(Q35631582)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

title

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

high-throughput sequencing

8 March 2020

main subject

1 reference

1 reference

Zewei Song

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Dan Schlatter

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Peter Kennedy

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Nhu Nguyen

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

Scott T Bates

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

language of work or name

English

0 references

publication date

14 May 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

page(s)

e0127234

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons CC0 License

8 March 2020

copyright license

start time

14 May 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

describes a project that uses

ggplot2

object named as

ggplot2

2 references

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4431839

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

cites work

Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Endemism and functional convergence across the North American soil mycobiome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Trimmomatic: a flexible trimmer for Illumina sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Soil biodiversity and soil community composition determine ecosystem multifunctionality

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Fungi at a small scale: spatial zonation of fungal assemblages around single trees

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Towards a unified paradigm for sequence-based identification of fungi

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Direct Detection of Cylindrocarpon destructans, Root Rot Pathogen of Ginseng by Nested PCR from Soil Samples

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Digging the New York City Skyline: soil fungal communities in green roofs and city parks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Unlocking the potential of metagenomics through replicated experimental design

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Search and clustering orders of magnitude faster than BLAST

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Co-invasion by Pinus and its mycorrhizal fungi

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

QIIME allows analysis of high-throughput community sequencing data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

The microbial engines that drive Earth's biogeochemical cycles.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Automated and manual methods of DNA extraction for Aspergillus fumigatus and Rhizopus oryzae analyzed by quantitative real-time PCR

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Innovative methods for soil DNA purification tested in soils with widely differing characteristics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Toward an ecological classification of soil bacteria.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

What is the extent of prokaryotic diversity?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

DNA extraction from soils: old bias for new microbial diversity analysis methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Inhibition and facilitation of nucleic acid amplification

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Parsing ecological signal from noise in next generation amplicon sequencing.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Commercial DNA extraction kits impact observed microbial community composition in permafrost 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=4431839

Development of an efficient fungal DNA extraction method to be used in random amplified polymorphic DNA-PCR analysis to differentiate cyclopiazonic acid mold producers

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

DNA extraction method affects microbial community profiles from soils and sediment.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4431839

Elevated CO2 stimulates grassland soil respiration by increasing carbon inputs rather than by enhancing soil moisture

25 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0127234

Antagonistic effects of species on C respiration and net N mineralization in soils from mixed coniferous plantations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0127234

Cutadapt removes adapter sequences from high-throughput sequencing reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0127234

Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0127234

Insidious effects of sequencing errors on perceived diversity in molecular surveys

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25974078

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0127234

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json

8 March 2020

PubMed publication ID

25974078

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25974078%20AND%20SRC:MED&resulttype=core&format=json