Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution (Q30835994)

13 November 2017

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution (English)

1 reference

13 November 2017

1 reference

Mikhail Tikhonov

1

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author name string

Robert W Leach

series ordinal

2

1 reference

PMCID

4274427

13 November 2017

Ned S Wingreen

series ordinal

3

1 reference

13 November 2017

11 July 2014

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13 November 2017

1 reference

13 November 2017

9

1 reference

13 November 2017

1

1 reference

13 November 2017

68-80

1 reference

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

13 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Improved inference of taxonomic richness from environmental DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

UPARSE: highly accurate OTU sequences from microbial amplicon reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

The long-term stability of the human gut microbiota

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Control of pathogens and pathobionts by the gut microbiota

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Commensal bacteria at the interface of host metabolism and the immune system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Cohabiting family members share microbiota with one another and with their dogs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

A meta-analysis of changes in bacterial and archaeal communities with time

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Fundamentals of microbial community resistance and resilience

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Denoising PCR-amplified metagenome data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Lineage-specific responses of microbial communities to environmental change

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Structure, function and diversity of the healthy human microbiome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

The application of ecological theory toward an understanding of the human microbiome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

UCHIME improves sensitivity and speed of chimera detection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Moving pictures of the human microbiome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

The generation and maintenance of diversity in microbial communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Removing noise from pyrosequenced amplicons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Search and clustering orders of magnitude faster than BLAST

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Comparison of 61 sequenced Escherichia coli genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

CD-HIT Suite: a web server for clustering and comparing biological sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Bacterial community variation in human body habitats across space and time

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Accurate determination of microbial diversity from 454 pyrosequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

The role of ecological theory in microbial ecology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

UniFrac: a new phylogenetic method for comparing microbial communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Neutral mutations and neutral substitutions in bacterial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4274427

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2014.117

[Copy number of ribosomal operons in prokaryotes and its effect on phylogenic analyses]

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25012900

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DySC: software for greedy clustering of 16S rRNA reads

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25012900

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/ISMEJ.2014.117

1 reference

Dimensions Publication ID

13 November 2017

1 reference

0 references

1 reference

13 November 2017

1 reference

PMCID

4274427