4.6 Article

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat

Vincent Ranwez et al.

BMC BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Ya Yang et al.

BMC GENOMICS (2013)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Update on activities at the Universal Protein Resource (UniProt) in 2013

Rolf Apweiler et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biotechnology & Applied Microbiology

Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis

Nicolas Sierro et al.

GENOME BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Separating homeologs by phasing in the tetraploid wheat transcriptome

Ksenia V. Krasileva et al.

GENOME BIOLOGY (2013)

Article Biochemical Research Methods

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Marcel H. Schulz et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

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

Nicole Gruenheit et al.

BMC GENOMICS (2012)

Article Biotechnology & Applied Microbiology

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

Aureliano Bombarely et al.

BMC GENOMICS (2012)

Article Biotechnology & Applied Microbiology

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

Jialei Duan et al.

BMC GENOMICS (2012)

Article Biotechnology & Applied Microbiology

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

Andreas W. Schreiber et al.

BMC GENOMICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Reorganizing the protein space at the Universal Protein Resource (UniProt)

Rolf Apweiler et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Marc Lohse et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Feature-by-Feature - Evaluating De Novo Sequence Assembly

Francesco Vezzi et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

Francesco Vezzi et al.

PLOS ONE (2012)

Article Biochemical Research Methods

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Qiong-Yi Zhao et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemical Research Methods

De novo assembly and analysis of RNA-seq data

Gordon Robertson et al.

NATURE METHODS (2010)

Article Biochemical Research Methods

De novo transcriptome assembly with ABySS

Inanc Birol et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Assessing the gene space in draft genomes

Genis Parra et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

NCBI Reference Sequences: current status, policy and new initiatives

Kim D. Pruitt et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

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

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Plant Sciences

Wheat FT protein regulates VRN1 transcription through interactions with FDL2

Chengxia Li et al.

PLANT JOURNAL (2008)

Article Biochemical Research Methods

UniRef: comprehensive and non-redundant UniProt reference clusters

Baris E. Suzek et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes

Genis Parra et al.

BIOINFORMATICS (2007)

Article Cell Biology

A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana

Ramya Rajagopalan et al.

GENES & DEVELOPMENT (2006)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation

ZX Xie et al.

CURRENT BIOLOGY (2003)

Article Biochemistry & Molecular Biology

The bioperl toolkit:: Perl modules for the life sciences

JE Stajich et al.

GENOME RESEARCH (2002)