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List of works by Agnès Bouchez

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

scientific article published on 15 September 2014

A taxonomy-free approach based on machine learning to assess the quality of rivers with diatoms

scientific article published on 12 March 2020

Antifouling coatings influence both abundance and community structure of colonizing biofilms: a case study in the Northwestern Mediterranean Sea

scientific article

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

scientific article published in March 2017

Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France)

scientific article published in November 2017

Assessment of toxicity thresholds in aquatic environments: does benthic growth of diatoms affect their exposure and sensitivity to herbicides?

scientific article published on 03 July 2013

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

scientific article published on 22 January 2018

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

scientific article published on 09 April 2019

Benthic diatom community dynamics in Mediterranean intermittent streams: Effects of water availability and their potential as indicators of dry-phase ecological status

scientific article published on 20 February 2020

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

scientific article published on 13 July 2018

Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability.

scientific article

Comparative sensitivity to the fungicide tebuconazole of biofilm and plankton microbial communities in freshwater ecosystems

scientific article published on 15 September 2013

Comparison of specific versus literature species sensitivity distributions for herbicides risk assessment

scientific article published on 23 September 2015

Comparison of the effects of two herbicides and an insecticide on tropical freshwater plankton in microcosms.

scientific article published on 22 February 2011

Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

scientific article published on 28 June 2019

Cyprus’ diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding

scientific article published in 2021

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

scientific article published on 27 April 2019

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

scientific article

DNAqua-Net or how to navigate on the stormy waters of standards and legislations

scientific article published on 18 May 2018

DNAqua-Net: Advancing Methods, Connecting Communities and Envisaging Standards

scientific article published in 2017

DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe

scientific article (publication date: 29 November 2016)

Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

scientific article published on 07 May 2018

Diat.barcode, an open-access curated barcode library for diatoms

scientific article published on 22 October 2019

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

article by Kálmán Tapolczai et al published 29 October 2019 in Frontiers in Ecology and Evolution

Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software

scientific article published in February 2020

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

scientific article published on 2 February 2018

ECOTOX, new questions for terrestrial and aquatic ecotoxicology

scientific article published on 19 September 2018

ECOTOX, the INRA's network of ecotoxicologists, a major structure involved for the coordination and structuring of the French research in ecotoxicology.

scientific article published on 22 December 2015

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

scientific article published on 16 May 2020

Effects of flow regime and pesticides on periphytic communities: evolution and role of biodiversity

scientific article

Effects of organic herbicides on phototrophic microbial communities in freshwater ecosystems

scientific article published on January 2011

Environmental filtering and limiting similarity as main forces driving diatom community structure in Mediterranean and continental temporary and perennial streams

scientific article published on 23 June 2020

Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers

scientific article published on 04 April 2020

Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms

scientific article published in 2023

Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

scientific article published on 25 December 2020

First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta).

scientific article published on 28 August 2013

Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects

scientific article published on 04 December 2021

Freshwater biomonitoring in the Information Age

scientific article published on 15 May 2017

Herbicide-Induced Shifts in the Periphyton Community Composition Indirectly Affect Feeding Activity and Physiology of the Gastropod Grazer Physella acuta

scientific article

How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams?

scientific article published in 2021

Impact of chronic and acute pesticide exposures on periphyton communities

scientific article

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

scientific article published in July 2018

In situ assessment of periphyton recovery in a river contaminated by pesticides

scientific article

Key Questions for Next-Generation Biomonitoring

scientific article published on 08 January 2020

Linking diatom sensitivity to herbicides to phylogeny: a step forward for biomonitoring?

scientific article published on 21 January 2014

Lotic biofilm community structure and pesticide tolerance along a contamination gradient in a vineyard area

scientific article published in 2007

Mangrove microbial diversity and the impact of trophic contamination

scientific article

Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines.

scientific article published on December 2002

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

scientific article published in 2021

Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status

scientific article published in 2019

Monitoring the ecological status of rivers with diatom eDNA metabarcoding: a comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index

scientific article published on 26 September 2020

Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations

scientific article

Pioneer marine biofilms on artificial surfaces including antifouling coatings immersed in two contrasting French Mediterranean coast sites.

scientific article published in January 2012

Pollution-induced community tolerance (PICT) as a tool for monitoring Lake Geneva long-term in situ ecotoxic restoration from herbicide contamination

scientific article published on 3 September 2015

Pollution-induced community tolerance (PICT): towards an ecologically relevant risk assessment of chemicals in aquatic systems

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

scientific article published on 17 March 2016

Report on the fifth meeting of INRA's national network of ecotoxicologists, ECOTOX.

scientific article

Responses of chronically contaminated biofilms to short pulses of diuron. An experimental study simulating flooding events in a small river.

scientific article published on 19 February 2008

Risk of herbicide mixtures as a key parameter to explain phytoplankton fluctuation in a great lake: the case of Lake Geneva, Switzerland.

scientific article

River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant

scientific article published on 8 September 2017

SIPIBEL observatory: Data on usual pollutants (solids, organic matter, nutrients, ions) and micropollutants (pharmaceuticals, surfactants, metals), biological and ecotoxicity indicators in hospital and urban wastewater, in treated effluent and sludge

scientific article

Seasonal shift in the sensitivity of a natural benthic microalgal community to a herbicide mixture: impact on the protective level of thresholds derived from species sensitivity distributions

scientific article

Sensitivities of seven algal species to triclosan, fluoxetine and their mixtures

scientific article published in Scientific Reports

Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities

scientific article published on 9 November 2015

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments.

scientific article

Species sensitivity analysis as a tool for interpreting diatom metabarcoding for WFD bioassessment

scientific article published in 2021

Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring

scientific article published in 2019

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

scientific article

The Fellowship of the Ring Test: DNAqua-Net WG2 initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardisation

The SIPIBEL project: treatment of hospital and urban wastewater in a conventional urban wastewater treatment plant

scientific article

The effect of temperature and a herbicide mixture on freshwater periphytic algae

scientific article published on 9 October 2013

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

scientific article published in October 2018

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

article

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

scientific article published on 31 March 2018

The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding

article by Kálmán Tapolczai et al published March 2021 in Ecological Indicators

The use of MapPop1.0 for choosing a QTL mapping sample from an advanced backcross population.

scientific article published on 14 February 2007

The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension

scientific article published on 01 February 2020

Trait-based ecological classifications for benthic algae: review and perspectives

scientific article published on 18 March 2016

Transplantation of microbenthic algal assemblages to assess structural and functional recovery after diuron exposure

scientific article published on 01 November 2010

Using bioassays and species sensitivity distributions to assess herbicide toxicity towards benthic diatoms

scientific article

When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta).

scientific article

Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

scientific article published in 2018

phylosignal: an R package to measure, test, and explore the phylogenetic signal

scientific article published on 19 March 2016

A strategy for successful integration of DNA-based methods in aquatic monitoring

scientific article published in 2022

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