(Q30424103)

13 August 2017

Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance (English)

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13 August 2017

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3

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PubMed publication ID

21 June 2017

Steven W Kembel

1

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Martin Wu

object named as

Martin Wu

series ordinal

2

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author name string

Jessica L Green

series ordinal

4

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13 August 2017

25 October 2012

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PLOS Computational Biology

13 August 2017

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13 August 2017

8

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13 August 2017

10

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13 August 2017

e1002743

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Creative Commons Attribution 4.0 International

13 August 2017

start time

25 October 2012

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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

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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

20 June 2018

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Unlocking short read sequencing for metagenomics

20 June 2018

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Picante: R tools for integrating phylogenies and ecology

20 June 2018

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QIIME allows analysis of high-throughput community sequencing data

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

A human gut microbial gene catalogue established by metagenomic sequencing

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

20 June 2018

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PyNAST: a flexible tool for aligning sequences to a template alignment

20 June 2018

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Bacterial community variation in human body habitats across space and time

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Visualization of ribosomal RNA operon copy number distribution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Polymerase chain reaction primers miss half of rRNA microbial diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

A simple, fast, and accurate method of phylogenomic inference

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Microbial biogeography: from taxonomy to traits

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

RNAmmer: consistent and rapid annotation of ribosomal RNA genes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

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

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Community genomics among stratified microbial assemblages in the ocean's interior

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Metagenomics: application of genomics to uncultured microorganisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Environmental genome shotgun sequencing of the Sargasso Sea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

New approaches to analyzing microbial biodiversity data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Testing for phylogenetic signal in comparative data: behavioral traits are more labile

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Biological identifications through DNA barcodes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Estimating prokaryotic diversity and its limits

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

rRNA operon copy number reflects ecological strategies of bacteria

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

A molecular view of microbial diversity and the biosphere

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002743

The Commonness, And Rarity, of Species

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002743

Phylogenies and the Comparative Method

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002743

Short pyrosequencing reads suffice for accurate microbial community analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002743

Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002743

Understanding Bias in Microbial Community Analysis Techniques due to rrn Operon Copy Number Heterogeneity

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

Using the Past to Predict the Present: Confidence Intervals for Regression Equations in Phylogenetic Comparative Methods.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3486904

10.1371/JOURNAL.PCBI.1002743

26 November 2018

Identifiers

DOI

1 reference

journals/ploscb/KembelWEG12

13 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3486904

13 August 2017

PubMed publication ID

23133348

1 reference

PMC publication ID

3486904