Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons (Q29614292)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons (English)

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

3

1 reference

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19 January 2020

Rob Knight

15

1 reference

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19 January 2020

9

Sarah K Highlander

1 reference

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19 January 2020

14

Joseph F Petrosino

1 reference

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19 January 2020

author name string

Brian J Haas

1

1 reference

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19 January 2020

Dirk Gevers

2

1 reference

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19 January 2020

Mike Feldgarden

4

1 reference

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19 January 2020

Doyle V Ward

5

1 reference

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19 January 2020

Georgia Giannoukos

6

1 reference

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19 January 2020

Dawn Ciulla

7

1 reference

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19 January 2020

Diana Tabbaa

8

1 reference

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19 January 2020

Erica Sodergren

10

1 reference

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19 January 2020

Barbara Methé

11

1 reference

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19 January 2020

Todd Z DeSantis

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Human Microbiome Consortium

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

Bruce W Birren

16

1 reference

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

19 January 2020

language of work or name

1 reference

30 April 2017

publication date

6 January 2011

1 reference

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19 January 2020

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

volume

21

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

page(s)

494-504

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

issue

3

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

QIIME allows analysis of high-throughput community sequencing data

19 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Microbial diversity in the deep sea and the underexplored "rare biosphere"

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

The Uncultured Microbial Majority

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

A molecular view of microbial diversity and the biosphere

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

A general method applicable to the search for similarities in the amino acid sequence of two proteins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Accurate determination of microbial diversity from 454 pyrosequencing data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

A renaissance for the pioneering 16S rRNA gene

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Short pyrosequencing reads suffice for accurate microbial community analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Amplification of complex gene libraries by emulsion PCR.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3044863

The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species

26 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/21212162

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/21212162

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.112730.110

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21212162%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21212162

30 April 2017