Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

(2012) S Samuel Yang et al.   BMC GENOMICS

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

(2011) Eshchar Mizrachi et al.   BMC GENOMICS

The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype

(2010) Nicholas D. Bonawitz et al.   Annual Review of Genetics

Towards reliable isoform quantification using RNA-SEQ data

(2010) Brian E Howard et al.   BMC BIOINFORMATICS

Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip(R) Soybean Genome Array: optimizing analysis by masking biased probes

(2010) S SAMUEL Yang et al.   BMC PLANT BIOLOGY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

(2010) V. M. Bruno et al.   GENOME RESEARCH

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

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

Sucrose Synthase is an Integral Component of the Cellulose Synthesis Machinery

(2010) S. Fujii et al.   PLANT AND CELL PHYSIOLOGY

Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology

(2010) Steven D. Rounsley et al.   PLANT JOURNAL

Understanding Lignification: Challenges Beyond Monolignol Biosynthesis

(2010) X. Li et al.   PLANT PHYSIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing

(2009) Wei Wang et al.   BMC GENOMICS

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

(2009) Diana Bellin et al.   BMC GENOMICS

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

RNA-seq: from technology to biology

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

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

(2009) Ryan Lister et al.   CURRENT OPINION IN PLANT BIOLOGY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

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

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

MATE Transporters Facilitate Vacuolar Uptake of Epicatechin 3'-O-Glucoside for Proanthocyanidin Biosynthesis in Medicago truncatula and Arabidopsis

(2009) J. Zhao et al.   PLANT CELL

The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis

(2009) Y.-F. Chen et al.   PLANT CELL

Single-Feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa

(2009) S. Samuel Yang et al.   Plant Genome

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME 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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. 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

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Dissecting the Molecular Basis of the Regulation of Wood Formation by Auxin in Hybrid Aspen

(2008) J. Nilsson et al.   PLANT CELL

Tracking Monolignols during Wood Development in Lodgepole Pine

(2008) M. Kaneda et al.   PLANT PHYSIOLOGY

Role of AUX1 in the control of organ identity during in vitro organogenesis and in mediating tissue specific auxin and cytokinin interaction in Arabidopsis

(2008) Aparna Kakani et al.   PLANTA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Pretreatment: the key to unlocking low-cost cellulosic ethanol

(2007) Bin Yang et al.   Biofuels Bioproducts & Biorefining-Biofpr