Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

(2017) Olivier Laroche et al.   PeerJ

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

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

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

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

(2015) Thierry Comtet et al.   BIOLOGICAL INVASIONS

The ecology of environmental DNA and implications for conservation genetics

(2015) Matthew A. Barnes et al.   CONSERVATION GENETICS

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

On the use of the serial dilution culture method to enumerate viable phytoplankton in natural communities of plankton subjected to ballast water treatment

(2015) John J. Cullen et al.   JOURNAL OF APPLIED PHYCOLOGY

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

(2015) X. Pochon et al.   MARINE POLLUTION BULLETIN

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

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity

(2015) Eric Capo et al.   MICROBIAL ECOLOGY

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library

(2015) Caryll Waugh et al.   Virology Journal

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

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

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

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

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

(2013) Xavier Pochon et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

Impacts of the invasive ascidian Didemnum vexillum on green-lipped mussel Perna canaliculus aquaculture in New Zealand

(2013) LM Fletcher et al.   Aquaculture Environment Interactions

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

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

The impact and control of biofouling in marine aquaculture: a review

(2012) Isla Fitridge et al.   BIOFOULING

Dead or alive? Viability assessment of micro- and mesoplankton

(2012) E.-M. Zetsche et al.   JOURNAL OF PLANKTON RESEARCH

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET 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

Biodiversity, evolution and adaptation of fungi in extreme environments

(2012) Laura Selbmann et al.   PLANT BIOSYSTEMS

Impacts of biological invasions: what's what and the way forward

(2012) Daniel Simberloff et al.   TRENDS IN ECOLOGY & EVOLUTION

The golden age of DNA metasystematics

(2012) Mehrdad Hajibabaei   TRENDS IN GENETICS

Resistance to UV-B induced DNA damage in extreme-tolerant cryptoendolithic Antarctic fungi: detection by PCR assays

(2011) Laura Selbmann et al.   Fungal Biology

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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Detection of a colonizing, aquatic, non-indigenous species

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

The spread of marine non-indigenous species via recreational boating: A conceptual model for risk assessment based on fault tree analysis

(2009) Hernando Acosta et al.   ECOLOGICAL MODELLING

Trade, transport and trouble: managing invasive species pathways in an era of globalization

(2009) Philip E. Hulme   JOURNAL OF APPLIED ECOLOGY

Macroalgal Introductions by Hull Fouling on Recreational Vessels: Seaweeds and Sailors

(2008) Frédéric Mineur et al.   ENVIRONMENTAL MANAGEMENT

Assessing the global threat of invasive species to marine biodiversity

(2008) Jennifer L Molnar et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY