Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

(2015) Alex Harkess et al.   NEW PHYTOLOGIST

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis Reveals the Same 17S-Locus F-BoxGenes in Two Haplotypes of the Self-Incompatibility Locus ofPetunia inflata

(2014) Justin S. Williams et al.   PLANT CELL

De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

(2013) Luca Venturini et al.   BMC GENOMICS

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

(2012) Jianan Zhang et al.   BMC GENOMICS

De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis

(2012) Hua-Hong Huang et al.   BMC GENOMICS

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

(2012) Parul Gahlan et al.   BMC GENOMICS

Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties

(2012) Ramasamy S Annadurai et al.   BMC GENOMICS

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing

(2012) Xiudong Sun et al.   PLANT CELL REPORTS

Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish

(2012) Shufen Wang et al.   PLANT CELL REPORTS

Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

(2011) Zhao Lai et al.   AMERICAN JOURNAL OF BOTANY

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis

(2011) Norman J. Wickett et al.   CURRENT BIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques

(2011) F. ANGELONI et al.   Molecular Ecology Resources

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

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

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Tissue- and Cell-Type Specific Transcriptome Profiling of Expanding Tomato Fruit Provides Insights into Metabolic and Regulatory Specialization and Cuticle Formation

(2011) Antonio J. Matas et al.   PLANT CELL

Journey through the past: 150 million years of plant genome evolution

(2011) Sebastian Proost et al.   PLANT JOURNAL

RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

(2011) Zhihui Xia et al.   PLANT MOLECULAR BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni 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