Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

Pollen DNA barcoding: current applications and future prospects

(2016) Karen L. Bell et al.   GENOME

What you need is what you eat? Prey selection by the bat Myotis daubentonii

(2016) Eero J. Vesterinen et al.   MOLECULAR ECOLOGY

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee

(2016) Quinn S. McFrederick et al.   MOLECULAR ECOLOGY

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

How to limit false positives in environmental DNA and metabarcoding?

(2016) Gentile Francesco Ficetola et al.   Molecular Ecology Resources

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

(2016) Kessy Abarenkov et al.   MycoKeys

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Statistical approaches to account for false-positive errors in environmental DNA samples

(2015) José J. Lahoz-Monfort et al.   Molecular Ecology Resources

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

(2015) Min Tang et al.   Methods in Ecology and Evolution

Climatic warming and the future of bison as grazers

(2015) Joseph M. Craine et al.   Scientific Reports

Rank-Based Characterization of Pollen Assemblages Collected by Honey Bees Using a Multi-Locus Metabarcoding Approach

(2015) Rodney T. Richardson et al.   Applications in Plant Sciences

Application of ITS2 Metabarcoding to Determine the Provenance of Pollen Collected by Honey Bees in an Agroecosystem

(2015) Rodney T. Richardson et al.   Applications in Plant Sciences

Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach

(2015) Wiebke Sickel et al.   BMC ECOLOGY

Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences

(2015) Jennifer Hawkins et al.   PLoS One

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

(2015) R. Scott Cornman et al.   PLoS One

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons

(2015) Magdalena Guardiola et al.   PLoS One

Improving ITS sequence data for identification of plant pathogenic fungi

(2014) R. Henrik Nilsson et al.   FUNGAL DIVERSITY

Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing

(2014) Ken Kraaijeveld et al.   Molecular Ecology Resources

Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples

(2014) A. Keller et al.   PLANT BIOLOGY

A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range

(2013) Erwan Quéméré et al.   PLoS One

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Screening mammal biodiversity using DNA from leeches

(2012) Ida Bærholm Schnell et al.   CURRENT BIOLOGY

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

(2012) Teresita M. Porter et al.   PLoS One

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota

(2009) Lance B. Price et al.   PLoS One

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY