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

Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species

(2017) Hannah Weigand et al.   MOLECULAR ECOLOGY

A DNA barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera)

(2017) Jérôme Morinière et al.   Molecular Ecology Resources

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

(2017) David A. Bohan et al.   TRENDS IN ECOLOGY & EVOLUTION

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

(2017) Iliana Bista et al.   Nature Communications

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Environmental DNA analysis for estimating the abundance and biomass of stream fish

(2016) Hideyuki Doi et al.   FRESHWATER BIOLOGY

Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

(2016) Anaïs Lacoursière-Roussel et al.   Molecular Ecology Resources

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

(2016) Nicole A. Fahner et al.   PLoS One

Mitochondrial metagenomics: letting the genes out of the bottle

(2016) Alex Crampton-Platt et al.   GigaScience

Phylogenetic incongruence inferred with two mitochondrial genes in Mepraia spp. and Triatoma eratyrusiformis (Hemiptera, Reduviidae)

(2015) Ricardo Campos-Soto et al.   GENETICS AND MOLECULAR BIOLOGY

Length–mass relationships for lake macroinvertebrates corrected for back-transformation and preservation effects

(2015) Marlen Mährlein et al.   HYDROBIOLOGIA

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

(2015) Alex Crampton-Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

(2015) Shanlin Liu et al.   Molecular Ecology Resources

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

(2014) Aibin Zhan et al.   CONSERVATION GENETICS

Genome size estimates for crustaceans using Feulgen image analysis densitometry of ethanol-preserved tissues

(2014) Nicholas W. Jeffery et al.   CYTOMETRY PART A

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

(2014) Inga Hiiesalu et al.   NEW PHYTOLOGIST

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

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

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

(2014) Elvira Mächler et al.   Freshwater Science

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

(2014) John K. Jackson et al.   Freshwater Science

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Biodiversity and ecosystem stability: a synthesis of underlying mechanisms

(2013) Michel Loreau et al.   ECOLOGY LETTERS

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

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

(2013) Xin Zhou et al.   GigaScience

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Implementing the Water Framework Directive: a transition from established monitoring networks in England and Wales

(2012) Alexandra Collins et al.   ENVIRONMENTAL SCIENCE & POLICY

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

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

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

Multi-locus species delimitation in closely related animals and fungi: one marker is not enough

(2012) JULIAN R. DUPUIS et al.   MOLECULAR ECOLOGY

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

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS