Designing a transcriptome next-generation sequencing project for a nonmodel plant species1
Published 2012 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Designing a transcriptome next-generation sequencing project for a nonmodel plant species1
Authors
Keywords
-
Journal
AMERICAN JOURNAL OF BOTANY
Volume 99, Issue 2, Pages 257-266
Publisher
Wiley
Online
2012-01-21
DOI
10.3732/ajb.1100292
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now