(Q43136047)

14 November 2017

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units (English)

1 reference

14 November 2017

2

1 reference

14 November 2017

Sarah L Westcott

1

1 reference

14 November 2017

8 December 2015

1 reference

14 November 2017

1 reference

14 November 2017

3

1 reference

14 November 2017

e1487

1 reference

Creative Commons Attribution 4.0 International

14 November 2017

start time

8 December 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

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Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

25 May 2018

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Swarm: robust and fast clustering method for amplicon-based studies

25 May 2018

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Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

25 May 2018

1 reference

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Advancing our understanding of the human microbiome using QIIME

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

UPARSE: highly accurate OTU sequences from microbial amplicon reads

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Secondary structure improves OTU assignments of 16S rRNA gene sequences

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Stabilization of the murine gut microbiome following weaning

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Defining seasonal marine microbial community dynamics

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

UCHIME improves sensitivity and speed of chimera detection

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Search and clustering orders of magnitude faster than BLAST

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

QIIME allows analysis of high-throughput community sequencing data

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Pyrosequencing enumerates and contrasts soil microbial diversity

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

25 May 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

25 May 2018

https://api.crossref.org/works/10.7717%2FPEERJ.1487

Comparing clustering and pre-processing in taxonomy analysis

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4675110

A new method for non-parametric multivariate analysis of variance

15 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.7717%2FPEERJ.1487

Structure, function and diversity of the healthy human microbiome

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.7717%2FPEERJ.1487

Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.7717%2FPEERJ.1487

21 January 2018

Identifiers

DOI

10.7717/PEERJ.1487

1 reference

14 November 2017

1 reference

PMC publication ID

4675110

14 November 2017

PubMed publication ID

26664811

1 reference

PMC publication ID

4675110