Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species

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

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

(2011) Massimo Iorizzo et al.   BMC GENOMICS

Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum

(2011) Kayvan Etebari et al.   BMC GENOMICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species

(2011) Andrea Bräutigam et al.   JOURNAL OF EXPERIMENTAL BOTANY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

(2011) Zhihui Xia et al.   PLANT MOLECULAR BIOLOGY

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

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

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

(2010) JULIE JEUKENS et al.   MOLECULAR ECOLOGY

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing

(2010) Fabian Birzele et al.   NUCLEIC ACIDS RESEARCH

De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

(2010) Jacob E. Crawford et al.   PLoS One

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

Expression profiling of microRNAs by deep sequencing

(2009) C. J. Creighton et al.   BRIEFINGS IN BIOINFORMATICS

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

(2009) J. G. Gibbons et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

(2008) Björn M Hallström et al.   BMC EVOLUTIONARY BIOLOGY

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

(2008) Evandro Novaes et al.   BMC GENOMICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE