Assessing De Novo transcriptome assembly metrics for consistency and utility

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867)

(2012) Huixia Du et al.   PLoS One

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

(2012) Marvin Mundry et al.   PLoS One

De novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus chalceus (Coleoptera, Carabidae)

(2012) Steven M. Van Belleghem et al.   PLoS One

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

(2011) Victor Zeng et al.   BMC GENOMICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

(2011) Thomas Sandmann et al.   GENOME BIOLOGY

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

(2010) Saneyoshi Ueno et al.   BMC GENOMICS

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

(2010) Shawn T O'Neil et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

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

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

(2009) Dietmar Schwarz et al.   BMC GENOMICS

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

(2009) Daniel A Hahn et al.   BMC GENOMICS

454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

(2009) Mika Zagrobelny et al.   BMC GENOMICS

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches

(2008) Foo Cheung et al.   BMC GENOMICS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

(2008) Christopher W. Wheat   GENETICA

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Modeling Transcriptome Based on Transcript-Sampling Data

(2008) Jiang Zhu et al.   PLoS One