COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

Metabarcoding of storage ethanol vs. conventional morphometric identification in relation to the use of stream macroinvertebrates as ecological indicators in forest management

(2019) Maitane Erdozain et al.   ECOLOGICAL INDICATORS

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

(2019) G. A. C. Singer et al.   Scientific Reports

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

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

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter 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

Over 2.5 million COI sequences in GenBank and growing

(2018) Teresita M. Porter et al.   PLoS One

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

(2018) Sydney I. Glassman et al.   mSphere

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

(2017) Jorge Lobo et al.   Scientific Reports

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Connecting Earth observation to high-throughput biodiversity data

(2017) Alex Bush et al.   Nature Ecology & Evolution

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

(2017) Caroline E. Emilson et al.   Scientific Reports

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

Evaluating a multigene environmental DNA approach for biodiversity assessment

(2015) Alexei J. Drummond et al.   GigaScience

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

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

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

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Redesign of PCR primers for mitochondrial cytochromecoxidase subunit I for marine invertebrates and application in all-taxa biotic surveys

(2013) J. Geller et al.   Molecular Ecology Resources

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

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

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

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

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

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology