Metagenomics - a guide from sampling to data analysis (Q21195892)

Dimensions

17 August 2022

2

Jack Gilbert

Jack

Gilbert

1 reference

Dimensions

17 August 2022

1

Torsten

Thomas

Torsten Thomas

1 reference

Dimensions

1015648092

Microbial informatics and experimentation

17 August 2022

language of work or name

English

0 references

publication date

2012

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published in

1 reference

Creative Commons Attribution 2.0 Generic

Crossref

volume

2

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issue

1

0 references

page(s)

3

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copyright license

start time

9 February 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

describes a project that uses

MIRA

object named as

MIRA

1 reference

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Environmental genome shotgun sequencing of the Sargasso Sea

19 March 2017

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Improved microbial gene identification with GLIMMER

19 March 2017

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Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

19 March 2017

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19 March 2017

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7 April 2017

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7 April 2017

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7 April 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Metagenomics and the protein universe

12 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Combining gene prediction methods to improve metagenomic gene annotation

12 September 2017

1 reference

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Metagenomic analyses: past and future trends

12 September 2017

1 reference

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12 September 2017

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12 September 2017

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Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

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12 September 2017

1 reference

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FragGeneScan: predicting genes in short and error-prone reads

12 September 2017

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12 September 2017

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12 September 2017

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Artificial and natural duplicates in pyrosequencing reads of metagenomic data

12 September 2017

1 reference

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Identifying and removing artificial replicates from 454 pyrosequencing data.

12 September 2017

1 reference

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Assembly algorithms for next-generation sequencing data

12 September 2017

1 reference

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Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Statistical methods for detecting differentially abundant features in clinical metagenomic samples

12 September 2017

1 reference

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Digital PCR provides sensitive and absolute calibration for high throughput sequencing

12 September 2017

1 reference

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Genomic DNA amplification by the multiple displacement amplification (MDA) method

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Short read DNA fragment anchoring algorithm

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Selective extraction of bacterial DNA from the surfaces of macroalgae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Binning sequences using very sparse labels within a metagenome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Metagenomics: read length matters

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

IMG/M: a data management and analysis system for metagenomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Accurate phylogenetic classification of variable-length DNA fragments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Metaproteomics: studying functional gene expression in microbial ecosystems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

12 September 2017

1 reference

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Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Orphelia: predicting genes in metagenomic sequencing reads

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Metagenomic comparison of direct and indirect soil DNA extraction approaches

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Bacterial carbon processing by generalist species in the coastal ocean.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Genome-wide experimental determination of barriers to horizontal gene transfer.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3351745

Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22587947

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Non-parametric multivariate analyses of changes in community structure

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F2042-5783-2-3

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1186/2042-5783-2-3

1 reference

171069

1015648092

0 references

171069

1 reference

1 reference

1 reference