Author

Renaud Bernatchez

Université Laval

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:dimensionality reduction· 2 Assay:imaging· 2 Approach:transformer / foundation model· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1

Frequent Co-Authors

Flavie Lavoie-CardinaliD· 2 shared Aitor González-MarfiliD· 1 shared ALAIN D. LESAGEiD· 1 shared Alain Lévesque· 1 shared Alexandre DumaisiD· 1 shared Amelie Felx· 1 shared Andre Lemieux· 1 shared André Luyet· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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2 shared papersBioinformatics

Flavie Lavoie-CardinalORCID

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Author profile →

3 papers

Recent·Most cited

PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping

Aitor González-Marfil, Lenka Backová, Renaud Bernatchez, Iván Hidalgo-Cenalmor, Antoine Dufour, Guillaume Jacquemet, Flavie Lavoie-Cardinal, Ignacio Arganda-Carreras, Estibaliz Gómez-de-Mariscal

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

bioRxiv · Nov 3, 2026 · PreprintBioinformatics

A Self-Supervised Foundation Model for Robust and Generalizable Representation Learning in STED Microscopy

Anthony Bilodeau, Frédéric Beaupré, Julia Chabbert, Kamylle Thériault, Andréanne Deschênes, Jean-Michel Bellavance, Koraly Lessard, Renaud Bernatchez, Paul De Koninck, Christian Gagné, Flavie Lavoie‐Cardinal

This paper introduces STED-FM, a foundation model for STED microscopy that learns robust representations without extensive annotations, improving downstream tasks like classification, segmentation, and image denoising.

bioRxiv · Jun 6, 2025 · PreprintBioinformatics

Chronic stress exposure alters the gut barrier: sex-specific effects on microbiota and jejunum tight junctions

Ellen Doney, Laurence Dion‐Albert, François Coulombe-Rozon, Natasha Osborne, Renaud Bernatchez, Sam E.J. Paton, Fernanda Neutzling Kaufmann, Roseline Olory Agomma, José L. Solano, Raphael Gaumond, Katarzyna Dudek, Joanna Kasia Szyszkowicz, Frederic Aardema, Lahcen Aït Bentaleb, Janique Beauchamp, , André Luyet

This study investigates how chronic stress affects intestinal barrier function and microbiota in mice, revealing sex-specific effects and potential translational relevance to human depression.

Biological Psychiatry Global Open Science · May 8, 2023Peer-reviewedNeuroscience