Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

eDNA metabarcoding as a biomonitoring tool for marine protected areas

(2021) Zachary Gold et al.   PLoS One

Natal origin of Pacific bluefin tuna from the California Current Large Marine Ecosystem

(2020) R. J. David Wells et al.   Biology Letters

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

(2020) Tamara Schenekar et al.   RIVER RESEARCH AND APPLICATIONS

Habitat compression and ecosystem shifts as potential links between marine heatwave and record whale entanglements

(2020) Jarrod A. Santora et al.   Nature Communications

Environmental DNA reveals seasonal shifts and potential interactions in a marine community

(2020) Anni Djurhuus et al.   Nature Communications

Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities

(2020) Elena M. Duke et al.   Ecology and Evolution

Unusual occurrences of fishes in the Southern California Current System during the warm water period of 2014–2018

(2020) H.J. Walker et al.   ESTUARINE COASTAL AND SHELF SCIENCE

The COVID-19 pandemic and research shutdown: staying safe and productive

(2020) M. Bishr Omary et al.   JOURNAL OF CLINICAL INVESTIGATION

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding

(2020) Kathleen J. Pitz et al.   PLoS One

Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United States

(2020) Mark Y. Stoeckle et al.   Frontiers in Marine Science

Plastics in the Pacific: Assessing risk from ocean debris for marine birds in the California Current Large Marine Ecosystem

(2020) Thomas P. Good et al.   BIOLOGICAL CONSERVATION

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

(2020) Masaki Miya et al.   FISHERIES SCIENCE

Disease epidemic and a marine heat wave are associated with the continental-scale collapse of a pivotal predator (Pycnopodia helianthoides)

(2019) C. D. Harvell et al.   Science Advances

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments

(2019) Lara Macheriotou et al.   Ecology and Evolution

Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast

(2019) Diana S. Baetscher et al.   MOLECULAR ECOLOGY

Anacapa Toolkit : an environmental DNA toolkit for processing multilocus metabarcode datasets

(2019) Emily E. Curd et al.   Methods in Ecology and Evolution

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

(2019) Lisa G. Crozier et al.   PLoS One

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

Assessing drivers of rocky reef fish biomass density from the Southern California Bight

(2019) II Pondella DJ et al.   MARINE ECOLOGY PROGRESS SERIES

GenBank is a reliable resource for 21st century biodiversity research

(2019) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine heat wave and multiple stressors tip bull kelp forest to sea urchin barrens

(2019) L. Rogers-Bennett et al.   Scientific Reports

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding

(2018) Yukuto Sato et al.   MOLECULAR BIOLOGY AND EVOLUTION

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

(2018) Tristan Cordier et al.   Molecular Ecology Resources

A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data

(2018) Rodney T. Richardson et al.   PeerJ

Taxonomy annotation and guide tree errors in 16S rRNA databases

(2018) Robert Edgar   PeerJ

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Environmental DNA illuminates the dark diversity of sharks

(2018) Germain Boussarie et al.   Science Advances

A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator

(2018) Philip Heller et al.   Scientific Data

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Complete Mitochondrial Genomes of the Cherskii’s Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

(2017) Evgeniy S Balakirev et al.   Evolutionary Bioinformatics

Satellite sea surface temperatures along the West Coast of the United States during the 2014-2016 northeast Pacific marine heat wave

(2017) Chelle L. Gentemann et al.   GEOPHYSICAL RESEARCH LETTERS

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA

(2017) Toshiaki Jo et al.   Molecular Ecology Resources

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

(2017) Léa Siegwald et al.   PLoS One

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

(2017) Iliana Bista et al.   Nature Communications

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Defining ecosystem thresholds for human activities and environmental pressures in the California Current

(2017) Jameal F. Samhouri et al.   Ecosphere

Spatial distribution of environmental DNA in a nearshore marine habitat

(2017) James L. O’Donnell et al.   PeerJ

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

Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area

(2017) Andrew R. Thompson et al.   Royal Society Open Science

Historical ecology and the conservation of large, hermaphroditic fishes in Pacific Coast kelp forest ecosystems

(2017) Todd J. Braje et al.   Science Advances

The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia

(2017) Emma Ransome et al.   PLoS One

Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes

(2017) Katy E. Klymus et al.   PLoS One

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

(2017) Satoshi Yamamoto et al.   Scientific Reports

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

(2016) Alexey M. Kozlov et al.   NUCLEIC ACIDS RESEARCH

Misannotation Awareness: A Tale of Two Gene-Groups

(2016) Tania Nobre et al.   Frontiers in Plant Science

Productivity and biomass of fishes in the California Current Large Marine Ecosystem: Comparison of fishery-dependent and -independent time series

(2016) J. Anthony Koslow et al.   Environmental Development

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

(2016) Philip Francis Thomsen et al.   PLoS One

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

(2015) Jon G. Sanders et al.   Nature Communications

Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected areas

(2015) Jennifer E. Caselle et al.   Scientific Reports

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

(2015) M. Miya et al.   Royal Society Open Science

The Geography of Morphological Convergence in the Radiations of Pacific Sebastes Rockfishes

(2014) Travis Ingram et al.   AMERICAN NATURALIST

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Environmental DNA for wildlife biology and biodiversity monitoring

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

A multi-decade time series of kelp forest community structure at the California Channel Islands

(2013) David J. Kushner et al.   ECOLOGY

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

(2013) W. Iwasaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Applications of DNA barcoding to fish landings: authentication and diversity assessmente

(2013) Alba Ardura et al.   ZooKeys

Global imprint of climate change on marine life

(2013) Elvira S. Poloczanska et al.   Nature Climate Change

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

Towards next-generation biodiversity assessment using DNA metabarcoding

(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

The Effect of Geographical Scale of Sampling on DNA Barcoding

(2012) J. Bergsten et al.   SYSTEMATIC BIOLOGY

Moorea BIOCODE barcode library as a tool for understanding predator–prey interactions: insights into the diet of common predatory coral reef fishes

(2011) M. Leray et al.   CORAL REEFS

Tracking apex marine predator movements in a dynamic ocean

(2011) B. A. Block et al.   NATURE

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

Comparisons between mitochondrial genomes of domestic goat (Capra hircus) reveal the presence of numts and multiple sequencing errors

(2010) Alexandre Hassanin et al.   Mitochondrial DNA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The campaign to DNA barcode all fishes, FISH-BOL

(2009) R. D. Ward et al.   JOURNAL OF FISH BIOLOGY

Patterns and processes in the California Current System

(2009) David M. Checkley et al.   PROGRESS IN OCEANOGRAPHY

Mapping cumulative human impacts to California Current marine ecosystems

(2009) Benjamin S. Halpern et al.   Conservation Letters

Research Review of Collaborative Ecosystem-Based Management in the California Current Large Marine Ecosystem

(2008) Kary Coleman   COASTAL MANAGEMENT

Emergence of Anoxia in the California Current Large Marine Ecosystem

(2008) F. Chan et al.   SCIENCE