Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

Author Correction: DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient

(2018) Caroline E. Emilson et al.   Scientific Reports

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

DNA metabarcoding reveals the complex and hidden responses of chironomids to multiple stressors

(2018) Arne J. Beermann et al.   Environmental Sciences Europe

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results

(2017) J. Vierna et al.   GENOME

A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

(2017) M. E. Carew et al.   MARINE AND FRESHWATER RESEARCH

Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

(2017) Iliana Bista et al.   Nature Communications

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

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

(2017) Matthieu Leray et al.   PeerJ

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

(2017) Satoshi Yamamoto et al.   Scientific Reports

Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

(2016) Vasco Elbrecht et al.   PeerJ

Open-Source Sequence Clustering Methods Improve the State Of the Art

(2016) Evguenia Kopylova et al.   mSystems

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

(2015) Liyou Wu et al.   BMC MICROBIOLOGY

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

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

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Recognizing false positives: synthetic oligonucleotide controls for environmental DNA surveillance

(2015) Chris C. Wilson et al.   Methods in Ecology and Evolution

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

(2015) Anja Lange 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

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

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

Stream biomonitoring using macroinvertebrates around the globe: a comparison of large-scale programs

(2014) Daniel F. Buss et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Does DNA barcoding improve performance of traditional stream bioassessment metrics?

(2014) Eric D. Stein et al.   Freshwater Science

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

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

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

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

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

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

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

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?

(2011) Bernard W. Sweeney et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results

(2010) Peter Haase et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Global threats to human water security and river biodiversity

(2010) C. J. Vörösmarty et al.   NATURE

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS