Discovery of replicating circular RNAs by RNA-seq and computational algorithms (Q30877994)

12 October 2017

Discovery of replicating circular RNAs by RNA-seq and computational algorithms (English)

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12 October 2017

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Zhixiang Zhang

1

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12 October 2017

Shuishui Qi

2

1 reference

12 October 2017

Nan Tang

3

1 reference

12 October 2017

Xinxin Zhang

4

1 reference

12 October 2017

Shanshan Chen

5

1 reference

12 October 2017

Pengfei Zhu

6

1 reference

12 October 2017

Lin Ma

7

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12 October 2017

Jinping Cheng

8

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12 October 2017

Yun Xu

9

1 reference

12 October 2017

Meiguang Lu

10

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12 October 2017

Hongqing Wang

11

1 reference

12 October 2017

Shou-Wei Ding

12

1 reference

12 October 2017

Shifang Li

13

1 reference

12 October 2017

Qingfa Wu

14

1 reference

12 October 2017

11 December 2014

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12 October 2017

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12 October 2017

10

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12 October 2017

12

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12 October 2017

e1004553

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Creative Commons Attribution 4.0 International

12 October 2017

start time

11 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

1 reference

Viroids: survivors from the RNA world?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Survey and analysis of simple sequence repeats (SSRs) present in the genomes of plant viroids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Search strategy has influenced the discovery rate of human viruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Characterization of a new apscaviroid from American persimmon

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Circular RNAs are a large class of animal RNAs with regulatory potency

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Natural RNA circles function as efficient microRNA sponges

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Circular RNAs are abundant, conserved, and associated with ALU repeats

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Comprehensive diversity analysis of viroids infecting grapevine in China and Japan

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Viroids: how to infect a host and cause disease without encoding proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Plant viroids: isolation, characterization/detection, and analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Viroid-specific small RNA in plant disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Virus-derived siRNAs and piRNAs in immunity and pathogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Transcriptome-wide discovery of circular RNAs in Archaea

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Satellite RNAs and Satellite Viruses of Plants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Viroid pathogenicity: one process, many faces

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Whole-transcriptome RNAseq analysis from minute amount of total RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: variations on a theme.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Comprehensive comparative analysis of strand-specific RNA sequencing methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Cultivated grapevines represent a symptomless reservoir for the transmission of hop stunt viroid to hop crops: 15 years of evolutionary analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

The biology of viroid-host interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Poly A- transcripts expressed in HeLa cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependent pathway

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Clustal W and Clustal X version 2.0

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

RNA intermediates in potato spindle tuber viroid replication

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Viroids and viroid-host interactions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Mfold web server for nucleic acid folding and hybridization prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Eggplant latent viroid, the candidate type species for a new genus within the family Avsunviroidae (hammerhead viroids)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Plant pathogenic RNAs and RNA catalysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Origin and evolution of viroids and viroid-like satellite RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

RNA-directed de novo methylation of genomic sequences in plants.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

A Replication Cycle for Viroids and Other Small Infectious RNA's

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Nucleotide sequence and secondary structure of apple scar skin viroid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Compilation of self-cleaving sequences from plant virus satellite RNAs and other sources

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Numbering system for the hammerhead

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Structure and structure formation of viroids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Fine structure melting of viroids as studied by kinetic methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4263765

Interplay between viroid-induced pathogenesis and RNA silencing pathways.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

Characterization of a new citrus viroid species tentatively termed Citrus viroid OS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

Identification and characterization of a new coleviroid (CbVd-5).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

RnaViz 2: an improved representation of RNA secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1004553

High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25503469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Discovering viroids — a personal perspective

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25503469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PPAT.1004553

1 reference

12 October 2017

1 reference

12 October 2017

1 reference