A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples (Q34770515)

4 August 2017

title

A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples (English)

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4 August 2017

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whole genome sequencing

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Paolo Piazza

20

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Elizabeth M Batty

Elizabeth M Batty

1

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Tanya Golubchik

Tanya Golubchik

8

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Kate E Dingle

Kate E Dingle

17

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Paul Klenerman

12

Paul Klenerman

1 reference

4 August 2017

Daniel J Wilson

16

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Eleanor J. Barnes

Eleanor Barnes

13

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Ann Sarah Walker

14

A Sarah Walker

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4 August 2017

19

Derrick W Crook

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4 August 2017

18

Tim E A Peto

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4 August 2017

5

Moustafa Attar

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4 August 2017

10

Rory Bowden

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4 August 2017

3

Amy Trebes

1 reference

4 August 2017

T H Nicholas Wong

2

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4 August 2017

Karène Argoud

4

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4 August 2017

David Buck

6

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4 August 2017

Camilla L C Ip

7

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4 August 2017

Madeleine Cule

9

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4 August 2017

Charis Manganis

11

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4 August 2017

David H Wyllie

15

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4 August 2017

language of work or name

English

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publication date

10 June 2013

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4 August 2017

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4 August 2017

volume

8

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4 August 2017

issue

6

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4 August 2017

page(s)

e66129

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Creative Commons Attribution 4.0 International

4 August 2017

copyright license

start time

10 June 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Indications for worldwide increased norovirus activity associated with emergence of a new variant of genotype II.4, late 2012.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational 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=3677912

De novo assembly of highly diverse viral populations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Constraints on viral evolution during chronic hepatitis C virus infection arising from a common-source exposure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Insights from genomics into bacterial pathogen populations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute 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=3677912

Bayesian phylogenetics with BEAUti and the BEAST 1.7

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

De novo assembly and genotyping of variants using colored de Bruijn graphs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation 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=3677912

Specific capture and whole-genome sequencing of viruses from clinical samples

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Inferring viral quasispecies spectra from 454 pyrosequencing 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=3677912

Mechanisms of GII.4 norovirus 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=3677912

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation 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=3677912

The origin of the Haitian cholera outbreak strain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

PriSM: a primer selection and matching tool for amplification and sequencing of viral 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=3677912

Development of a low bias method for characterizing viral populations using next generation sequencing technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence 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=3677912

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

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=3677912

Target-enrichment strategies for next-generation 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=3677912

RNA-Seq: a method for comprehensive transcriptome analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute 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=3677912

Evolutionary analysis of the dynamics of viral infectious disease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

RNA-Seq: a revolutionary tool for transcriptomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Systematic literature review of role of noroviruses in sporadic gastroenteritis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

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=3677912

The transcriptional landscape of the yeast genome defined by 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=3677912

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Mutation in a Lordsdale norovirus epidemic strain as a potential indicator of transmission routes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Is the quasispecies concept relevant to RNA viruses?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

The Staden sequence analysis package

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3677912

Rational optimization of generic primers used for Norwalk-like virus detection by reverse transcriptase polymerase chain reaction

7 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0066129

Oxford Nanopore announcement sets sequencing sector abuzz.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0066129

Genome sequencing in clinical microbiology

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23762474

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0066129

1 reference

4 August 2017

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1 reference

4 August 2017

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