Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

(2013) Joshua P Der et al.   BMC GENOMICS

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

(2011) Zhangying Wang et al.   BMC GENOMICS

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

(2011) Cheng-Ying Shi et al.   BMC GENOMICS

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

(2011) Fengyi Hu et al.   BMC PLANT BIOLOGY

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi 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

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

(2010) Jeremy Kapteyn et al.   BMC GENOMICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

(2010) Xiao-Wei Wang et al.   BMC GENOMICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics

(2010) A. L. Schilmiller et al.   PLANT PHYSIOLOGY

Comparative Functional Genomic Analysis of Solanum Glandular Trichome Types

(2010) E. T. McDowell et al.   PLANT PHYSIOLOGY

Increased Food and Ecosystem Security via Perennial Grains

(2010) J. D. Glover et al.   SCIENCE

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PAVE: Program for assembling and viewing ESTs

(2009) Carol Soderlund et al.   BMC GENOMICS

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Is sequencing enlightenment ending the dark age of the transcriptome?

(2009) Piero Carninci   NATURE METHODS

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Hormonal Regulation of Branching in Grasses

(2009) P. McSteen   PLANT PHYSIOLOGY

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

(2009) Carol Soderlund et al.   PLoS Genetics

Spectral Index for Assessment of Differential Protein Expression in Shotgun Proteomics

(2008) Xiaoyun Fu et al.   JOURNAL OF PROTEOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Characterization of TCTP, the Translationally Controlled Tumor Protein, from Arabidopsis thaliana

(2008) O. Berkowitz et al.   PLANT CELL