Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale (Q35156891)

6 August 2017

Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale (English)

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6 August 2017

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3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

Thomas S.B. Schmidt

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1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

João F Matias Rodrigues

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2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

author name string

Thomas S B Schmidt

series ordinal

1

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PubMed ID

24763141

6 August 2017

language of work or name

English

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publication date

24 April 2014

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PLOS Computational Biology

6 August 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

volume

10

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1 June 2020

issue

4

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1 June 2020

page(s)

e1003594

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Creative Commons Attribution 4.0 International

1 June 2020

copyright license

start time

24 April 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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maintained by WikiProject

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HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Distribution-based clustering: using ecology to refine the operational taxonomic unit

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

M-pick, a modularity-based method for OTU picking of 16S rRNA sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

CD-HIT: accelerated for clustering the next-generation sequencing data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Structure, function and diversity of the healthy human microbiome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Lineage-dependent ecological coherence in bacteria

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Fine-scale distribution patterns of Synechococcus ecological diversity in microbial mats of Mushroom Spring, Yellowstone National Park

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

UCHIME improves sensitivity and speed of chimera detection

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

A species concept for bacteria based on adaptive divergence

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Search and clustering orders of magnitude faster than BLAST

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

QIIME allows analysis of high-throughput community sequencing data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Topographical and temporal diversity of the human skin microbiome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

On the origin of prokaryotic species.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Infernal 1.0: inference of RNA alignments

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Microbial diversity and the genetic nature of microbial species

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

A systematics for discovering the fundamental units of bacterial diversity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Opinion: Re-evaluating prokaryotic species

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

What are bacterial species?

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

A natural species concept for prokaryotes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Comparing clustering and pre-processing in taxonomy analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Population genomics: how bacterial species form and why they don't exist

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

The ecological coherence of high bacterial taxonomic ranks

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Genomics and the bacterial species problem

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998914

Information theoretic measures for clusterings comparison

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003594

10.1371/JOURNAL.PCBI.1003594

21 January 2018

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/SchmidtRM14

1 June 2020

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24763141%20AND%20SRC:MED&resulttype=core&format=json