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

Protist metabarcoding and environmental biomonitoring: Time for change

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

Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms

(2016) François Keck et al.   JOURNAL OF APPLIED ECOLOGY

Foram-AMBI: A sensitivity index based on benthic foraminiferal faunas from North-East Atlantic and Arctic fjords, continental shelves and slopes

(2016) Elisabeth Alve et al.   MARINE MICROPALEONTOLOGY

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

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

Genetic and Physiological Diversity in the DiatomNitzschia inconspicua

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

Hidden diversity in the freshwater planktonic diatomAsterionella formosa

(2015) S. Van den Wyngaert et al.   MOLECULAR ECOLOGY

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Benthic foraminifera assemblages as elemental pollution bioindicator in marine sediments around fish farm (Vrgada Island, Central Adriatic, Croatia)

(2014) Jelena Vidović et al.   MARINE POLLUTION BULLETIN

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

Transport Distance of Invertebrate Environmental DNA in a Natural River

(2014) Kristy Deiner et al.   PLoS One

Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research

(2014) Jonas Zimmermann et al.   PLoS One

When is Sampling Complete? The Effects of Geographical Range and Marker Choice on Perceived Diversity in Nitzschia palea (Bacillariophyta)

(2014) Frédéric Rimet et al.   PROTIST

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

(2014) Lenaïg Kermarrec et al.   Freshwater Science

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

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

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

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

(2013) Alexander Eiler et al.   PLoS One

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

(2013) Alexandra A-T. Weber et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

The FOBIMO (FOraminiferal BIo-MOnitoring) initiative—Towards a standardised protocol for soft-bottom benthic foraminiferal monitoring studies

(2012) Joachim Schönfeld et al.   MARINE MICROPALEONTOLOGY

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

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

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Survey of the Efficacy of a Short Fragment of the rbcL Gene as a Supplemental DNA Barcode for Diatoms

(2011) Michael L. MacGillivary et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

(2011) Jonas Zimmermann et al.   ORGANISMS DIVERSITY & EVOLUTION

An approach to analyzing spatial patterns of planktonic ciliate communities for monitoring water quality in Jiaozhou Bay, northern China

(2010) Yong Jiang et al.   MARINE POLLUTION BULLETIN

Diatom teratological forms and environmental alterations: a review

(2009) Elisa Falasco et al.   HYDROBIOLOGIA

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR

(2008) A. Godhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2008) M. Coste et al.   ECOLOGICAL INDICATORS

A comparison of national approaches to setting ecological status boundaries in phytobenthos assessment for the European Water Framework Directive: results of an intercalibration exercise

(2008) Martyn Kelly et al.   HYDROBIOLOGIA

Use of ciliates (Protozoa: Ciliophora) as bioindicator to assess sediment quality of two constructed mangrove sewage treatment belts in Southern China

(2008) Qing-Hua Chen et al.   MARINE POLLUTION BULLETIN

Assessing the environmental quality status in estuarine and coastal systems: Comparing methodologies and indices

(2007) A. Borja et al.   ECOLOGICAL INDICATORS