Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition (Q28596947)

6

Frank M Aarestrup

0 references

Berith E Knudsen

Berith E Knudsen

1

0 references

Lasse Bergmark

Lasse Bergmark

2

0 references

Patrick Munk

Patrick Munk

3

0 references

Oksana Lukjancenko

Oksana Lukjancenko

4

0 references

Sünje Johanna Pamp

Sünje J Pamp

7

0 references

Anders Priemé

5

describes a project that uses

Anders Priemé

0 references

language of work or name

English

0 references

publication date

18 October 2016

1 reference

1 reference

1

0 references

issue

5

0 references

page(s)

e00095-16

0 references

phyloseq

phyloseq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Plankton networks driving carbon export in the oligotrophic ocean

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

The changing face of pathogen discovery and surveillance

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

QIIME allows analysis of high-throughput community sequencing data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

UPARSE: highly accurate OTU sequences from microbial amplicon reads

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Actionable sequence data on infectious diseases in the clinical workplace

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Dynamics and associations of microbial community types across the human body

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Waste not, want not: why rarefying microbiome data is inadmissible

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Genomic variation landscape of the human gut microbiome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Evaluation of methods for the extraction and purification of DNA from the human microbiome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Pre-PCR processing: strategies to generate PCR-compatible samples

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5080404

Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.

29 September 2017

1 reference