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

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

(2018) Frederic Rimet et al.   Fottea

Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

(2018) Frédéric Rimet et al.   ORGANISMS DIVERSITY & EVOLUTION

DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

(2018) Sinziana F. Rivera et al.   PLoS One

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

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

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

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

The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

(2017) Sophie Groendahl et al.   PLoS One

Combined eco-morphological functional groups are reliable indicators of colonisation processes of benthic diatom assemblages in a lowland stream

(2016) Viktória B-Béres et al.   ECOLOGICAL INDICATORS

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

(2016) Frédéric Rimet et al.   Database-The Journal of Biological Databases and Curation

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

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

Genetic and Physiological Diversity in the DiatomNitzschia inconspicua

(2015) Laia Rovira et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions

(2015) Julia Birtel et al.   PLoS One

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

Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy

(2014) Irena Kaczmarska et al.   AMERICAN JOURNAL OF BOTANY

Characterizing the niches of two very similarNitzschiaspecies and implications for ecological assessment

(2014) Martyn G. Kelly et al.   DIATOM RESEARCH

DNA-based species delimitation in algae

(2014) Frederik Leliaert et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Functional classifications and their application in phytoplankton ecology

(2014) Nico Salmaso et al.   FRESHWATER BIOLOGY

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

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

(2014) Paul J. McMurdie 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

An Inordinate Fondness? The Number, Distributions, and Origins of Diatom Species

(2013) David G. Mann et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Are diatom diversity indices reliable monitoring metrics?

(2012) Saúl Blanco et al.   HYDROBIOLOGIA

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

(2012) Maria Kahlert et al.   HYDROBIOLOGIA

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

(2012) Nastassia V. Patin et al.   MICROBIAL ECOLOGY

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

Molecular Evidence for Distinct Antarctic Lineages in the Cosmopolitan Terrestrial Diatoms Pinnularia borealis and Hantzschia amphioxys

(2012) Caroline Souffreau et al.   PROTIST

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

Biomonitoring river diatoms: Implications of taxonomic resolution

(2011) Frédéric Rimet et al.   ECOLOGICAL INDICATORS

Barcoding Diatoms: Exploring Alternatives to COI-5P

(2011) Sarah E. Hamsher et al.   PROTIST

Evaluation of European diatom trophic indices

(2010) Anna Besse-Lototskaya et al.   ECOLOGICAL INDICATORS

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

The effect of excluding diatom taxa and reducing taxonomic resolution on multivariate analyses and stream bioassessment

(2008) Isabelle Lavoie et al.   ECOLOGICAL INDICATORS

Improvements of the Biological Diatom Index (BDI): Description and efficiency of the new version (BDI-2006)

(2008) M. Coste et al.   ECOLOGICAL INDICATORS

Validation of diatoms as proxies for phytobenthos when assessing ecological status in lakes

(2008) M. G. Kelly et al.   HYDROBIOLOGIA

Harmonization is more important than experience—results of the first Nordic–Baltic diatom intercalibration exercise 2007 (stream monitoring)

(2008) Maria Kahlert et al.   JOURNAL OF APPLIED PHYCOLOGY

A MOLECULAR SYSTEMATIC APPROACH TO EXPLORE DIVERSITY WITHIN THESELLAPHORA PUPULASPECIES COMPLEX (BACILLARIOPHYTA)

(2008) Katharine M. Evans et al.   JOURNAL OF PHYCOLOGY

Algae–P relationships, thresholds, and frequency distributions guide nutrient criterion development

(2008) R. Jan Stevenson et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY