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

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

(2013) Joshua P Der 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

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

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

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants

(2011) Stéphanie M. Swarbreck et al.   PLANT AND CELL PHYSIOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types

(2010) Shaogui Guo et al.   BMC GENOMICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

(2010) RICHARD J. A. BUGGS et al.   MOLECULAR ECOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

(2010) A. M. Smith et al.   NUCLEIC ACIDS RESEARCH

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

(2010) A. Bombarely et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes

(2010) Chance W Riggins et al.   PEST MANAGEMENT SCIENCE

An mRNA Blueprint for C4 Photosynthesis Derived from Comparative Transcriptomics of Closely Related C3 and C4 Species

(2010) A. Brautigam et al.   PLANT PHYSIOLOGY

Reference-Free Validation of Short Read Data

(2010) Jan Schröder et al.   PLoS One

High-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing

(2010) Hideo Matsumura et al.   PLoS One

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li 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

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

(2009) Fiammetta Alagna et al.   BMC GENOMICS

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

(2009) Abdelali Barakat et al.   BMC PLANT BIOLOGY

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Shedding light on an extremophile lifestyle through transcriptomics

(2009) M. Dassanayake et al.   NEW PHYTOLOGIST

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Probabilistic base calling of Solexa sequencing data

(2008) Jacques Rougemont et al.   BMC BIOINFORMATICS

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

(2008) Carlos Molina et al.   BMC GENOMICS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

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

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY