Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes

Circadian oscillatory transcriptional programs in grapevine ripening fruits

(2014) Pablo Carbonell-Bejerano et al.   BMC PLANT BIOLOGY

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

(2014) Jie Xu et al.   BMC PLANT BIOLOGY

Transcriptome profiling of genes and pathways associated with arsenic toxicity and tolerance in Arabidopsis

(2014) Shih-Feng Fu et al.   BMC PLANT BIOLOGY

Applications of next-generation sequencing to unravelling the evolutionary history of algae

(2014) K. M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments

(2014) Javier Canales et al.   Frontiers in Plant Science

Transcriptome analysis of rice root heterosis by RNA-Seq

(2013) Rongrong Zhai et al.   BMC GENOMICS

De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing

(2013) Ying Yang et al.   GENE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

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

(2012) Jialei Duan et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

(2012) J. A. O'Rourke et al.   PLANT PHYSIOLOGY

De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

(2012) Miao He et al.   PLoS One

De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

(2012) Xue-Mei Zhang et al.   PLoS One

SEPALLATA1/2-suppressed mature apples have low ethylene, high auxin and reduced transcription of ripening-related genes

(2012) Robert J. Schaffer et al.   AoB Plants

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

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

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

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

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

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

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

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

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

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

(2008) E. Paux et al.   SCIENCE