De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana (Q34651478)

3 August 2017

De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana (English)

1 reference

3 August 2017

0 references

0 references

1 reference

Nicotiana benthamiana

Nicotiana benthamiana

1 reference

5

1 reference

3 August 2017

Julia Bally

3

0 references

Peter M. Waterhouse

Peter M Waterhouse

series ordinal

6

0 references

Ross N Crowhurst

series ordinal

2

Ross N Crowhurst

1 reference

3 August 2017

Kenlee Nakasugi

1

1 reference

PubMed ID

23555698

3 August 2017

Craig C Wood

series ordinal

4

1 reference

PubMed ID

23555698

3 August 2017

language of work or name

English

0 references

publication date

28 March 2013

1 reference

3 August 2017

1 reference

3 August 2017

8

1 reference

3 August 2017

e59534

1 reference

3 August 2017

3

1 reference

Creative Commons Attribution 4.0 International

3 August 2017

start time

28 March 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

edgeR

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

0 references

cites work

Advanced engineering of lipid metabolism in Nicotiana benthamiana using a draft genome and the V2 viral silencing-suppressor protein

1 reference

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Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

7 July 2018

1 reference

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RNA-Seq Assembly - Are We There Yet?

7 July 2018

1 reference

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Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

The transcriptome of Verticillium dahliae-infected Nicotiana benthamiana determined by deep RNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

The tomato genome sequence provides insights into fleshy fruit evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Characterization of the Conus bullatus genome and its venom-duct transcriptome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

From RNA-seq reads to differential expression results

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

De novo assembly and analysis of RNA-seq data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Biases in Illumina transcriptome sequencing caused by random hexamer priming

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Control of female gamete formation by a small RNA pathway in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

A scaling normalization method for differential expression analysis of RNA-seq data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

BLAST+: architecture and applications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Virus-induced gene silencing: a versatile tool for discovery of gene functions in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

De novo transcriptome assembly with ABySS.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

SHRiMP: accurate mapping of short color-space reads

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

RNA-mediated chromatin-based silencing in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Assessing the gene space in draft genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

NCBI Reference Sequences: current status, policy and new initiatives

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

RNA silencing in plants: yesterday, today, and tomorrow.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

UniRef: comprehensive and non-redundant UniProt reference clusters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Nicotiana (Nicotiana tobaccum, Nicotiana benthamiana).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

RETRACTED: Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

A leaf-based assay using interchangeable design principles to rapidly assemble multistep recombinant pathways.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

SHORT HYPOCOTYL UNDER BLUE1 truncations and mutations alter its association with a signaling protein complex in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

RNA silencing: an antiviral mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

InterPro and InterProScan: tools for protein sequence classification and comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

Virus-induced gene silencing of argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1-like and Argonaute4-like genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

The evolution and diversification of Dicers in plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

DICER-LIKE 4 but not DICER-LIKE 2 may have a positive effect on potato spindle tuber viroid accumulation in Nicotiana benthamiana

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

RNA-dependent RNA polymerase 1 from Nicotiana tabacum suppresses RNA silencing and enhances viral infection in Nicotiana benthamiana.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Optimization of transient Agrobacterium-mediated gene expression system in leaves of Nicotiana benthamiana.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3610648

Comparative morphology and phylogeny of Nicotiana section Suaveolentes (Solanaceae) in Australia and the South Pacific

26 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059534

Viral suppressors of RNA silencing

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23555698

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0059534

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference

PubMed ID

23555698