Optimization of de novo transcriptome assembly from next-generation sequencing data.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68

Next-generation transcriptome assembly. Nat Rev Genet (2011) 5.89

Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol Biol (2011) 2.98

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics (2011) 2.88

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics (2010) 2.62

De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One (2010) 2.19

Sequence assembly demystified. Nat Rev Genet (2013) 2.09

De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS One (2010) 1.95

Incorporating RNA-seq data into the zebrafish Ensembl genebuild. Genome Res (2012) 1.89

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One (2012) 1.82

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics (2011) 1.77

NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genomics (2012) 1.76

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics (2012) 1.54

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

Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms. Genome Biol Evol (2012) 1.50

Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PLoS One (2012) 1.47

Graph accordance of next-generation sequence assemblies. Bioinformatics (2011) 1.47

Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol (2014) 1.46

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics (2011) 1.45

Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol (2013) 1.45

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics (2011) 1.43

De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics (2012) 1.40

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. Evodevo (2011) 1.38

De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. BMC Genomics (2013) 1.30

Assessing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics (2013) 1.28

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics (2012) 1.28

De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism. Plant Physiol (2014) 1.27

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. Genome Biol (2013) 1.26

Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc Biol Sci (2014) 1.20

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics (2012) 1.17

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool (2012) 1.17

Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PLoS One (2012) 1.16

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. Bioinformatics (2013) 1.16

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics (2012) 1.15

De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genomics (2013) 1.13

Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. Biotechnol Biofuels (2012) 1.13

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). Brief Bioinform (2011) 1.12

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biol (2014) 1.12

The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector. G3 (Bethesda) (2013) 1.10

Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. DNA Res (2012) 1.05

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species. BMC Genomics (2013) 1.04

Gene discovery in the horned beetle Onthophagus taurus. BMC Genomics (2010) 1.03

Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida. BMC Genomics (2012) 1.02

RNA-Seq technology and its application in fish transcriptomics. OMICS (2013) 1.02

Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome. PLoS One (2012) 1.02

Quantitative proteomic analysis reveals that antioxidation mechanisms contribute to cold tolerance in plantain (Musa paradisiaca L.; ABB Group) seedlings. Mol Cell Proteomics (2012) 1.00

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. BMC Bioinformatics (2012) 0.99

Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics (2015) 0.96

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics (2012) 0.96

Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea. BMC Plant Biol (2015) 0.96

High-throughput sequencing of black pepper root transcriptome. BMC Plant Biol (2012) 0.95

Deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts. PLoS One (2012) 0.95

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput Biol (2012) 0.95

Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum 'Sonate'. Front Plant Sci (2015) 0.95

RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis. BMC Res Notes (2014) 0.95

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. ISME J (2012) 0.94

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics (2013) 0.94

Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris. BMC Genomics (2012) 0.94

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs. BMC Genomics (2012) 0.94

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway. BMC Plant Biol (2014) 0.93

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics (2014) 0.93

Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles. PLoS One (2013) 0.92

Rapid speciation with gene flow following the formation of Mt. Etna. Genome Biol Evol (2013) 0.92

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome. Front Genet (2014) 0.92

A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Mol Cell Proteomics (2012) 0.90

In silico secretome analysis approach for next generation sequencing transcriptomic data. BMC Genomics (2011) 0.89

Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly. Comp Biochem Physiol C Toxicol Pharmacol (2011) 0.89

The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. BMC Genomics (2012) 0.89

Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol (2013) 0.89

Scaffolding low quality genomes using orthologous protein sequences. Bioinformatics (2012) 0.89

Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu. PLoS One (2011) 0.89

Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS One (2014) 0.88

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data. PLoS One (2014) 0.88

De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number. BMC Genomics (2015) 0.88

New approaches to Prunus transcriptome analysis. Genetica (2011) 0.88

Echidna venom gland transcriptome provides insights into the evolution of monotreme venom. PLoS One (2013) 0.87

Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome. PLoS One (2013) 0.87

Transcriptomic changes during regeneration of the central nervous system in an echinoderm. BMC Genomics (2014) 0.87

Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PLoS One (2012) 0.87

Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol (2013) 0.87

Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger mosquito, Aedes albopictus. Physiol Entomol (2013) 0.86

Advances in genomics for flatfish aquaculture. Genes Nutr (2012) 0.86

Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum. BMC Genomics (2015) 0.85

Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves). BMC Genomics (2012) 0.84

Investigation of de novo unique differentially expressed genes related to evolution in exercise response during domestication in Thoroughbred race horses. PLoS One (2014) 0.84

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. BMC Genomics (2013) 0.84

Global transcriptional dynamics of diapause induction in non-blood-fed and blood-fed Aedes albopictus. PLoS Negl Trop Dis (2015) 0.84

De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PLoS One (2013) 0.83

Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Mar Biotechnol (NY) (2012) 0.83

De novo assembly of mud loach (Misgurnus anguillicaudatus) skin transcriptome to identify putative genes involved in immunity and epidermal mucus secretion. PLoS One (2013) 0.83

De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Sci Rep (2016) 0.82

Isolation and characterization of a R2R3-MYB transcription factor gene related to anthocyanin biosynthesis in the spathes of Anthurium andraeanum (Hort.). Plant Cell Rep (2016) 0.82

Comparative transcriptome analysis of lufenuron-resistant and susceptible strains of Spodoptera frugiperda (Lepidoptera: Noctuidae). BMC Genomics (2015) 0.82

Enhancing de novo transcriptome assembly by incorporating multiple overlap sizes. ISRN Bioinform (2012) 0.82

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. Database (Oxford) (2012) 0.82

Transcriptome analysis of two buffalograss cultivars. BMC Genomics (2013) 0.82

In silico identification of transcription factors in Medicago sativa using available transcriptomic resources. Mol Genet Genomics (2014) 0.82

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. G3 (Bethesda) (2014) 0.82

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach. PLoS One (2014) 0.82

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. BMC Genomics (2014) 0.81

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68

ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20

An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84

Short read fragment assembly of bacterial genomes. Genome Res (2007) 15.40

Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res (2008) 14.90

Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85

Next-generation sequencing transforms today's biology. Nat Methods (2007) 11.93

Broad phylogenomic sampling improves resolution of the animal tree of life. Nature (2008) 11.84

mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71

Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol (2008) 9.09

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76

Gene expression profiling by massively parallel sequencing. Genome Res (2007) 6.69

A contig assembly program based on sensitive detection of fragment overlaps. Genomics (1992) 6.53

Next-generation tag sequencing for cancer gene expression profiling. Genome Res (2009) 6.50

Fragment assembly with double-barreled data. Bioinformatics (2001) 6.04

SNP discovery via 454 transcriptome sequencing. Plant J (2007) 5.92

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res (2008) 3.41

Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol (2009) 2.65

Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science (2007) 2.60

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol (2009) 2.42

Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol (2009) 2.32

Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett (2008) 2.30

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics (2009) 2.21

Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol (2008) 2.04

An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Inform (2008) 2.01

Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol (2006) 1.91

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics (2009) 1.90

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. Genes Genet Syst (2006) 1.70

An ancient gene network is co-opted for teeth on old and new jaws. PLoS Biol (2009) 1.60

Allele-specific expression assays using Solexa. BMC Genomics (2009) 1.41

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol Biol Evol (2005) 1.23

Teeth outside the mouth in teleost fishes: how to benefit from a developmental accident. Evol Dev (2001) 1.02

Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH). BMC Genomics (2010) 0.88

Tissue compartment analysis for biomarker discovery by gene expression profiling. PLoS One (2009) 0.85

Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. Plant Signal Behav (2009) 0.84

Hunting hidden transcripts. Nat Methods (2008) 0.83

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05

Molecular systematic and historical biogeography of the armored Neotropical catfishes Hypoptopomatinae and Neoplecostominae (Siluriformes: Loricariidae). Mol Phylogenet Evol (2008) 2.51

Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet (2007) 1.92

Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium. Mol Phylogenet Evol (2005) 1.82

Changes in Hox genes' structure and function during the evolution of the squamate body plan. Nature (2010) 1.43

Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A (2007) 1.28

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard. Genome Res (2009) 1.06

Divergent evolution among teleost V1r receptor genes. PLoS One (2007) 0.87

Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: the Guyanas Region. Mol Ecol (2009) 0.84

Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes. Mol Phylogenet Evol (2007) 0.81