Limits to robustness and reproducibility in the demarcation of operational taxonomic units (Q35231650)

7 August 2017

Limits to robustness and reproducibility in the demarcation of operational taxonomic units (English)

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7 August 2017

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João F Matias Rodrigues

object named as

João F Matias Rodrigues

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2

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Christian von Mering

object named as

Christian von Mering

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3

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author name string

Thomas S B Schmidt

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1

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7 August 2017

29 September 2014

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Environmental Microbiology

7 August 2017

1 reference

7 August 2017

17

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7 August 2017

5

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7 August 2017

1689-1706

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Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

7 August 2017

1 reference

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Comparing clustering and pre-processing in taxonomy analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

An Ordination of the Upland Forest Communities of Southern Wisconsin

21 January 2018

1 reference

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

21 January 2018

1 reference

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QIIME allows analysis of high-throughput community sequencing data

21 January 2018

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21 January 2018

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MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence

21 January 2018

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A comparison of methods for clustering 16S rRNA sequences into OTUs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Bayesian estimation of bacterial community composition from 454 sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Ribosomal Database Project: data and tools for high throughput rRNA analysis

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

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Measures of the Amount of Ecologic Association Between Species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Genomics and the bacterial species problem

21 January 2018

1 reference

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On the origin of prokaryotic species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Search and clustering orders of magnitude faster than BLAST

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

UPARSE: highly accurate OTU sequences from microbial amplicon reads

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12610

UCHIME improves sensitivity and speed of chimera detection

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

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Opinion: Re-evaluating prokaryotic species

21 January 2018

1 reference

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Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

21 January 2018

1 reference

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Topographical and temporal diversity of the human skin microbiome

21 January 2018

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

21 January 2018

1 reference

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

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Ultrafast clustering algorithms for metagenomic sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Infernal 1.0: inference of RNA alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Microbial ecology and evolution: a ribosomal RNA approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

21 January 2018

Measurement of Diversity

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

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A framework for human microbiome research

21 January 2018

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Structure, function and diversity of the healthy human microbiome

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12610

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

A novel hierarchical clustering algorithm for gene sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12610

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks

21 January 2018

1 reference

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A general species delimitation method with applications to phylogenetic placements

21 January 2018

1 reference

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21 January 2018

Identifiers

DOI

10.1111/1462-2920.12610

1 reference

7 August 2017

1 reference

PubMed ID

25156547