reconstituted human epidermis suggest potential roles in cutaneous innate defense and pathogenic adaptive immunity in psoriasis. J Immunol (2007) 3.06
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics (2006) 2.96
Distinctive proliferative phase differences in gene expression in human myometrium and leiomyomata. Fertil Steril (2003) 2.89
Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms. BMC Genomics (2006) 2.86