Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities

(2015) C Sun et al.   Aquatic Biology

DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens

(2015) Thierry Comtet et al.   BIOLOGICAL INVASIONS

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

Next generation sequencing for characterizing biodiversity: promises and challenges

(2015) François Pompanon et al.   GENETICA

Ascidians as models for studying invasion success

(2015) Aibin Zhan et al.   MARINE BIOLOGY

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

Metabarcoding approach for the ballast water surveillance – An advantageous solution or an awkward challenge?

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast

(2015) Jorge Lobo et al.   Molecular Ecology Resources

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

(2014) Aibin Zhan et al.   CONSERVATION GENETICS

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

(2014) Amrita Srivathsan et al.   Molecular Ecology Resources

Influence of Artifact Removal on Rare Species Recovery in Natural Complex Communities Using High-Throughput Sequencing

(2014) Aibin Zhan et al.   PLoS One

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities

(2014) Aibin Zhan et al.   Methods in Ecology and Evolution

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi

(2013) Otso Ovaskainen et al.   ISME Journal

Arctic root-associated fungal community composition reflects environmental filtering

(2013) Rakel Blaalid et al.   MOLECULAR ECOLOGY

Low host specificity of root-associated fungi at an Arctic site

(2013) Synnøve Botnen et al.   MOLECULAR ECOLOGY

DNA barcoding commercially important fish species of Turkey

(2013) Emre Keskİn et al.   Molecular Ecology Resources

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

Introduction and use of non-native species for aquaculture in China: status, risks and management solutions

(2013) Yaping Lin et al.   Reviews in Aquaculture

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

(2013) Shanlin Liu et al.   Methods in Ecology and Evolution

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

(2012) DAVID M. LODGE et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

(2012) Robin van Velzen et al.   PLoS One

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences

(2012) Ryuji J. Machida et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

(2011) John A. Darling et al.   ENVIRONMENTAL RESEARCH

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

(2011) SANNE BOESSENKOOL et al.   MOLECULAR ECOLOGY

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Molecular Detection of Invasive Species in Heterogeneous Mixtures Using a Microfluidic Carbon Nanotube Platform

(2011) Andrew R. Mahon et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs

(2010) Elizabeta Briski et al.   BIOLOGICAL INVASIONS

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

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

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

A pound of prevention, plus a pound of cure: Early detection and eradication of invasive species in the Laurentian Great Lakes

(2010) M. Jake Vander Zanden et al.   JOURNAL OF GREAT LAKES RESEARCH

Experimental parameters affecting quantitative PCR ofArtemia franciscana: a model for a marine zooplanktonic target in natural plankton samples

(2010) Joshua A. Mackie et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

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

(2010) SIMON CREER   MOLECULAR ECOLOGY

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Detection of a colonizing, aquatic, non-indigenous species

(2009) Chad T. Harvey et al.   DIVERSITY AND DISTRIBUTIONS

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

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

(2008) Hege Vestheim et al.   Frontiers in Zoology