Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture

An eDNA-qPCR assay to detect the presence of the parasiteSchistocephalus solidusinside its threespine stickleback host

(2018) Chloé Suzanne Berger et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

(2018) Iliana Bista et al.   Molecular Ecology Resources

PCR Technologies for Point of Care Testing: Progress and Perspectives

(2017) Salvatore Petralia et al.   ACS Sensors

Trends during development of Scottish salmon farming: An example of sustainable intensification?

(2016) Tim Ellis et al.   AQUACULTURE

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish

(2016) Lauren M. Sassoubre et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

(2016) Tae-Ho Yoon et al.   PeerJ

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

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

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

A longitudinal study of amoebic gill disease on a marine Atlantic salmon farm utilising a real-time PCR assay for the detection of Neoparamoeba perurans

(2015) JK Downes et al.   Aquaculture Environment Interactions

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

(2015) Dáithí C. Murray et al.   PLoS One

Determining Microeukaryotic Plankton Community around Xiamen Island, Southeast China, Using Illumina MiSeq and PCR-DGGE Techniques

(2015) Lingyu Yu et al.   PLoS One

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantifying Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms

(2014) Lucas M. Nathan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

Estimating costs of sea lice control strategy in Norway

(2014) Yajie Liu et al.   PREVENTIVE VETERINARY MEDICINE

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Salmon lice - impact on wild salmonids and salmon aquaculture

(2013) O Torrissen et al.   JOURNAL OF FISH DISEASES

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

(2013) SA Wood et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

(2013) Alexander Eiler et al.   PLoS One

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

(2013) Alexandra A-T. Weber et al.   PLoS One

Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments

(2013) Andrew R. Mahon et al.   PLoS One

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

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

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

(2013) Zachary H. Olson et al.   WILDLIFE RESEARCH

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Toxic marine microalgae and shellfish poisoning in the British isles: history, review of epidemiology, and future implications

(2011) Stephanie L Hinder et al.   Environmental Health

Incorporating molecular tools into routine HAB monitoring programs: Using qPCR to track invasive Prymnesium

(2011) Richard M. Zamor et al.   HARMFUL ALGAE

Monitoring endangered freshwater biodiversity using environmental DNA

(2011) PHILIP FRANCIS THOMSEN et al.   MOLECULAR ECOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prymnesins: Toxic Metabolites of the Golden Alga, Prymnesium parvum Carter (Haptophyta)

(2010) Schonna R. Manning et al.   Marine Drugs

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Development of a diagnostic PCR to detect Neoparamoeba perurans, agent of amoebic gill disease

(2008) N D Young et al.   JOURNAL OF FISH DISEASES