Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol

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

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

(2018) Ahmed Abdelfattah et al.   BIOLOGICAL CONTROL

Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution

(2018) Mark A Phuong et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

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

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

(2018) Lynsey R. Harper et al.   HYDROBIOLOGIA

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms

(2018) C. Mariac et al.   PLoS One

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals

(2018) Michelle A. Jusino et al.   Molecular Ecology Resources

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Matthieu Leray et al.   PeerJ

DNA Metabarcoding of Amazonian Ichthyoplankton Swarms

(2017) M. E. Maggia et al.   PLoS One

Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps

(2016) Marie Leys et al.   BMC EVOLUTIONARY BIOLOGY

Synthesising the trait information of European Chironomidae (Insecta: Diptera): Towards a new database

(2016) Sónia R.Q. Serra et al.   ECOLOGICAL INDICATORS

The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding

(2016) Trevor T. Bringloe et al.   GENOME

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design

(2016) Christoph Mayer et al.   MOLECULAR BIOLOGY AND EVOLUTION

An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

(2016) Daniel M. Portik et al.   Molecular Ecology Resources

A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring

(2016) Mehrdad Hajibabaei et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure

(2016) Gillian K. Martin et al.   Freshwater Science

Taxonomic resolution based on DNA barcoding affects environmental signal in metacommunity structure

(2016) Gillian K. Martin et al.   Freshwater Science

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

(2016) Vasco Elbrecht et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics

(2015) Benjamin Linard et al.   Genome Biology and Evolution

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

(2015) Johanna L. A. Paijmans 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

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

(2015) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

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

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

(2014) J. Piñol et al.   Molecular Ecology Resources

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data

(2014) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity

(2013) Sébastien Calvignac-Spencer et al.   MOLECULAR ECOLOGY

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France

(2013) Gontran Sonet et al.   ZooKeys

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

(2013) Xin Zhou et al.   GigaScience

Screening mammal biodiversity using DNA from leeches

(2012) Ida Bærholm Schnell et al.   CURRENT BIOLOGY

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

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

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto 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

Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals

(2011) I.A. Arif et al.   GENETICS AND MOLECULAR RESEARCH

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

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Expanding whole exome resequencing into non-human primates

(2011) Eric J Vallender   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

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

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae

(2010) Nicolas Hubert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A customized and versatile high-density genotyping array for the mouse

(2009) Hyuna Yang et al.   NATURE METHODS

Error Cascades in the Biological Sciences: The Unwanted Consequences of Using Bad Taxonomy in Ecology

(2008) Alejandro Bortolus   AMBIO

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY