(Q35693671)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

Søren M Karst

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

Rasmus H Kirkegaard

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

Per Halkjær Nielsen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

author name string

Anja S Ziegler

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

language of work or name

English

0 references

publication date

16 July 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

page(s)

e0132783

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

19 February 2020

copyright license

start time

16 July 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ggplot2

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4504704

ggplot2

2 references

10 June 2022

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

RStudio

1 reference

18 June 2022

https://europepmc.org/article/PMC/4504704

based on heuristic

inferred from PubMed Central ID database lookup

phyloseq

phyloseq

1 reference

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

dplyr

dplyr

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

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

1 reference

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Dead or alive: molecular assessment of microbial viability

27 July 2018

1 reference

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Evaluating bias of illumina-based bacterial 16S rRNA gene profiles

27 July 2018

1 reference

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A hundred years of activated sludge: time for a rethink

27 July 2018

1 reference

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Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment

27 July 2018

1 reference

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

27 July 2018

1 reference

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

27 July 2018

1 reference

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Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Evaluation of 16S rDNA-based community profiling for human microbiome research

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Fast gapped-read alignment with Bowtie 2

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

FLASH: fast length adjustment of short reads to improve genome assemblies

27 July 2018

1 reference

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A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Extracting nucleic acids from activated sludge which reflect community population diversity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Efficient recovery of environmental DNA for expression cloning by indirect extraction methods

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

MiDAS: the field guide to the microbes of activated sludge.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

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

25 September 2018

1 reference

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Microbial communities involved in enhanced biological phosphorus removal from wastewater--a model system in environmental biotechnology

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

QIIME allows analysis of high-throughput community sequencing data

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Purification of total DNA extracted from activated sludge

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Characterization of the loosely attached fraction of activated sludge bacteria

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

A novel approach for extraction of PCR-compatible DNA from activated sludge samples collected from different biological effluent treatment plants

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504704

DNA extraction from activated sludges

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26182345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Eikelboom's morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26182345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0132783

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json

19 February 2020

PubMed publication ID

26182345

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26182345%20AND%20SRC:MED&resulttype=core&format=json