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Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes
scientific article published on 24 July 2019
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Europe PubMed Central
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6655640
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
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27 April 2020
title
Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes
(English)
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Europe PubMed Central
PMC publication ID
6655640
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
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27 April 2020
author
Robyn L Allscheid
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3
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Europe PubMed Central
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6655640
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
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27 April 2020
James C. Carrington
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4
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Europe PubMed Central
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6655640
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
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27 April 2020
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Kerrigan B Gilbert
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1
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6655640
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27 April 2020
Emily E Holcomb
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2
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27 April 2020
publication date
24 July 2019
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27 April 2020
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PLOS One
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Europe PubMed Central
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6655640
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27 April 2020
volume
14
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Europe PubMed Central
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6655640
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27 April 2020
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7
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27 April 2020
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e0219207
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27 April 2020
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24 July 2019
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PdbrlA, PdabaA and PdwetA control distinct stages of conidiogenesis in Penicillium digitatum
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23 February 2021
A novel single-stranded RNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix, with similarity to hypo-like viruses
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Molecular characterisation of an endornavirus infecting the phytopathogen Sclerotinia sclerotiorum
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Hypovirulence of the phytopathogenic fungus Botryosphaeria dothidea: association with a coinfecting chrysovirus and a partitivirus
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Gene silencing and gene expression in phytopathogenic fungi using a plant virus vector.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
A novel dsRNA element isolated from the Aspergillus foetidus mycovirus complex
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
The family narnaviridae: simplest of RNA viruses.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Overexpression of ShCYP51B and ShatrD in Sclerotinia homoeocarpa isolates exhibiting practical field resistance to a demethylation inhibitor fungicide
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Sequence determination of a quadripartite dsRNA virus isolated from Aspergillus foetidus.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Fast gapped-read alignment with Bowtie 2
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Molecular characterization of a new hypovirus infecting a phytopathogenic fungus, Valsa ceratosperma
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
RNA sequence determinants of a coupled termination-reinitiation strategy for downstream open reading frame translation in Helminthosporium victoriae virus 190S and other victoriviruses (Family Totiviridae)
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Discovery and initial analysis of novel viral genomes in the soybean cyst nematode
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
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23 February 2021
The good viruses: viral mutualistic symbioses
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Nucleotide sequences of four segments of chrysovirus in Korean Cryphonectria nitschkei BS122 strain
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A novel mycovirus associated with four double-stranded RNAs affects host fungal growth in Alternaria alternata
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Victorivirus, a new genus of fungal viruses in the family Totiviridae
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Virus population dynamics and acquired virus resistance in natural microbial communities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Sequences of the smallest double-stranded RNAs associated with cherry chlorotic rusty spot and Amasya cherry diseases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Evidence that RNA silencing functions as an antiviral defense mechanism in fungi
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A totivirus infecting the mutualistic fungal endophyte Epichloë festucae
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Mycovirus Cryphonectria Hypovirus 1 Elements Cofractionate with trans-Golgi Network Membranes of the Fungal Host Cryphonectria parasitica
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Cherry chlorotic rusty spot and Amasya cherry diseases are associated with a complex pattern of mycoviral-like double-stranded RNAs. I. Characterization of a new species in the genus Chrysovirus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Transfection of Diaporthe perjuncta with Diaporthe RNA virus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
The viral killer system in yeast: from molecular biology to application
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A novel RNA mycovirus in a hypovirulent isolate of the plant pathogen Diaporthe ambigua
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Mutation analysis of the GDD sequence motif of a calicivirus RNA-dependent RNA polymerase
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Genetic interrelationships and genome organization of double-stranded RNA elements of Fusarium poae
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Molecular characterization of two endogenous double-stranded RNAs in rice and their inheritance by interspecific hybrids
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Coinfection of a fungal pathogen by two distinct double-stranded RNA viruses
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Structure of the RNA-dependent RNA polymerase of poliovirus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Organization and expression of the double-stranded RNA genome of Helminthosporium victoriae 190S virus, a totivirus infecting a plant pathogenic filamentous fungus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Membrane-associated replication of an unencapsidated double-strand RNA of the fungus, Cryphonectria parasitica
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
A viral dsRNA element of the chestnut blight fungus with a distinct genetic organization
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Mutation of the aspartic acid residues of the GDD sequence motif of poliovirus RNA-dependent RNA polymerase results in enzymes with altered metal ion requirements for activity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Double-stranded RNA in rice: a novel RNA replicon in plants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Identification of four conserved motifs among the RNA-dependent polymerase encoding elements
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Recent evidence for evolution of the genetic code
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6655640
retrieved
23 February 2021
Identifiers
DOI
10.1371/JOURNAL.PONE.0219207
1 reference
stated in
Europe PubMed Central
PMC publication ID
6655640
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
retrieved
27 April 2020
PMC publication ID
6655640
1 reference
stated in
Europe PubMed Central
PMC publication ID
6655640
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
retrieved
27 April 2020
PubMed publication ID
31339899
1 reference
stated in
Europe PubMed Central
PMC publication ID
6655640
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31339899%20AND%20SRC:MED&resulttype=core&format=json
retrieved
27 April 2020
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