Metabarcoding reveals hidden species and improves identification of marine zooplankton communities in the North Sea

Marine clade sensitivities to climate change conform across timescales

(2020) Carl J. Reddin et al.   Nature Climate Change

Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator

(2019) E. L. Carroll et al.   Scientific Reports

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

(2019) Henrik Krehenwinkel et al.   GigaScience

Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

(2019) Tina E. Berry et al.   PLoS Genetics

Metabarcoding a Diverse Arthropod Mock Community

(2019) Thomas W. A. Braukmann et al.   Molecular Ecology Resources

Time-series metabarcoding analysis of zooplankton diversity of the NW Atlantic continental shelf

(2019) Ann Bucklin et al.   ICES JOURNAL OF MARINE SCIENCE

A rapid eDNA method for detecting white sharks in the open ocean

(2019) Nathan K. Truelove et al.   Methods in Ecology and Evolution

LifeWatch observatory data: Zooplankton observations in the Belgian part of the North Sea

(2019) Jonas Mortelmans et al.   Geoscience Data Journal

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

(2019) Joeselle M. Serrana et al.   ECOLOGICAL INDICATORS

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

(2019) Alexander M Piper et al.   GigaScience

Global Trends in Marine Plankton Diversity across Kingdoms of Life

(2019) Federico M. Ibarbalz et al.   CELL

Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community

(2019) Ilias Semmouri et al.   MARINE ENVIRONMENTAL RESEARCH

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

A Sequel to Sanger: amplicon sequencing that scales

(2018) Paul D. N. Hebert et al.   BMC GENOMICS

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

(2018) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

A MinION™-based pipeline for fast and cost-effective DNA barcoding

(2018) Amrita Srivathsan et al.   Molecular Ecology Resources

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

(2018) Aaron Pomerantz et al.   GigaScience

Distribution of the invasive calanoid copepod Pseudodiaptomus marinus (Sato, 1913) in the Belgian part of the North Sea

(2018) Yana Deschutter et al.   BioInvasions Records

Zooplankton monitoring to contribute towards addressing global biodiversity conservation challenges

(2018) Sanae Chiba et al.   JOURNAL OF PLANKTON RESEARCH

Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

(2017) Robert G. Young et al.   GENOME

Relative contribution of multiple stressors on copepod density and diversity dynamics in the Belgian part of the North Sea

(2017) Yana Deschutter et al.   MARINE POLLUTION BULLETIN

Indigenous species barcode database improves the identification of zooplankton

(2017) Jianghua Yang et al.   PLoS One

On site DNA barcoding by nanopore sequencing

(2017) Michele Menegon et al.   PLoS One

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

(2017) Alfonso Benítez-Páez et al.   GigaScience

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports

(2016) Frédéric J. J. Chain et al.   DIVERSITY AND DISTRIBUTIONS

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

(2016) Ann Bucklin et al.   JOURNAL OF PLANKTON RESEARCH

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2

(2016) Jana Batovska et al.   G3-Genes Genomes Genetics

Distribution of dominant zooplankton species along a latitudinal gradient in China sea during spring

(2016) Jiayi Xu et al.   Journal of Ocean University of China

Role of DNA barcoding in marine biodiversity assessment and conservation: An update

(2016) Subrata Trivedi et al.   SAUDI JOURNAL OF BIOLOGICAL SCIENCES

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

How will the ‘molecular revolution’ contribute to biological recording?

(2015) Lori Lawson Handley   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Automated identification of copepods using digital image processing and artificial neural network

(2015) Lee Kien Leow et al.   BMC BIOINFORMATICS

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

(2015) G.-J. Brandon-Mong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

The ecology of environmental DNA and implications for conservation genetics

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

Next generation sequencing and its applications in forensic genetics

(2015) Claus Børsting et al.   Forensic Science International-Genetics

Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

(2015) Austen C. Thomas et al.   Molecular Ecology Resources

Looking back on a decade of barcoding crustaceans

(2015) Michael J. Raupach et al.   ZooKeys

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing

(2015) Adam D. Hargreaves et al.   PeerJ

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

(2015) Shu Wu et al.   PLoS One

Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea

(2015) John K. Pearman et al.   PLoS One

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

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

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

(2014) Kenan Hadziavdic et al.   PLoS One

Estimation of Density-Dependent Mortality of Juvenile Bivalves in the Wadden Sea

(2014) Henrike Andresen et al.   PLoS One

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

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

The mesozooplankton community of the Belgian shelf (North Sea)

(2013) Karl Van Ginderdeuren et al.   JOURNAL OF SEA RESEARCH

Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences

(2013) S. Laakmann et al.   Molecular Ecology Resources

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar 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

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque 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

Potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of freshwater zooplankton: a pilot study with three Eudiaptomus (Copepoda: Diaptomidae) species

(2012) Nicoletta Riccardi et al.   JOURNAL OF PLANKTON RESEARCH

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

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

Multi-Gene Analysis Reveals a Lack of Genetic Divergence between Calanus agulhensis and C. sinicus (Copepoda; Calanoida)

(2012) Robert Kozol 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

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Molecular phylogeny of the Calanoida (Crustacea: Copepoda)

(2011) Leocadio Blanco-Bercial et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

DNA Barcoding of Marine Metazoa

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

Dissimilarity of Species and Forms of Planktonic Neocalanus Copepods Using Mitochondrial COI, 12S, Nuclear ITS, and 28S Gene Sequences

(2010) Ryuji J. Machida et al.   PLoS One

Express barcodes: racing from specimen to identification

(2009) NATALIA V. IVANOVA et al.   Molecular Ecology Resources

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

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

(2008) Danwei Huang et al.   JOURNAL OF MOLECULAR EVOLUTION

“compositions”: A unified R package to analyze compositional data

(2007) K. Gerald van den Boogaart et al.   COMPUTERS & GEOSCIENCES