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An introduction to the analysis of shotgun metagenomic data
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title
An introduction to the analysis of shotgun metagenomic data
(English)
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main subject
metagenomics
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author name string
Thomas J. Sharpton
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1
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English
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publication date
2014
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published in
Frontiers in Plant Science
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volume
5
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page(s)
209
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PubMed
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Horizontal gene exchange in environmental microbiota
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Metagenomic biomarker discovery and explanation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Meta-IDBA: a de Novo assembler for metagenomic data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
The human gut microbiome: ecology and recent evolutionary changes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Illumina-based analysis of microbial community diversity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
CoMet--a web server for comparative functional profiling of metagenomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Metagenomics and the protein universe
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Combining gene prediction methods to improve metagenomic gene annotation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Metagenomic analyses: past and future trends
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
FragGeneScan: predicting genes in short and error-prone reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Polymerase chain reaction primers miss half of rRNA microbial diversity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Plant-rhizobacteria interactions alleviate abiotic stress conditions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Rhizosphere bacteria help plants tolerate abiotic stress.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
A bioinformatician's guide to metagenomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Global patterns in bacterial diversity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Accurate phylogenetic classification of variable-length DNA fragments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Symbiosis insights through metagenomic analysis of a microbial consortium
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Colonization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Marine microorganisms and global nutrient cycles
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Molecular mechanisms of defense by rhizobacteria against root disease
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
Identifying microbial diversity in the natural environment: a molecular phylogenetic approach.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 September 2017
PhyloSift: phylogenetic analysis of genomes and metagenomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
The automatic annotation of bacterial genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
Individual genome assembly from complex community short-read metagenomic datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
Taxonomic metagenome sequence assignment with structured output models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
Metagenome fragment classification using N-mer frequency profiles
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
Orphelia: predicting genes in metagenomic sequencing reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
31 May 2018
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Advances in computational analysis of metagenome sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Genovo: de novo assembly for metagenomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Suppression subtractive hybridisation allows selective sampling of metagenomic subsets of interest.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Mixtures of plant growth-promoting rhizobacteria enhance biological control of multiple cucumber pathogens
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059276
retrieved
28 November 2018
Enrichment for microbes living in association with plant tissues
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24982662
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Thermotolerance generated by plant/fungal symbiosis
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24982662
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.3389/FPLS.2014.00209
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
564972
OpenCitations bibliographic resource ID
564972
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
564972
PMC publication ID
4059276
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
564972
PubMed publication ID
24982662
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
564972
ResearchGate publication ID
263585285
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