Experimental and analytical tools for studying the human microbiome (Q34241426)

31 July 2017

Experimental and analytical tools for studying the human microbiome (English)

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31 July 2017

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Rob Knight

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Dirk Gevers

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6

object named as

Dirk Gevers

1 reference

31 July 2017

Laura Wegener Parfrey

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4

object named as

Laura Wegener Parfrey

1 reference

31 July 2017

1

Justin Kuczynski

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31 July 2017

3

William A Walters

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31 July 2017

Christian L Lauber

2

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31 July 2017

José C Clemente

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5

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31 July 2017

language of work or name

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16 December 2011

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31 July 2017

Nature Reviews Genetics

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31 July 2017

13

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31 July 2017

47-58

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https://scigraph.springernature.com/pub.10.1038/nrg3129

31 July 2017

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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PhymmBL expanded: confidence scores, custom databases, parallelization and more

6 July 2018

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6 July 2018

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Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads

6 July 2018

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Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

6 July 2018

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6 July 2018

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Host-associated and free-living phage communities differ profoundly in phylogenetic composition

6 July 2018

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PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

6 July 2018

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Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

6 July 2018

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Microbial metagenomics: beyond the genome

6 July 2018

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The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

6 July 2018

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6 July 2018

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PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

6 July 2018

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Removing noise from pyrosequenced amplicons

6 July 2018

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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

6 July 2018

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Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

6 July 2018

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High-quality draft assemblies of mammalian genomes from massively parallel sequence data

6 July 2018

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Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products

6 July 2018

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6 July 2018

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BIPES, a cost-effective high-throughput method for assessing microbial diversity.

6 July 2018

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SmashCommunity: a metagenomic annotation and analysis tool

6 July 2018

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Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

6 July 2018

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Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

6 July 2018

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Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

6 July 2018

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Deep sequencing of the vaginal microbiota of women with HIV.

6 July 2018

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Unlocking short read sequencing for metagenomics

6 July 2018

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Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

6 July 2018

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Succession of microbial consortia in the developing infant gut microbiome

6 July 2018

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Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis

6 July 2018

1 reference

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Viruses in the faecal microbiota of monozygotic twins and their mothers

6 July 2018

1 reference

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The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

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

6 July 2018

1 reference

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Prokaryotic and eukaryotic diversity of the human gut.

6 July 2018

1 reference

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Vaginal microbiome of reproductive-age women

6 July 2018

1 reference

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

6 July 2018

1 reference

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Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

6 July 2018

1 reference

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QIIME allows analysis of high-throughput community sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice

6 July 2018

1 reference

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Harnessing the power of the human microbiome

6 July 2018

1 reference

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FastTree 2--approximately maximum-likelihood trees for large alignments

6 July 2018

1 reference

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A human gut microbial gene catalogue established by metagenomic sequencing

6 July 2018

1 reference

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6 July 2018

A primer on metagenomics

1 reference

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Characterization of the oral fungal microbiome (mycobiome) in healthy individuals

6 July 2018

1 reference

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Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

PyNAST: a flexible tool for aligning sequences to a template alignment

6 July 2018

1 reference

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eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Bacterial community variation in human body habitats across space and time

6 July 2018

1 reference

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KEGG for representation and analysis of molecular networks involving diseases and drugs

6 July 2018

1 reference

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The NIH Human Microbiome Project

6 July 2018

1 reference

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Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

6 July 2018

1 reference

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Bacteriophages encode factors required for protection in a symbiotic mutualism

6 July 2018

1 reference

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ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Redefining chronic viral infection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

A core gut microbiome in obese and lean twins

6 July 2018

1 reference

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

6 July 2018

1 reference

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The influence of sex, handedness, and washing on the diversity of hand surface bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The rational exploration of microbial diversity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Fungi and inflammatory bowel diseases: Alterations of composition and diversity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Viral diversity and dynamics in an infant gut.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

A diversity profile of the human skin microbiota

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Microbial influences in inflammatory bowel diseases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The Pfam protein families database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The human microbiome project

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Accuracy and quality of massively parallel DNA pyrosequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Development of the human infant intestinal microbiota

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Metaproteomics: a new approach for studying functional microbial ecology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Molecular analysis of human forearm superficial skin bacterial biota

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

6 July 2018

1 reference

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A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

UniFrac: a new phylogenetic method for comparing microbial communities

6 July 2018

1 reference

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Bioinformatics for whole-genome shotgun sequencing of microbial communities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Obesity alters gut microbial ecology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Comparative metagenomics of microbial communities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Community structure and metabolism through reconstruction of microbial genomes from the environment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Evaluation of three different forward primers by terminal restriction fragment length polymorphism analysis for determination of fecal bifidobacterium spp. in healthy subjects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

The Uncultured Microbial Majority

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Recurrent Clostridium difficile colitis: case series involving 18 patients treated with donor stool administered via a nasogastric tube

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

Phylogenetic identification and in situ detection of individual microbial cells without cultivation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5119550

DNA microarray analysis of predominant human intestinal bacteria in fecal samples

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRG3129

Short pyrosequencing reads suffice for accurate microbial community analysis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRG3129

A comparison of five methods for extraction of bacterial DNA from human faecal samples

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRG3129

31 March 2020

Identifiers

DOI

10.1038/NRG3129

1 reference

Dimensions Publication ID

31 July 2017

0 references

1 reference

31 July 2017

1 reference