Related references
Note: Only part of the references are listed.Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat
Vincent Ranwez et al.
BMC BIOINFORMATICS (2013)
Characterisation of the wheat (triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat
Youko Oono et al.
BMC GENOMICS (2013)
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
Ya Yang et al.
BMC GENOMICS (2013)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Update on activities at the Universal Protein Resource (UniProt) in 2013
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2013)
De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana
Kenlee Nakasugi et al.
PLOS ONE (2013)
Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis
Nicolas Sierro et al.
GENOME BIOLOGY (2013)
Separating homeologs by phasing in the tetraploid wheat transcriptome
Ksenia V. Krasileva et al.
GENOME BIOLOGY (2013)
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
Marcel H. Schulz et al.
BIOINFORMATICS (2012)
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms
Berat Z. Haznedaroglu et al.
BMC BIOINFORMATICS (2012)
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants
Nicole Gruenheit et al.
BMC GENOMICS (2012)
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
Aureliano Bombarely et al.
BMC GENOMICS (2012)
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
Jialei Duan et al.
BMC GENOMICS (2012)
Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat
Andreas W. Schreiber et al.
BMC GENOMICS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Reorganizing the protein space at the Universal Protein Resource (UniProt)
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2012)
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
Marc Lohse et al.
NUCLEIC ACIDS RESEARCH (2012)
Feature-by-Feature - Evaluating De Novo Sequence Assembly
Francesco Vezzi et al.
PLOS ONE (2012)
Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
Francesco Vezzi et al.
PLOS ONE (2012)
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
Qiong-Yi Zhao et al.
BMC BIOINFORMATICS (2011)
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li et al.
BMC BIOINFORMATICS (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
De novo assembly and analysis of RNA-seq data
Gordon Robertson et al.
NATURE METHODS (2010)
De novo transcriptome assembly with ABySS
Inanc Birol et al.
BIOINFORMATICS (2009)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Assessing the gene space in draft genomes
Genis Parra et al.
NUCLEIC ACIDS RESEARCH (2009)
NCBI Reference Sequences: current status, policy and new initiatives
Kim D. Pruitt et al.
NUCLEIC ACIDS RESEARCH (2009)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
Wheat FT protein regulates VRN1 transcription through interactions with FDL2
Chengxia Li et al.
PLANT JOURNAL (2008)
UniRef: comprehensive and non-redundant UniProt reference clusters
Baris E. Suzek et al.
BIOINFORMATICS (2007)
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes
Genis Parra et al.
BIOINFORMATICS (2007)
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
Ramya Rajagopalan et al.
GENES & DEVELOPMENT (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li et al.
BIOINFORMATICS (2006)
Virus-induced gene silencing of Argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1-like and Argonaute4-like genes
Louise Jones et al.
PLANT PHYSIOLOGY (2006)
Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation
ZX Xie et al.
CURRENT BIOLOGY (2003)
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
G Pertea et al.
BIOINFORMATICS (2003)
The bioperl toolkit:: Perl modules for the life sciences
JE Stajich et al.
GENOME RESEARCH (2002)
Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice
T Izawa et al.
GENES & DEVELOPMENT (2002)