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Agnès BOUCHEZ

26
Documents

Présentation

Ecologie microbienne aquatique

Publications

valentin-vasselon
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Recommendations for the preservation of environmental samples in diatom metabarcoding studies

Ana Baricevic , Cécile Chardon , Maria Kahlert , Satu Maaria Karjalainen , Daniela Maric Pfannkuchen
Metabarcoding and Metagenomics, 2022, 6 (e85844), ⟨10.3897/mbmg.6.85844⟩
Article dans une revue hal-03976810v1

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

Philippe Blancher , Estelle Lefrançois , Frédéric Rimet , Valentin Vasselon , Christine Argillier
Metabarcoding and Metagenomics, 2022, 6 (e85652), ⟨10.3897/mbmg.6.85652⟩
Article dans une revue hal-03976834v1

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

Laure Apothéloz‐perret‐gentil , Agnes Bouchez , Tristan Cordier , Arielle Cordonier , Julie Guéguen
Molecular Ecology, 2021, 30 (13), pp.2959-2968. ⟨10.1111/mec.15646⟩
Article dans une revue hal-02955898v1
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Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Frédéric Rimet , Eva Aylagas , Ángel Borja , Agnes Bouchez , Alexis Canino
Metabarcoding and Metagenomics, 2021, 5, pp.e58056. ⟨10.3897/mbmg.5.58056⟩
Article dans une revue pasteur-03159791v1
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Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

Sinziana Rivera , Valentin Vasselon , Nathalie Mary , Olivier Monnier , Fréderic Rimet
Science of the Total Environment, 2021, 763, pp.144208. ⟨10.1016/j.scitotenv.2020.144208⟩
Article dans une revue hal-03103971v1

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

Maria João Feio , Sonia R.Q. Serra , Andreia Mortágua , Agnes Bouchez , Frédéric Rimet
Science of the Total Environment, 2020, 722, ⟨10.1016/j.scitotenv.2020.137900⟩
Article dans une revue hal-02520169v1
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Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software

Sinziana Rivera , Valentin Vasselon , Agnes Bouchez , Frédéric Rimet
Ecological Indicators, 2020, 109, ⟨10.1016/j.ecolind.2019.105775⟩
Article dans une revue hal-02518194v1

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

Javier Pérez-Burillo , Rosa Trobajo , Valentin Vasselon , Frédéric Rimet , Agnes Bouchez
Science of the Total Environment, 2020, 727, ⟨10.1016/j.scitotenv.2020.138445⟩
Article dans une revue hal-02557859v1
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Key questions for next-generation biomonitoring

Andreas Makiola , Zacchaeus G. Compson , Donald J Baird , Matthew A. Barnes , Sam Philip Boerlijst
Frontiers in Environmental Science, inPress, 7, ⟨10.3389/fenvs.2019.00197⟩
Article dans une revue hal-02402296v1
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Diatom DNA metabarcoding for biomonitoring: strategies to avoid major taxonomical and bioinformatical biases Llmiting molecular indices capacities

Kálmán Tapolczai , François Keck , Agnes Bouchez , Frédéric Rimet , Maria Kahlert
Frontiers in Ecology and Evolution, 2019, 7, ⟨10.3389/fevo.2019.00409⟩
Article dans une revue hal-02624302v1

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

Frédéric Rimet , Evgenuy Gusev , Maria Kahlert , Martyn G. Kelly , Maxim Kulikovskiy
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-51500-6⟩
Article dans une revue hal-02619171v1
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Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Teofana Chonova , Rainer Kurmayer , Frédéric Rimet , Jérôme Labanowski , Valentin Vasselon
Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.00653⟩
Article dans une revue hal-02381793v1

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

Andreia Mortágua , Valentin Vasselon , Ricardo Oliveira , Carmen Elias , Cécile Chardon
Ecological Indicators, 2019, 106, pp.105470. ⟨10.1016/j.ecolind.2019.105470⟩
Article dans une revue hal-02623986v1

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

Kalman Tapolczai , Valentin Vasselon , Agnes Bouchez , Csilla Stenger-Kovács , Judit Padisák
Ecology and Evolution, 2019, 9 (1), pp.166-179. ⟨10.1002/ece3.4701⟩
Article dans une revue hal-02619428v1

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

S. F. Rivera , Valentin Vasselon , Stéphan Jacquet , Agnes Bouchez , D. Ariztegui
Hydrobiologia, 2018, 807 (1), pp.37-51. ⟨10.1007/s10750-017-3381-2⟩
Article dans une revue hal-02621047v1
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DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

Sinziana Rivera , Valentin Vasselon , Katia Ballorain , Alice Carpentier , Carlos E. Wetzel
PLoS ONE, 2018, 13 (4), pp.e0195770. ⟨10.1371/journal.pone.0195770⟩
Article dans une revue hal-02624564v1

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles

F Keck , Valentin Vasselon , Frédéric Rimet , Agnes Bouchez , M Kahlert
Molecular Ecology Resources, 2018, 18 (6), pp.1299-1309. ⟨10.1111/1755-0998.12919⟩
Article dans une revue hal-02625977v1

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

Frédéric Rimet , Valentin Vasselon , Barbara A.-Keszte , Agnes Bouchez
Organisms Diversity and Evolution, 2018, 18 (1), pp.51-62. ⟨10.1007/s13127-018-0359-5⟩
Article dans une revue hal-02625205v1

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

Jan Pawlowski , Mary Kelly-Quinn , Florian Altermatt , Laure Apothéloz-Perret-Gentil , Pedro Beja
Science of the Total Environment, 2018, 637-638, pp.1295-1310. ⟨10.1016/j.scitotenv.2018.05.002⟩
Article dans une revue hal-02629210v1

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

Teofana Chonova , Jérôme Labanowski , Benoit Cournoyer , Cècile Chardon , François Keck
Environmental Science and Pollution Research, 2018, 25 (10), pp.9254-9264. ⟨10.1007/s11356-017-0024-0⟩
Article dans une revue hal-01859406v1

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

Frédéric Rimet , Nelida Abarca , Agnes Bouchez , Wolf-Henning Kusber , Regine Jahn
Fottea (Praha), 2018, 18 (1), pp.37-54. ⟨10.5507/fot.2017.013⟩
Article dans une revue hal-02624468v1

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

Valentin Vasselon , Frédéric Rimet , Kalman Tapolczai , Agnes Bouchez
Ecological Indicators, 2017, 82, pp.1-12. ⟨10.1016/j.ecolind.2017.06.024⟩
Article dans une revue hal-02622658v1
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Freshwater biomonitoring in the Information age

Francois Keck , Valentin Vasselon , Kalman Tapolczai , Frédéric Rimet , Agnes Bouchez
Frontiers in Ecology and the Environment, 2017, 15 (5), pp.266-274. ⟨10.1002/fee.1490⟩
Article dans une revue hal-01604509v1
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Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

Valentin Vasselon , Isabelle Domaizon , Frédéric Rimet , Maria Kahlert , Agnes Bouchez
Freshwater Science, 2017, 36 (1), pp.162-177. ⟨10.1086/690649⟩
Article dans une revue hal-01606868v1
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Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring

Valentin Vasselon , Agnes Bouchez , Frédéric Rimet , Stéphan Jacquet , Rosa Trobajo
Methods in Ecology and Evolution, 2017, 9 (4), pp.1060-1069. ⟨10.1111/2041-210X.12960⟩
Article dans une revue hal-02916343v1
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R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Frédéric Rimet , Philippe Chaumeil , François Keck , Lenaïg Kermarrec , Valentin Vasselon
Database - The journal of Biological Databases and Curation, 2016, 2016, pp.baw016. ⟨10.1093/database/baw016⟩
Article dans une revue hal-01426772v1