Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species

(2018) Ryan Scott et al.   Evolutionary Applications

Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay

(2018) Yaisel J. Borrell et al.   JOURNAL FOR NATURE CONSERVATION

The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis

(2018) Ulla von Ammon et al.   MARINE ENVIRONMENTAL RESEARCH

Enhancing passive sampling tools for detecting marine bioinvasions

(2018) Leigh Tait et al.   MARINE POLLUTION BULLETIN

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

(2018) David López-Escardó et al.   Scientific Reports

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples

(2017) Susanna A. Wood et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs

(2017) Anett S. Trebitz et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Invasion Science: A Horizon Scan of Emerging Challenges and Opportunities

(2017) Anthony Ricciardi et al.   TRENDS IN ECOLOGY & EVOLUTION

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

(2017) Matthieu Leray et al.   PeerJ

Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples

(2017) Ryuji J. Machida et al.   Scientific Data

The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

(2017) Sophie Groendahl et al.   PLoS One

DNA in a bottle—Rapid metabarcoding survey for early alerts of invasive species in ports

(2017) Yaisel J. Borrell et al.   PLoS One

Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species

(2017) Chelsea Hatzenbuhler et al.   Scientific Reports

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

(2016) Anastasija Zaiko et al.   BIOFOULING

Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports

(2016) Emily A. Brown et al.   DIVERSITY AND DISTRIBUTIONS

Protist metabarcoding and environmental biomonitoring: Time for change

(2016) J. Pawlowski et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Survival of ship biofouling assemblages during and after voyages to the Canadian Arctic

(2016) Farrah T. Chan et al.   MARINE BIOLOGY

Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy

(2016) David Abad et al.   MARINE BIOLOGY

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

(2016) Wei Xiong et al.   MARINE BIOLOGY

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

(2015) Xavier Pochon et al.   BIOFOULING

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

(2015) Thierry Comtet et al.   BIOLOGICAL INVASIONS

MOLTOOLS: a workshop on “Molecular tools for monitoring marine invasive species”

(2015) John A. Darling et al.   BIOLOGICAL INVASIONS

Marine urbanization: an ecological framework for designing multifunctional artificial structures

(2015) Katherine A Dafforn et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes

(2015) O Berry et al.   MARINE ECOLOGY PROGRESS SERIES

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

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

(2015) Eddy J. Dowle et al.   Molecular Ecology Resources

A DNA Barcoding system integrating multigene sequence data

(2015) Douglas Chesters et al.   Methods in Ecology and Evolution

Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes

(2015) O Berry et al.   MARINE ECOLOGY PROGRESS SERIES

The Marine Biosecurity Porthole – a web-based information system on non-indigenous marine species in New Zealand

(2015) Kimberley Seaward et al.   Management of Biological Invasions

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

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

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

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

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

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

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Rarefaction and extrapolation of phylogenetic diversity

(2014) Anne Chao et al.   Methods in Ecology and Evolution

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

The risk of marine bioinvasion caused by global shipping

(2013) H. Seebens et al.   ECOLOGY LETTERS

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

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

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

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

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

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

DNA Barcoding of Marine Metazoa

(2010) Ann Bucklin et al.   Annual Review of Marine Science

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

(2008) Julio B.J. Harvey et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY