(Q34630217)

3 August 2017

title

Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity (English)

1 reference

3 August 2017

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1 reference

1 reference

1 reference

Jean-François Mangot

2

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Isabelle Domaizon

object named as

Isabelle Domaizon

series ordinal

3

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Didier Debroas

series ordinal

5

object named as

Didier Debroas

1 reference

3 August 2017

Najwa Taib

1

1 reference

3 August 2017

Gisèle Bronner

series ordinal

4

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3 August 2017

language of work or name

English

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publication date

14 March 2013

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3 August 2017

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3 August 2017

volume

8

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3 August 2017

issue

3

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3 August 2017

page(s)

e58950

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Creative Commons Attribution 4.0 International

3 August 2017

copyright license

start time

14 March 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Vertical structure of small eukaryotes in three lakes that differ by their trophic status: a quantitative approach

7 July 2018

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VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences.

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

QIIME allows analysis of high-throughput community sequencing data

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

FastTree 2--approximately maximum-likelihood trees for large alignments

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

PANGEA: pipeline for analysis of next generation amplicons

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Mapping the protistan 'rare biosphere'.

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Ecology of the rare microbial biosphere of the Arctic Ocean

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

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

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

New insights into the diversity of marine picoeukaryotes

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Microbial community structure in the North Pacific ocean

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Defining DNA-based operational taxonomic units for microbial-eukaryote ecology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag 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=3597552

The Ribosomal Database Project: improved alignments and new tools for rRNA 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=3597552

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Comparative analysis of human gut microbiota by barcoded 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=3597552

An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

The diversity of small eukaryotic phytoplankton (< or =3 microm) in marine ecosystems.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Microbial diversity and the genetic nature of microbial species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Species divergence and the measurement of microbial diversity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Unexpected importance of potential parasites in the composition of the freshwater small-eukaryote community

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Pyrosequencing enumerates and contrasts soil microbial diversity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Genomics, environmental genomics and the issue of microbial species.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Genetic diversity of small eukaryotes in lakes differing by their trophic status

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

SAR11 clade dominates ocean surface bacterioplankton communities.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Global dispersal of free-living microbial eukaryote species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Exploring prokaryotic diversity in the genomic era

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

EMBOSS: the European Molecular Biology Open Software Suite

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Profile hidden Markov models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Archaea in coastal marine environments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3597552

Perkinsozoa, a well-known marine protozoan flagellate parasite group, newly identified in lacustrine systems: a review

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Short pyrosequencing reads suffice for accurate microbial community analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Freshwater Foraminiferans Revealed by Analysis of Environmental DNA Samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Using ecological diversity measures with bacterial communities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058950

10.1371/JOURNAL.PONE.0058950

21 January 2018

Identifiers

DOI

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3 August 2017

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3 August 2017

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