Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Integrating C4 photosynthesis into C3 crops to increase yield potential

(2012) Sarah Covshoff et al.   CURRENT OPINION IN BIOTECHNOLOGY

RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

(2012) Chao Li et al.   FISH & SHELLFISH IMMUNOLOGY

Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirds

(2012) Yuhong Zhang et al.   GENOMICS

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

From Bench to Bountiful Harvests: A Road Map for the Next Decade ofArabidopsisResearch

(2012) Irene Lavagi et al.   PLANT CELL

Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research

(2012) Eli Meyer et al.   PLANT JOURNAL

De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome

(2012) Fuliang Xie et al.   PLANTA

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

(2012) Yixing Wang et al.   PLoS One

The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers

(2012) Huang Lulin et al.   PLoS One

Molecular evolution of genes recruited into C4 photosynthesis

(2012) Ben P. Williams et al.   TRENDS IN PLANT SCIENCE

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences

(2011) Juan E. Zalapa et al.   AMERICAN JOURNAL OF BOTANY

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Best practice procedures for the establishment of a C4 cycle in transgenic C3 plants

(2011) C. Peterhansel   JOURNAL OF EXPERIMENTAL BOTANY

Exploiting the engine of C4 photosynthesis

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses

(2011) P. Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types?

(2011) R. T. Furbank   JOURNAL OF EXPERIMENTAL BOTANY

Next-generation transcriptome assembly

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

Regulatory mechanisms underlying C4 photosynthesis

(2011) Lin Wang et al.   NEW PHYTOLOGIST

C4Cycles: Past, Present, and Future Research on C4Photosynthesis

(2011) Jane A. Langdale   PLANT CELL

The Regulation of Gene Expression Required for C4Photosynthesis

(2010) Julian M. Hibberd et al.   Annual Review of Plant Biology

C4 Rice - an Ideal Arena for Systems Biology Research

(2010) Xin-Guang Zhu et al.   Journal of Integrative Plant Biology

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Setaria viridis: A Model for C4 Photosynthesis

(2010) T. P. Brutnell et al.   PLANT CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Foxtail Millet: A Sequence-Driven Grass Model System

(2009) A. N. Doust et al.   PLANT PHYSIOLOGY

What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?

(2008) Xin-Guang Zhu et al.   CURRENT OPINION IN BIOTECHNOLOGY