Reproducible protocols for metagenomic analysis of human faecal phageomes. (Q52327730)

http://europepmc.org/abstract/PMC/5892011

15 June 2018

title

Reproducible protocols for metagenomic analysis of human faecal phageomes. (English)

1 reference

http://europepmc.org/abstract/PMC/5892011

15 June 2018

1 reference

1 reference

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1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Feargal J Ryan

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Stephen R Stockdale

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Marion Dalmasso

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Reynolds Paul Ross

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Colin Hill

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

author name string

Lorraine A Draper

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Amanda Forde

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Karen M Daly

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Siobhan A McDonnell

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

James A Nolan

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Thomas D S Sutton

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Angela McCann

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

publication date

10 April 2018

1 reference

http://europepmc.org/abstract/PMC/5892011

15 June 2018

published in

Microbiome

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

volume

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

page(s)

68

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

10 June 2020

copyright license

start time

10 April 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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=5892011

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

DESeq2

object named as

DESeq2

1 reference

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

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Normalization and microbial differential abundance strategies depend upon data characteristics

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16 June 2018

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16 June 2018

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16 June 2018

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16 June 2018

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Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

16 June 2018

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Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.

16 June 2018

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The human gut microbiome in health: establishment and resilience of microbiota over a lifetime

16 June 2018

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Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

16 June 2018

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Hyperexpansion of RNA Bacteriophage Diversity

16 June 2018

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Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

16 June 2018

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Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

16 June 2018

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Sample storage conditions significantly influence faecal microbiome profiles.

16 June 2018

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Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

16 June 2018

1 reference

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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

16 June 2018

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SPINGO: a rapid species-classifier for microbial amplicon sequences

16 June 2018

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Early life dynamics of the human gut virome and bacterial microbiome in infants.

16 June 2018

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Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

16 June 2018

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Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool

16 June 2018

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16 June 2018

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The virome in host health and disease

16 June 2018

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Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria

16 June 2018

1 reference

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The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations.

16 June 2018

1 reference

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Disease-specific alterations in the enteric virome in inflammatory bowel disease

16 June 2018

1 reference

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Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

16 June 2018

1 reference

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Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond

16 June 2018

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Temporal variability is a personalized feature of the human microbiome

16 June 2018

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

16 June 2018

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Characterization of virus-like particles associated with the human faecal and caecal microbiota

16 June 2018

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16 June 2018

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A large spectrum of alpha and beta papillomaviruses are detected in human stool samples

16 June 2018

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A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

16 June 2018

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The first 1000 cultured species of the human gastrointestinal microbiota.

16 June 2018

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Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

16 June 2018

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Trimmomatic: a flexible trimmer for Illumina sequence data

16 June 2018

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Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.

16 June 2018

1 reference

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

16 June 2018

1 reference

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Rapid evolution of the human gut virome

16 June 2018

1 reference

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Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach.

16 June 2018

1 reference

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Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

16 June 2018

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Bacteriophage adhering to mucus provide a non-host-derived immunity.

16 June 2018

1 reference

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Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13.

16 June 2018

1 reference

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Identification of viral pathogen diversity in sewage sludge by metagenome analysis

16 June 2018

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16 June 2018

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16 June 2018

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Storage conditions of intestinal microbiota matter in metagenomic analysis

16 June 2018

1 reference

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Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads

16 June 2018

1 reference

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Sequence analysis of the human virome in febrile and afebrile children

16 June 2018

1 reference

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High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature

16 June 2018

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The human microbiome: at the interface of health and disease

16 June 2018

1 reference

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Fast gapped-read alignment with Bowtie 2

16 June 2018

1 reference

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Diversity and abundance of single-stranded DNA viruses in human feces.

16 June 2018

1 reference

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Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses

16 June 2018

1 reference

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The human gut virome: inter-individual variation and dynamic response to diet

16 June 2018

1 reference

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Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions

16 June 2018

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Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes

16 June 2018

1 reference

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Enterotypes of the human gut microbiome

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

16 June 2018

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Viruses in the faecal microbiota of monozygotic twins and their mothers

16 June 2018

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A human gut microbial gene catalogue established by metagenomic sequencing

16 June 2018

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

16 June 2018

1 reference

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FastTree: computing large minimum evolution trees with profiles instead of a distance matrix

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Viral diversity and dynamics in an infant gut.

16 June 2018

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Metagenomic analysis of the human distal gut microbiome

16 June 2018

1 reference

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RNA viral community in human feces: prevalence of plant pathogenic viruses

16 June 2018

1 reference

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Diversity of the human intestinal microbial flora

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

cpnDB: a chaperonin sequence database

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Metagenomic analyses of an uncultured viral community from human feces

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Effect of multiple freeze-thaw cycles on hepatitis B virus DNA and hepatitis C virus RNA quantification as measured with branched-DNA technology

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Pepper (Capsicum annuum) Is a Dead-End Host for Tomato yellow leaf curl virus

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5892011

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

13 August 2018

1 reference

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10.1186/S40168-018-0446-Z

30 November 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

10 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29631623%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

PubMed publication ID

29631623

1 reference