Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

(2013) Yvan Wenger et al.   BMC GENOMICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq

(2013) BingXin Lu et al.   Science China-Life Sciences

Comparative analysis of de novo transcriptome assembly

(2013) Kaitlin Clarke et al.   Science China-Life Sciences

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

(2012) Berat Z Haznedaroglu et al.   BMC BIOINFORMATICS

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

(2012) Hilary C Miller et al.   BMC GENOMICS

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

(2012) Jialei Duan et al.   BMC GENOMICS

Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette

(2012) Nathan J Kenny et al.   DEVELOPMENT GENES AND EVOLUTION

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

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 sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

(2011) Maria D Logacheva et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FACT: Functional annotation transfer between proteins with similar feature architectures.

(2010) Tina Koestler et al.   BMC BIOINFORMATICS

De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis

(2010) Chao Sun et al.   BMC GENOMICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

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

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

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

ESTPiper – a web-based analysis pipeline for expressed sequence tags

(2009) Zuojian Tang et al.   BMC GENOMICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

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

An overview of the wcd EST clustering tool

(2008) Scott Hazelhurst et al.   BIOINFORMATICS

Predicting protein function from domain content

(2008) Kristoffer Forslund et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Generations of sequencing technologies

(2008) Erik Pettersson et al.   GENOMICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH