Pôles techniques

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

2023

Article dans une revue

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Beyond accuracy : score calibration in deep learning models for camera trap image sequences

Gaspard Dussert, Simon Chamaillé-Jammes, Stéphane Dray, Vincent Miele

DOI: 10.1101/2023.11.10.566512

2023

Pré-publication

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The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Noa Rigoudy, Gaspard Dussert, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Jérome Boyer...

European Journal of Wildlife Research . 69 : 24 p.

DOI: 10.1007/s10344-023-01742-7

2023

Article dans une revue

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Validation of a field-friendly faeces drying and storage method for quantifying faecal glucocorticoid metabolites in African elephants (Loxodonta africana) opens up new perspectives for conservationists

Laura Lacomme, Chloé Guerbois, Hervé Fritz, André Ganswindt, Benjamin Rey

Conservation Physiology . 11 ( 1 ) : coad053

DOI: 10.1093/conphys/coad053

2023

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Oak masting drivers vary between populations depending on their climatic environments

Emilie Fleurot, Jean R Lobry, Vincent Boulanger, François Débias, Camille Mermet-Bouvier, Thomas Caignard...

Current Biology - CB . 33 ( 6 ) : 1117-1124.e4

DOI: 10.1016/j.cub.2023.01.034

2023

Article dans une revue

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DRomics, a workflow to exploit dose-response omics data in ecotoxicology

Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir

Peer Community Journal . 3 : e90

DOI: 10.24072/pcjournal.325

2023

Article dans une revue

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Universal DNA methylation age across mammalian tissues

A T Lu, Z Fei, A Haghani, T R Robeck, J A Zoller, C Z Li...

Nature Aging . 3 : 1144 - 1166

DOI: 10.1038/s43587-023-00462-6

2023

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DNA methylation networks underlying mammalian traits

Amin Haghani, Caesar Li, Todd Robeck, Joshua Zhang, Ake Lu, Julia Ablaeva...

Science . 381 ( 6658 )

DOI: 10.1126/science.abq5693

2023

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Nine tips for ecologists using machine learning

Marine Desprez, Vincent Miele, Olivier Gimenez

2023

Pré-publication

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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

2023

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The for gene as one of the drivers of foraging variations in a parasitic wasp

Aurore Gallot, Emmanuel Desouhant, Vincent Lhuillier, David Lepetit, Adil El Filali, Laurence Mouton...

Molecular Ecology . 32 ( 7 ) : 1760-1776

DOI: 10.1111/mec.16834

2023

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PhylteR: efficient identification of outlier sequences in phylogenomic datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msad234

2023

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Neural Networks beyond explainability: Selective inference for sequence motifs

Antoine Villié, Philippe Veber, Yohann de Castro, Laurent Jacob

Transactions on Machine Learning Research Journal .

2023

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Age and spatio-temporal variations in food resources modulate stress-immunity relationships in three populations of wild roe deer

Jeffrey Carbillet, Marine Hollain, B. Rey, Rupert Palme, Maryline Pellerin, Corinne Régis...

General and Comparative Endocrinology . 330 : 114141

DOI: 10.1016/j.ygcen.2022.114141

2023

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Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Marc Ohlmann, Catherine Matias, Giovanni Poggiato, Stéphane Dray, Wilfried Thuiller, Vincent Miele

Ecological Modelling . 483 : 110424

DOI: 10.1016/j.ecolmodel.2023.110424

2023

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Meta-transcriptomics reveals stress adaptation processes in microbial communities differing in exposure history

Floriane Larras, Elise Billoir, Stefan Lips, Stephan Schreiber, Philippe Veber, Marie Laure Delignette-Muller...

"Ecology and Evolution: New perspectives and societal challenges" SFE2-GfÖ-EEF joint meeting, International conference on ecological sciences .

2022

Acte de congrès

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Influence of bacterial symbionts on host niche and ecological diversification: an integrative approach in a whitefly model

Sylvain Benhamou, Isabelle Rahioui, Hélène Henri, Pedro da Silva, Hubert Charles, Abdelaziz Heddi...

26.International Congress of Entomology .

2022

Poster

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Decline in telomere length with increasing age across nonhuman vertebrates: A meta‐analysis

Florentin Remot, Victor Ronget, Hannah Froy, Benjamin Rey, Jean‐michel Gaillard, Daniel Nussey...

Molecular Ecology . 31 ( 23 ) : 5917-5932

DOI: 10.1111/mec.16145

2022

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tidy tree : A New Layout for Phylogenetic Trees

Simon Penel, Damien de Vienne

Molecular Biology and Evolution . 39 ( 10 ) : msac204

DOI: 10.1093/molbev/msac204

2022

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The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images

Noa Rigoudy, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Yoann Bollet, Yoann Bunz...

DOI: 10.1101/2022.03.15.484324

2022

Pré-publication

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Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks

Julie J. Aubert, Pierre M Barbillon, Sophie Donnet, Vincent Miele

Statistical Approaches for Hidden Variables in Ecology. . : 117-134

DOI: 10.1002/9781119902799.ch6

2022

Chapitre d'ouvrage

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Bayesian investigation of SARS-CoV-2-related mortality in France

Louis Duchemin, Philippe Veber, Bastien Boussau

Peer Community Journal . 2 ( e6 )

DOI: 10.1101/2020.06.09.20126862

2022

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An appraisal of graph embeddings for comparing trophic network architectures

Christophe Botella, Stéphane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller

Methods in Ecology and Evolution . 13 ( 1 ) : 203-216

DOI: 10.1111/2041-210X.13738

2022

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The oxidative cost of helping and its minimization in a cooperative breeder.

Rita Covas, Sophie Lardy, Liliana R. Silva, Benjamin Rey, André C. Ferreira, Franck Theron...

Behavioral Ecology . 33 ( 3 ) : 504-517

DOI: 10.1093/beheco/arab152

2022

Article dans une revue

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Co-variation between glucocorticoids, behaviour and immunity supports the pace-of-life syndrome hypothesis: an experimental approach

Jeffrey Carbillet, Benjamin Rey, Rupert Palme, Chloé Monestier, Luca Börger, Typhaine Lavabre...

Proceedings of the Royal Society B: Biological Sciences . 289 ( 1975 ) : 20220464

DOI: 10.1098/rspb.2022.0464

2022

Article dans une revue

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Litter characteristics and helping context during early life shape the responsiveness of the stress axis in a wild cooperative breeder

Aurélie Cohas, Coraline Bichet, Rébecca Garcia, Sylvia Pardonnet, Sophie Lardy, Benjamin Rey

BioRxiv . 75 : 171

DOI: 10.1101/2021.06.11.448015

2022

Article dans une revue

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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

2022

Article dans une revue

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DNA methylation as a tool to explore ageing in wild roe deer populations

Jean-François Lemaître Lemaître, Benjamin Rey, Jean-Michel Gaillard, Corinne Régis, Emmanuelle Gilot-Fromont, François Débias...

Molecular Ecology Resources . 22 ( 3 ) : 1002-1015

DOI: 10.1111/1755-0998.13533

2022

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Taking full advantage of modelling to better assess environmental risk due to xenobiotics

Sandrine Charles, Aude Ratier, Virgile Baudrot, Gauthier Multari, Aurélie Siberchicot, Dan Wu...

Environmental Science and Pollution Research .

DOI: 10.1007/s11356-021-15042-7

2022

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Influence of secondary symbionts on host plant utilization and selection in the whitefly Bemisia tabaci.

Sylvain Benhamou, Isabelle Rahioui, Hélène Henri, Zainab Belgaidi, Hubert Charles, Pedro da Silva...

10. Congress of the International Symbiosis Society - 3rd International Conference on Holobionts .

2021

Poster

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Pôles techniques

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Publications

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Beyond accuracy : score calibration in deep learning models for camera trap image sequences

The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Validation of a field-friendly faeces drying and storage method for quantifying faecal glucocorticoid metabolites in African elephants (Loxodonta africana) opens up new perspectives for conservationists

Oak masting drivers vary between populations depending on their climatic environments

DRomics, a workflow to exploit dose-response omics data in ecotoxicology

Universal DNA methylation age across mammalian tissues

DNA methylation networks underlying mammalian traits

Nine tips for ecologists using machine learning

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

The for gene as one of the drivers of foraging variations in a parasitic wasp

PhylteR: efficient identification of outlier sequences in phylogenomic datasets

Neural Networks beyond explainability: Selective inference for sequence motifs

Age and spatio-temporal variations in food resources modulate stress-immunity relationships in three populations of wild roe deer

Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Meta-transcriptomics reveals stress adaptation processes in microbial communities differing in exposure history

Influence of bacterial symbionts on host niche and ecological diversification: an integrative approach in a whitefly model

Decline in telomere length with increasing age across nonhuman vertebrates: A meta‐analysis

tidy tree : A New Layout for Phylogenetic Trees

The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images

Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks

Bayesian investigation of SARS-CoV-2-related mortality in France

An appraisal of graph embeddings for comparing trophic network architectures

The oxidative cost of helping and its minimization in a cooperative breeder.

Co-variation between glucocorticoids, behaviour and immunity supports the pace-of-life syndrome hypothesis: an experimental approach

Litter characteristics and helping context during early life shape the responsiveness of the stress axis in a wild cooperative breeder

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

DNA methylation as a tool to explore ageing in wild roe deer populations

Taking full advantage of modelling to better assess environmental risk due to xenobiotics

Influence of secondary symbionts on host plant utilization and selection in the whitefly Bemisia tabaci.