High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

(2015) Anthony A. Chariton et al.   ENVIRONMENTAL POLLUTION

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

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

The transcriptional response of microbial communities in thawing Alaskan permafrost soils

(2015) Marco J. L. Coolen et al.   Frontiers in Microbiology

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

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

(2015) Shadi Shokralla et al.   Scientific Reports

Assessment of the production and dispersal of faecal waste from the sea-cage aquaculture of spiny lobsters

(2014) Soxi Lee et al.   AQUACULTURE RESEARCH

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

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

Development of a new biotic index for ecological status assessment of Italian coastal waters based on coralligenous macroalgal assemblages

(2014) Enrico Cecchi et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

(2014) Eva Aylagas et al.   PLoS One

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

A next-generation sequencing approach to river biomonitoring using benthic diatoms

(2014) Lenaïg Kermarrec et al.   Freshwater Science

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

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

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

M-AMBI revisited: looking inside a widely-used benthic index

(2013) Marco Sigovini et al.   HYDROBIOLOGIA

Exploiting salmon farm benthic enrichment gradients to evaluate the regional performance of biotic indices and environmental indicators

(2012) Nigel B. Keeley et al.   ECOLOGICAL INDICATORS

Can marine fisheries and aquaculture meet fish demand from a growing human population in a changing climate?

(2012) Gorka Merino et al.   GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS

Changes in sedimentation, sediment characteristics, and benthic macrofaunal assemblages around marine cage culture under seasonal monsoon scales in a shallow-water bay in Taiwan

(2012) Yuan-Chao Angelo Huang et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Cosmopolitanism of microbial eukaryotes in the global deep seas

(2012) SIMON CREER et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

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

Salmon farm impacts on muddy-sediment megabenthic assemblages on the west coast of Scotland

(2012) TA Wilding et al.   Aquaculture Environment Interactions

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fin and shellfish aquaculture located in sites across Europe

(2009) Ángel Borja et al.   AQUACULTURE

Main meiofauna taxa as an indicator for assessing the spatial and seasonal impact of fish farming

(2009) M. Grego et al.   MARINE POLLUTION BULLETIN

Species’ traits predict the effects of disturbance and productivity on diversity

(2008) Nick M. Haddad et al.   ECOLOGY LETTERS

Using M-AMBI in assessing benthic quality within the Water Framework Directive: Some remarks and recommendations

(2008) Angel Borja et al.   MARINE POLLUTION BULLETIN

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY