Publications
- Publications on ORCiD
- Publications on ResearchGate
- Publications on Google Scholar
Scientific articles
The distribution of coastal fish eDNA sequences in the Anthropocene
Laetitia Mathon, Virginie Marques, Stéphanie Manel, Camille Albouy, Marco Andrello, Emilie Boulanger, Julie Deter, Régis Hocdé, Fabien Leprieur, Tom B Letessier, Nicolas Loiseau, Eva Maire, Alice Valentini, Laurent Vigliola, Florian Baletaud, Sandra Bessudo, Tony Dejean, Nadia Faure, Pierre‐edouard Guerin, Meret Jucker, Jean‐baptiste Juhel, Kadarusman, Andrea Polanco F, Laurent Pouyaud, Dario Schwörer, Kirsten F Thompson, Marc Troussellier, Hagi Yulia Sugeha, Laure Velez, Xiaowei Zhang, Wenjun Zhong, Loïc Pellissier, David Mouillot
Global Ecology and Biogeography. 2023 August 08. DOI: 10.1111/geb.13698
Contrasting influence of seascape, space and marine reserves on genomic variation in multiple species
Laura Benestan, Nicolas Loiseau, Pierre‐edouard Guérin, Angel Pérez‐Ruzafa, Aitor Forcada, Esther Arcas, Philippe Lenfant, Sandra Mallol, Raquel Goñi, Laure Velez, David Mouillot, Oscar Puebla, Stéphanie Manel
Ecography. 2023 January 01. DOI: 10.1111/ecog.06127
Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
Bastien Macé, Régis Hocdé, Virginie Marques, Pierre‐Edouard Guerin, Alice Valentini, Véronique Arnal, Loïc Pellissier, Stéphanie Manel
Environmental DNA. 2022 February 08. DOI: 10.1002/edn3.269
Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
Laetitia Mathon, Virginie Marques, David Mouillot, Camille Albouy, Marco Andrello, Florian Baletaud, Giomar H Borrero-Pérez, Tony Dejean, Graham J Edgar, Jonathan Grondin, Pierre-Edouard Guerin, Régis Hocdé, Jean-Baptiste Juhel, Kadarusman, Eva Maire, Gael Mariani, Matthew Mclean, Andrea Polanco F, Laurent Pouyaud, Rick D Stuart-Smith, Hagi Yulia Sugeha, Alice Valentini, Laurent Vigliola, Indra B Vimono, Loïc Pellissier, Stéphanie Manel
Proceedings of the Royal Society B. 2022 April 20. DOI: 10.1098/rspb.2022.0162
Climate differently influences the genomic patterns of two sympatric marine fish species
Emilie Boulanger, Laura Benestan, Pierre‐Edouard Guerin, Alicia Dalongeville, David Mouillot, Stéphanie Manel
Journal of Animal Ecology. 2021 October 30. DOI: 10.1111/1365-2656.13623
Use of environmental DNA in assessment of fish functional and phylogenetic diversity
Virginie Marques, Paul Castagne, Andréa Polanco Fernandez, Giomar Helena Borrero-Perez, Regis Hocde, Pierre-Edouard Guerin, Jean-Baptiste Juhel, Laure Velez, Nicolas Loiseau, Tom Bech Letessier, Sandra Bessudo, Alice Valentini, Tony Dejean, David Mouillot, Loïc Pellissier, Sébastien Villéger
Conservation Biology. 2021 July 18. DOI: 10.1111/cobi.13802
Restricted dispersal in a sea of gene flow
Laura Benestan, Nicolas Loiseau, Pierre-Edouard Guerin, Katarina Fietz, Elena Trofimenko, Siren Rühs, Willi Rath, Arne Biastoch, Angel Perez-Ruzafa, Pilar Baixauli, Aitor Forcada, Philippe Lenfant, Sandra Mallol, Rachel Goni, Laure Velez, Marc Höppner, Stuart Kininmonth, David Mouillot, Oscar Puebla, Stephanie Manel
Proceedings of the Royal Society B. 2021 May 18. DOI: 10.1098/rspb.2021.0458
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification
Laetitia Mathon, Alice Valentini, Pierre-Edouard Guerin, Eric Normandeau, Cyril Noel, Clément Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stephanie Manel
Molecular Ecology Resources. 2021 May 17. DOI: 10.1111/1755-0998.13430
Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences
Virginie Marques, Pierre‐Edouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, David Mouillot, Tony Dejean
Ecography. 2020 Aug 04. DOI: 10.1111/ecog.05049
New genomic ressources for three exploited Mediterranean fishes
Katharina Fietz, Elena Trofimenko, Pierre-Edouard Guerin, Veronique Arnal, Montserrat Torres-Oliva, Stephane Lobreaux,Angel Perez-Ruzafa, Stephanie Manel, Oscar Puebla
Genomics. 2020 July 03. DOI: 10.1016/j.ygeno.2020.06.041
Global determinants of freshwater and marine fish genetic diversity
Stephanie Manel, Pierre-Edouard Guerin, David Mouillot, Simon Blanchet, Laure Velez, Camille Albouy & Loic Pellissier
Nature communications. 2020 Feb 10. DOI: 10.1038/s41467-020-14409-7
Predicting genotype environmental range from genome–environment associations
Stephanie Manel, Marco Andrello, Karine Henry, Daphne Verdelet, Aude Darracq, Pierre‐Edouard Guerin, Bruno Desprez, Pierre Devaux
Molecular Ecology. 2018 May 17. DOI: 10.1111/mec.14723
ORION : a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles
Yassine Ghouzam, Guillaume Postic, Pierre-Edouard Guerin, Alexandre G. de Brevern & Jean-Christophe Gelly
Scientific Reports. 2016 Jun 20. DOI: 10.1038/srep28268
Softwares
Florimond Desprez Group (2021-)
- My software developed for the company is confidential. Please contact me for more information.
Public research (2015-2021)
- WFGD (main contributor): interactive worldmap of fish genetic diversity.
- ANVAGE (main contributor): ANnotation Variants GEnome is a python toolkit software to perform routine operations such as detecting synonymous genetic variants from VCF, GFF3 and FASTA genome files.
- Rgeogendiv (main contributor): R package for downloading, preparing and aligning georeferenced DNA sequences on Genbank to calculate genetic diversity at different geographical scales
- Workflow to process environmental DNA sequencing data (main contributor): this workflow is open-source and was co-developped by the CEFE (lead stakeholder) and the company SPYGEN (data and tests), including interactions IFREMER, ETH Zurich and the marine explorations of Monaco.
- Workflow to genotype reduced genome sequencing data (main contributor): this workflow processed over 3000 fish genomes in the context of the european project RESERVEBENEFIT in collaboration with Helmholtz-Zentrum für Ozeanforschung Kiel and Instituto Español de Oceanografía.
- Genbar2 (main contributor): identify genetic boundaries between populations using individual spatial coordinates and genetic variants.
- DEMORT (main contributor): a DEmultiplexing MOnitoring Report Tool
- EXAM (contributor): a whole exome sequencing analysis and its graphical interface
- ORION (contributor): a sensivitive method for protein template detection