Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

(2020) Teresita M. Porter et al.   Frontiers in Ecology and Evolution

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

(2019) Mehrdad Hajibabaei et al.   PLoS One

Can Environmental RNA Revolutionize Biodiversity Science?

(2019) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Automated high throughput animal CO1 metabarcode classification

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

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

Over 2.5 million COI sequences in GenBank and growing

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

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

(2017) Benjamin J Callahan et al.   ISME Journal

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

(2017) Olivier Laroche et al.   PeerJ

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

(2017) Matthieu Leray et al.   PeerJ

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

Counting animal species with DNA barcodes: Canadian insects

(2016) Paul D. N. Hebert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Uncovering species boundaries in the Neotropical ant complexEctatomma ruidum(Ectatomminae) under the presence of nuclear mitochondrial paralogues

(2016) Reina Gabriela Aguilar-Velasco et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

(2016) Mikko Pentinsaari et al.   Scientific Reports

DNA barcoding largely supports 250 years of classical taxonomy: identifications for Central European bees (Hymenoptera, Apoideapartim)

(2015) Stefan Schmidt et al.   Molecular Ecology Resources

The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions

(2015) Michael J. Raupach et al.   PLoS One

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

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

Demographic Trends in Mixed Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Populations in Commercial Poinsettia Under Biological Control- and Insecticide-Based Management

(2014) Andrew J. Frewin et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

(2014) Muhammad Ashfaq et al.   PLoS One

Rampant Nuclear Insertion of mtDNA across Diverse Lineages within Orthoptera (Insecta)

(2014) Hojun Song et al.   PLoS One

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

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Misconceptions regarding nuclear mitochondrial pseudogenes (Numts) may obscure detection of mitochondrial evolutionary novelties

(2012) NV Schizas   Aquatic Biology

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Extensive Settlement of the Invasive Meam1 population ofBemisia tabaci(Hemiptera: Aleyrodidae) in the Caribbean and Rare Detection of Indigenous Populations

(2011) Y. Muñiz et al.   ENVIRONMENTAL ENTOMOLOGY

Hit or miss in phylogeographic analyses: the case of the cryptic NUMTs

(2011) CORALIE BERTHEAU et al.   Molecular Ecology Resources

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta)

(2010) MATTHEW J. MOULTON et al.   Molecular Ecology Resources

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

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

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

(2009) Frederic Austerlitz et al.   BMC BIOINFORMATICS

“COI-like” Sequences Are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies

(2009) Jennifer E. Buhay   JOURNAL OF CRUSTACEAN BIOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Mitochondrial DNA repair in aging and disease

(2008) Nadiya M. Druzhyna et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA