Published in Biol Direct on April 16, 2009
A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol (2010) 22.10
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol (2010) 10.05
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol (2013) 4.67
GC-content normalization for RNA-Seq data. BMC Bioinformatics (2011) 3.89
Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol (2009) 3.86
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS One (2011) 3.01
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol Biol (2011) 2.98
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics (2010) 2.95
RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol (2011) 2.77
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics (2011) 2.49
Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol (2010) 2.44
A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 2.37
Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics (2011) 2.36
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res (2011) 2.23
RNA-seq: technical variability and sampling. BMC Genomics (2011) 2.19
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics (2012) 2.19
De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One (2010) 2.19
Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods (2010) 2.07
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res (2010) 2.07
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics (2011) 2.00
Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics (2011) 1.93
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
Evaluation of normalization methods in mammalian microRNA-Seq data. RNA (2012) 1.68
Digital gene expression for non-model organisms. Genome Res (2011) 1.66
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol (2010) 1.56
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One (2011) 1.53
Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One (2011) 1.43
Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics (2011) 1.43
Characterizing natural variation using next-generation sequencing technologies. Trends Genet (2009) 1.39
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 1.34
RNA-Seq analysis in MeV. Bioinformatics (2011) 1.33
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics (2011) 1.24
A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis (2011) 1.23
RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics (2012) 1.22
Calculating sample size estimates for RNA sequencing data. J Comput Biol (2013) 1.21
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res (2011) 1.19
Protocol dependence of sequencing-based gene expression measurements. PLoS One (2011) 1.19
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics (2012) 1.17
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates. BMC Bioinformatics (2010) 1.16
Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics (2012) 1.16
Length bias correction for RNA-seq data in gene set analyses. Bioinformatics (2011) 1.15
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics (2011) 1.13
Data-based filtering for replicated high-throughput transcriptome sequencing experiments. Bioinformatics (2013) 1.13
Transforming RNA-Seq data to improve the performance of prognostic gene signatures. PLoS One (2014) 1.10
Comparing bioinformatic gene expression profiling methods: microarray and RNA-Seq. Med Sci Monit Basic Res (2014) 1.09
Probabilistic error correction for RNA sequencing. Nucleic Acids Res (2013) 1.08
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res (2012) 1.08
Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics (2010) 1.08
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data. Genome Biol (2011) 1.07
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res (2015) 1.05
A normalization strategy for comparing tag count data. Algorithms Mol Biol (2012) 1.03
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. BMC Med Genomics (2014) 1.02
A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLoS One (2012) 1.01
Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. Biotechnol Biofuels (2013) 1.00
PROPER: comprehensive power evaluation for differential expression using RNA-seq. Bioinformatics (2014) 1.00
Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser. Methods Mol Biol (2015) 0.99
S-MART, a software toolbox to aid RNA-Seq data analysis. PLoS One (2011) 0.99
Statistical Analyses of Next Generation Sequence Data: A Partial Overview. J Proteomics Bioinform (2010) 0.98
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. Genome Res (2015) 0.97
Statistical methods on detecting differentially expressed genes for RNA-seq data. BMC Syst Biol (2011) 0.95
Single-molecule direct RNA sequencing without cDNA synthesis. Wiley Interdiscip Rev RNA (2011) 0.95
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism. BMC Genomics (2014) 0.94
Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm Genome (2015) 0.91
On differential gene expression using RNA-Seq data. Cancer Inform (2011) 0.91
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database (Oxford) (2013) 0.90
RNA Sequencing and Analysis. Cold Spring Harb Protoc (2015) 0.90
DFI: gene feature discovery in RNA-seq experiments from multiple sources. BMC Genomics (2012) 0.90
Comparative studies of differential gene calling using RNA-Seq data. BMC Bioinformatics (2013) 0.90
miRNA-Seq normalization comparisons need improvement. RNA (2013) 0.89
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics (2014) 0.89
Determinants of expression variability. Nucleic Acids Res (2014) 0.89
Quantitative transcriptomics using designed primer-based amplification. Sci Rep (2013) 0.88
Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinformatics (2014) 0.88
Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights (2015) 0.88
A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays. Nucleic Acids Res (2015) 0.87
Global Approaches to the Role of miRNAs in Drug-Induced Changes in Gene Expression. Front Genet (2012) 0.87
Uncovering RNA Editing Sites in Long Non-Coding RNAs. Front Bioeng Biotechnol (2014) 0.87
Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq. PLoS One (2013) 0.87
RNA-Seq and find: entering the RNA deep field. Genome Med (2011) 0.87
In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines. PLoS One (2010) 0.86
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology. BMC Genomics (2012) 0.86
Pathway Analysis: State of the Art. Front Physiol (2015) 0.86
Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics (2014) 0.86
Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes. Commun Integr Biol (2013) 0.85
Data- and knowledge-based modeling of gene regulatory networks: an update. EXCLI J (2015) 0.85
PhysioSpace: relating gene expression experiments from heterogeneous sources using shared physiological processes. PLoS One (2013) 0.85
High-resolution transcriptome analysis with long-read RNA sequencing. PLoS One (2014) 0.84
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
The significance of digital gene expression profiles. Genome Res (1997) 23.90
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res (2011) 2.23
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res (2007) 1.79
PyEvolve: a toolkit for statistical modelling of molecular evolution. BMC Bioinformatics (2004) 1.75
Mechanisms that determine the internal environment of the developing brain: a transcriptomic, functional and ultrastructural approach. PLoS One (2013) 1.64
The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. Chromosome Res (2007) 1.27
Rates of genome evolution and branching order from whole genome analysis. Mol Biol Evol (2007) 1.21
Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosome Res (2008) 1.15
RegA, an AraC-like protein, is a global transcriptional regulator that controls virulence gene expression in Citrobacter rodentium. Infect Immun (2008) 1.11
Smchd1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation. Epigenetics Chromatin (2013) 1.06
The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution. Mol Biol Evol (2003) 0.98
Cone visual pigments of the Australian marsupials, the stripe-faced and fat-tailed dunnarts: sequence and inferred spectral properties. Vis Neurosci (2004) 0.93
Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals. Chromosome Res (2005) 0.86
Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933. Appl Environ Microbiol (2012) 0.81
RegR virulence regulon of rabbit-specific enteropathogenic Escherichia coli strain E22. Infect Immun (2013) 0.81
Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium. PLoS One (2012) 0.80
A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). BMC Genet (2011) 0.78
Control of bacterial virulence by the RalR regulator of the rabbit-specific enteropathogenic Escherichia coli strain E22. Infect Immun (2013) 0.76
Correction: Mechanisms That Determine the Internal Environment of the Developing Brain: A Transcriptomic, Functional and Ultrastructural Approach. PLoS One (2016) 0.75
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Autofluorescence Signatures of Seven Pathogens: Preliminary in Vitro Investigations of a Potential Diagnostic for Acanthamoeba Keratitis. Cornea (2015) 0.75