Sequencing our way towards understanding global eukaryotic biodiversity (Q28730952)

5

0 references

J Gregory Caporaso

4

object named as

J Gregory Caporaso

0 references

Simon Creer

3

object named as

Simon Creer

0 references

author name string

Dorota L Porazinska

2

0 references

W Kelley Thomas

Trends in Ecology & Evolution

6

0 references

language of work or name

English

0 references

publication date

April 2012

0 references

published in

0 references

volume

27

0 references

page(s)

233-43

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issue

4

0 references

cites work

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

17 March 2017

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A core gut microbiome in obese and lean twins

17 March 2017

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

17 March 2017

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Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss

17 March 2017

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Integration of biological networks and gene expression data using Cytoscape

17 March 2017

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

17 March 2017

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CAMERA: a community resource for metagenomics

17 March 2017

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Microbial diversity in the deep sea and the underexplored "rare biosphere"

17 March 2017

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Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway)

17 March 2017

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A molecular view of microbial diversity and the biosphere

17 March 2017

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Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago

17 March 2017

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UCHIME improves sensitivity and speed of chimera detection

23 March 2017

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Search and clustering orders of magnitude faster than BLAST

7 April 2017

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

7 April 2017

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

7 April 2017

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

7 April 2017

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

7 April 2017

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

7 April 2017

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Accuracy and quality of massively parallel DNA pyrosequencing

7 April 2017

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Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison

7 April 2017

1 reference

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Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

20 June 2018

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TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

20 June 2018

1 reference

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Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi

20 June 2018

1 reference

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

20 June 2018

1 reference

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Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Discovery of novel intermediate forms redefines the fungal tree of life

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Global sequencing: a review of current molecular data and new methods available to assess microbial diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Eukaryotic richness in the abyss: insights from pyrotag sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Second-generation environmental sequencing unmasks marine metazoan biodiversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

UniFrac: an effective distance metric for microbial community comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Diversity of 16S rRNA genes within individual prokaryotic genomes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Polymerase chain reaction primers miss half of rRNA microbial diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Accurate determination of microbial diversity from 454 pyrosequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

GenGIS: A geospatial information system for genomic data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

A comparative analysis of microscopy and PCR-based detection methods for blood parasites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Microbial population structures in the deep marine biosphere

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

The influence of biotic interactions on soil biodiversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Lateral gene transfer in eukaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Molecular drive: a cohesive mode of species evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Aligning short reads to reference alignments and trees.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Reducing chimera formation during PCR amplification to ensure accurate genotyping.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Assessment of bias associated with incomplete extraction of microbial DNA from soil.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Extracellular DNA plays a key role in deep-sea ecosystem functioning

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

The correlation between rDNA copy number and genome size in eukaryotes.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3311718

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

27 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.TREE.2011.11.010

Systems Biology for Ecology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TREE.2011.11.010

Universal primer cocktails for fish DNA barcoding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TREE.2011.11.010

Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TREE.2011.11.010

Theoretical Considerations of Lifecycle Modeling: An Analysis of the Dryad Repository Demonstrating Automatic Metadata Propagation, Inheritance, and Value System Adoption

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TREE.2011.11.010

10.1016/J.TREE.2011.11.010

7 January 2021

Identifiers

DOI

1 reference

416754

416754

1 reference

1 reference

1 reference