Published in Methods on March 29, 2009
Next-generation transcriptome assembly. Nat Rev Genet (2011) 5.89
Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res (2011) 3.44
Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) (2010) 3.22
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Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS One (2011) 3.01
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics (2010) 2.95
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Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol (2011) 2.36
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res (2010) 2.34
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Dual RNA-seq of pathogen and host. Nat Rev Microbiol (2012) 2.32
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3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics (2010) 1.68
Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA (2010) 1.59
Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay. Mol Biol Cell (2011) 1.54
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One (2011) 1.53
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics (2011) 1.52
Mechanisms of specificity in neuronal activity-regulated gene transcription. Prog Neurobiol (2011) 1.49
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics (2010) 1.31
Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One (2012) 1.28
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. BMC Genomics (2011) 1.24
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing. PLoS One (2012) 1.19
NanoStriDE: normalization and differential expression analysis of NanoString nCounter data. BMC Bioinformatics (2011) 1.19
Defining transcribed regions using RNA-seq. Nat Protoc (2010) 1.17
Gene expression studies in major depression. Curr Psychiatry Rep (2010) 1.17
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. PLoS One (2013) 1.11
RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and -susceptible alleles. DNA Res (2011) 1.10
Digital gene expression analysis of the zebra finch genome. BMC Genomics (2010) 1.10
Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes. J Biomol Tech (2010) 1.09
De novo assembly and characterization of the Barnyardgrass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing. PLoS One (2013) 1.08
Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PLoS One (2012) 1.08
Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways. BMC Genomics (2014) 1.06
Genomic toolboxes for conservation biologists. Evol Appl (2011) 1.06
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol (2015) 1.03
RNA-Seq technology and its application in fish transcriptomics. OMICS (2013) 1.02
RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes. Plant Mol Biol (2011) 1.00
Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing. Front Neurosci (2011) 0.99
Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. BMC Genomics (2014) 0.96
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics (2010) 0.96
Exome RNA sequencing reveals rare and novel alternative transcripts. Nucleic Acids Res (2012) 0.96
Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique. PLoS One (2013) 0.95
The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol (2013) 0.95
The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach. BMC Genomics (2011) 0.95
Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics (2013) 0.93
Statistical methods for identifying differentially expressed genes in RNA-Seq experiments. Cell Biosci (2012) 0.93
Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA. PLoS One (2013) 0.93
RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells. PLoS One (2013) 0.92
Unravelling global genome organization by 3C-seq. Semin Cell Dev Biol (2011) 0.92
Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome. PLoS One (2010) 0.92
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. BMC Genomics (2013) 0.91
Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling. PLoS One (2013) 0.91
Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genomics (2012) 0.91
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics (2014) 0.91
Identification of staphylococcal phage with reduced transcription in human blood through transcriptome sequencing. Front Microbiol (2015) 0.90
Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol (2012) 0.89
Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb Biotechnol (2010) 0.88
Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics (2011) 0.88
New approaches to Prunus transcriptome analysis. Genetica (2011) 0.88
Transcript assembly and quantification by RNA-Seq reveals differentially expressed genes between soft-endocarp and hard-endocarp hawthorns. PLoS One (2013) 0.88
Transcriptomic analysis brings new insight into the biological role of the prion protein during mouse embryogenesis. PLoS One (2011) 0.88
Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC Syst Biol (2011) 0.88
RNA-Seq and find: entering the RNA deep field. Genome Med (2011) 0.87
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. Front Cell Dev Biol (2014) 0.86
The de novo transcriptome and its analysis in the worldwide vegetable pest, Delia antiqua (Diptera: Anthomyiidae). G3 (Bethesda) (2014) 0.86
Identification of internal reference genes for gene expression normalization between the two sexes in dioecious white Campion. PLoS One (2014) 0.86
RNA-Seq analysis using de novo transcriptome assembly as a reference for the salmon louse Caligus rogercresseyi. PLoS One (2014) 0.86
Comparison of parallel high-throughput RNA sequencing between knockout of TDP-43 and its overexpression reveals primarily nonreciprocal and nonoverlapping gene expression changes in the central nervous system of Drosophila. G3 (Bethesda) (2012) 0.86
Interrogating genomic and epigenomic data to understand prostate cancer. Biochim Biophys Acta (2012) 0.85
Detoxification and stress response genes expressed in a western North American bumble bee, Bombus huntii (Hymenoptera: Apidae). BMC Genomics (2013) 0.85
Transcriptome characterization by RNA-Seq reveals the involvement of the complement components in noise-traumatized rat cochleae. Neuroscience (2013) 0.84
Towards an improved apple reference transcriptome using RNA-seq. Mol Genet Genomics (2014) 0.84
Genomics in mammalian cell culture bioprocessing. Biotechnol Adv (2011) 0.84
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq. BMC Genomics (2014) 0.83
Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress. Planta (2012) 0.83
Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates. BMC Genomics (2015) 0.83
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. Evol Bioinform Online (2015) 0.83
Application of resequencing to rice genomics, functional genomics and evolutionary analysis. Rice (N Y) (2014) 0.82
Transcriptome analysis on the inflammatory cell infiltration of nonalcoholic steatohepatitis in bama minipigs induced by a long-term high-fat, high-sucrose diet. PLoS One (2014) 0.82
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. Comput Struct Biotechnol J (2015) 0.82
Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca. PLoS One (2015) 0.82
Do housekeeping genes exist? PLoS One (2015) 0.81
Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.). PLoS One (2013) 0.81
Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res (2011) 0.81
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae). Parasit Vectors (2014) 0.81
Comprehensive transcriptome analysis of developing xylem responding to artificial bending and gravitational stimuli in Betula platyphylla. PLoS One (2014) 0.80
Analysis of the transcriptomes downstream of Eyeless and the Hedgehog, Decapentaplegic and Notch signaling pathways in Drosophila melanogaster. PLoS One (2012) 0.80
Elucidation of the regulon and cis-acting regulatory element of HrpB, the AraC-type regulator of a plant pathogen-like type III secretion system in Burkholderia pseudomallei. J Bacteriol (2011) 0.80
Omics strategies for revealing Yersinia pestis virulence. Front Cell Infect Microbiol (2012) 0.80
High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases. RNA (2015) 0.80
Suppression subtractive hybridization (SSH) combined with bioinformatics method: an integrated functional annotation approach for analysis of differentially expressed immune-genes in insects. Bioinformation (2013) 0.80
A review of the evolution of viviparity in squamate reptiles: the past, present and future role of molecular biology and genomics. J Comp Physiol B (2011) 0.80
The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species. PLoS One (2015) 0.80
Genome-wide identification and comparative analysis of grafting-responsive mRNA in watermelon grafted onto bottle gourd and squash rootstocks by high-throughput sequencing. Mol Genet Genomics (2015) 0.79
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection. Parasit Vectors (2015) 0.79
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics (2016) 0.79
Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet (2003) 3.49
Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. Proc Natl Acad Sci U S A (2007) 2.15
The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity. Proc Natl Acad Sci U S A (2007) 1.36
Endoglin expression in blood and endothelium is differentially regulated by modular assembly of the Ets/Gata hemangioblast code. Blood (2008) 1.16
Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell (2009) 1.08
Impaired natural killer cell self-education and "missing-self" responses in Ly49-deficient mice. Blood (2012) 0.96
Transcriptional control of murine CD94 gene: differential usage of dual promoters by lymphoid cell types. J Immunol (2003) 0.89
Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation. Nucleic Acids Res (2010) 0.83