Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities

Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

(2019) Teofana Chonova et al.   Frontiers in Microbiology

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms

(2019) Andreia Mortágua et al.   ECOLOGICAL INDICATORS

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

(2018) Tristan Cordier et al.   Molecular Ecology Resources

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

(2018) Jan Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring

(2018) Valentin Vasselon et al.   Methods in Ecology and Evolution

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

(2018) Kálmán Tapolczai et al.   Ecology and Evolution

Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning

(2017) Tristan Cordier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Freshwater biomonitoring in the Information Age

(2017) François Keck et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

(2017) S. F. Rivera et al.   HYDROBIOLOGIA

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

(2017) Benjamin J Callahan et al.   ISME Journal

Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms

(2017) Kristin Hardge et al.   Molecular Ecology Resources

Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring

(2017) Laure Apothéloz-Perret-Gentil et al.   Molecular Ecology Resources

Taxonomy- or trait-based ecological assessment for tropical rivers? Case study on benthic diatoms in Mayotte island (France, Indian Ocean)

(2017) Kálmán Tapolczai et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

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

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

(2017) Valentin Vasselon et al.   Freshwater Science

Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

(2017) Valentin Vasselon et al.   Freshwater Science

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

(2017) Sarah L. Westcott et al.   mSphere

Protist metabarcoding and environmental biomonitoring: Time for change

(2016) J. Pawlowski et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

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

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

cocor: A Comprehensive Solution for the Statistical Comparison of Correlations

(2015) Birk Diedenhofen et al.   PLoS One

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

(2014) Mohamed Mysara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

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

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

The application and testing of diatom-based indices of stream water quality in Chinhoyi Town, Zimbabwe

(2014) T Bere et al.   WATER SA

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

(2014) Lenaïg Kermarrec et al.   Freshwater Science

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

(2014) Thomas S. B. Schmidt et al.   PLoS Computational Biology

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

(2013) Sarah P. Preheim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

(2013) L. Kermarrec et al.   Molecular Ecology Resources

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque et al.   PLoS One

Identification versus counting protocols as sources of uncertainty in diatom-based ecological status assessments

(2012) Maria Kahlert et al.   HYDROBIOLOGIA

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

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

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

The European reference condition concept: A scientific and technical approach to identify minimally-impacted river ecosystems

(2012) Isabel Pardo et al.   SCIENCE OF THE TOTAL ENVIRONMENT

THE CONCEPTUAL BASIS OF ECOLOGICAL-STATUS ASSESSMENTS USING DIATOMS

(2010) Martyn Kelly et al.   BIOLOGY AND ENVIRONMENT-PROCEEDINGS OF THE ROYAL IRISH ACADEMY

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

Numerical simulations suggest that counting sums and taxonomic resolution of diatom analyses to determine IPS pollution and ACID acidity indices can be reduced

(2009) Christian Bigler et al.   JOURNAL OF APPLIED PHYCOLOGY