Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches

The risks of using molecular biodiversity data for incidental detection of species of concern

(2020) John A. Darling et al.   DIVERSITY AND DISTRIBUTIONS

Have the cake and eat it: Optimising non‐destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

(2019) Filipa M.S. Martins et al.   Molecular Ecology Resources

SPIKEPIPE : A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes

(2019) Yinqiu Ji et al.   Molecular Ecology Resources

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

(2019) Alexander M Piper et al.   GigaScience

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Non‐destructive DNA extractions from fly larvae (Diptera: Muscidae) enable molecular identification of species and enhance morphological features

(2019) Francesco Martoni et al.   Austral Entomology

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

(2018) Laura E. MacConaill et al.   BMC GENOMICS

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

(2018) Josep Piñol et al.   MOLECULAR ECOLOGY

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

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

(2018) Iliana Bista et al.   Molecular Ecology Resources

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

(2018) Maxime Galan et al.   Molecular Ecology Resources

Capture enrichment of aquatic environmental DNA: A first proof of concept

(2018) Taylor M. Wilcox et al.   Molecular Ecology Resources

Computational correction of index switching in multiplexed sequencing libraries

(2018) Anton J M Larsson et al.   NATURE METHODS

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

Taxonomy annotation and guide tree errors in 16S rRNA databases

(2018) Robert Edgar   PeerJ

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?

(2018) Melissa E. Carew et al.   PeerJ

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

(2018) Yi-Chun Yeh et al.   mSystems

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

(2018) Daniel Marquina et al.   Molecular Ecology Resources

DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method

(2018) Vera M A Zizka et al.   GENOME

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

(2018) Leho Tedersoo et al.   Molecular Ecology Resources

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

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

The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA

(2017) Joanna R. Freeland   GENOME

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

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Effective mosquito and arbovirus surveillance using metabarcoding

(2017) J. Batovska et al.   Molecular Ecology Resources

Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication

(2017) Ancuta Cristina Raclariu et al.   PHYTOCHEMICAL ANALYSIS

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

(2017) Henrik Krehenwinkel et al.   Scientific Reports

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples

(2017) Alfred J. Arulandhu et al.   GigaScience

Advances in DNA metabarcoding for food and wildlife forensic species identification

(2016) Martijn Staats et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Eradication of Invading Insect Populations: From Concepts to Applications

(2016) Andrew M. Liebhold et al.   Annual Review of Entomology

Active and passive environmental DNA surveillance of aquatic invasive species

(2016) Megan Simmons et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

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

A quantitative protocol for DNA metabarcoding of springtails (Collembola)

(2016) Seikoh Saitoh et al.   GENOME

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

(2016) Muhammad Ashfaq et al.   GENOME

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

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

Strategies to improve usability and preserve accuracy in biological sequence databases

(2016) Johan Bengtsson-Palme et al.   PROTEOMICS

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

(2015) Thierry Comtet et al.   BIOLOGICAL INVASIONS

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

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

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

Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

(2015) Eddy J. Dowle et al.   Molecular Ecology Resources

Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis

(2015) Shanlin Liu et al.   Molecular Ecology Resources

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

Effect of Propylene Glycol Concentration on Mid-Term DNA Preservation of Coleoptera

(2014) Michael L. Ferro et al.   COLEOPTERISTS BULLETIN

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Rapid and accurate taxonomic classification of insect (class Insecta) cytochromecoxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

(2014) Teresita M. Porter et al.   Molecular Ecology Resources

Description of a robust interception trap for collecting airborne arthropods in climatically challenging regions

(2013) Roger Farrow et al.   ANTARCTIC SCIENCE

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

Assessing DNA Barcoding as a Tool for Species Identification and Data Quality Control

(2013) Yong-Yi Shen 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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Optimal surveillance and eradication of invasive species in heterogeneous landscapes

(2012) Rebecca S. Epanchin-Niell et al.   ECOLOGY LETTERS

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

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Two new species ofAcizziaCrawford (Hemiptera: Psyllidae) from the Solanaceae with a potential new economic pest of eggplant,Solanum melongena

(2010) Deborah Kent et al.   AUSTRALIAN JOURNAL OF ENTOMOLOGY

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH