Marie Brunet

Prix et distinctions

• (2026) Dean's Honor List. Université de Sherbrooke.
• (2025) Junior 2 Career Award. FRQS.
• (2024) ECR Award. Canadian National Proteomics Network.
• (2024) Outstanding Contribution to Peer Review. CIHR.
• (2021) Junior 1 Career Award. FRQS.

Financement

• Subvention. Leveraging non-canonical translation in pediatric neuroblastoma. Cancer Research Society (QC, Canada). 140 000 $. (2026-2028).
• Subvention. Cannabis Exposure from Pregnancy to Early Childhood: A Family-Triad Brain Health Program CAN-B+FAM. CIHR (Ottawa, Canada). 2 000 000 $. (2026-2029).
• Subvention. Environmental eXposure Profiling for Signatures of Early ColoRectal Cancer (EXPOSECRC). CIHR (Ottawa, Canada). 2 000 000 $. (2026-2031).
• Subvention. Osteoclast-Related cells as Biomarkers for Bone homeostasis in Osteoporosis. CIHR (Ottawa, Canada). 635 000 $. (2025-2030).
• Subvention. Evolutionary and Functional Dynamics of Cytochrome P450 Genes and Pseudogenes. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2024-2025).
  Numéro de subvention : 586846-2023. Voir plus
• Subvention. Deep Learning and Multi-omics to study Pediatric Diseases. Centre de Recherche Medicale de l'Universite de Sherbrooke (Sherbrooke, Canada). Research Chair. 200 000 $. (2023-2028).
• Subvention. Pseudogenization: the overlooked recycling centre of coding DNA. NSERC (Ottawa, Canada). 262 500 $. (2023-2028).
• Subvention. Developing a real-time proteogenomics pipeline. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2023-2024).
  Numéro de subvention : grant.14460729. Voir plus
• Subvention. Informatic infrastructure to foster omics discoveries and innovations. Natural Sciences and Engineering Research Council (Ottawa, Canada). 142 374 $. (2023-2024).
  Numéro de subvention : grant.14453868. Voir plus
• Subvention. Evolutionary and Functional Dynamics of Cytochrome P450 Genes and Pseudogenes. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2023-2024).
  Numéro de subvention : grant.14460462. Voir plus
• Subvention. Developing a real-time proteogenomics pipeline. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2023-2024).
  Numéro de subvention : 571433-2021. Voir plus
• Subvention. Developing a real-time proteogenomics pipeline. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2022-2023).
  Numéro de subvention : grant.13604654. Voir plus
• Subvention. HeLTI cooperative research project: A Multifaceted Maternal-Child Health Intervention Cohort Study for the prevention of childhood obesity. Canadian Institutes of Health Research (Ottawa, Canada). 2 500 000 $. (2022-2027).
  Numéro de subvention : 202112HTC. Voir plus
• Subvention salariée. Developing the intelligence of trans-omics data. Fonds de Recherche du Québec - Santé (QC, Canada). Research Scholars - Junior 1. 235 698 $. (2021-2025).
• Subvention. Developing the intelligence of trans-omics data. Fonds de Recherche du Québec - Santé (QC, Canada). Starting Grant for Young Investigators - Junior 1. 80 000 $. (2021-2025).
• Subvention. Challenging the dogmas of monocistronic genes and pseudogenes using proteogenomics and systems biology approaches to better define the human proteome in health and diseases. Canadian Institutes of Health Research (Ottawa, Canada). 1 166 625 $. (2021-2026).
  Numéro de subvention : 202010PJT. Voir plus
• Subvention. Developing a real-time proteogenomics pipeline. Natural Sciences and Engineering Research Council (Ottawa, Canada). 45 000 $. (2021-2022).
  Numéro de subvention : grant.12997330. Voir plus
• Subvention. Assessing the clinical stages of Alzheimer's disease: identification of molecular biomarkers in blood cells. Réseau québécois de recherche sur le vieillissement (QC, Canada). 20 000 $. (2021-2022).
• Subvention. Développer l’intelligence des données trans-omiques pour révéler les relations génotype – phénotype. Fonds de Recherche du Québec - Santé (Montreal, Canada). 235 698 $. (2020-2024).
  Numéro de subvention : 307936. Voir plus

Publications

Articles

• Zhenfang Du, Felix-Antoine Trifiro, Marie A. Brunet, John R. Prensner. (2026). Microproteins in Human Physiology and Pathology. Biochemistry. DOI
• Amélie Taschereau, Jenna Wong, Soren Harnois-Leblanc, Marie Brunet, Myriam Doyon, Mélina Arguin, Sheryl Rifas-Shiman, Emily Oken, Patrice Perron, Pierre-Étienne Jacques, Luigi Bouchard, Marie-France Hivert. (2026). Machine Learning-Derived Predictive Risk Score for Prediabetes and Type 2 Diabetes Development in Parous Women. Diabetes, Metabolic Syndrome and Obesity. DOI
• Chothani, Sonia, Ruiz-Orera, Jorge, Tierney, Jack AS, Swirski, Michal I, Tjeldnes, Hakon, Kok, Leron W, Clauwaert, Jim, Deutsch, Eric W, Alba, M Mar, Aspden, Julie L, others. (2026). An expanded reference catalog of translated open reading frames for biomedical research. Nucleic acids research.
• Shajari, E, Gagné, D, Malick, M, Roy, P, Delisle, M, Brunet, M, Boisvert, F, Beaulieu, J. (2026). CAG Student Prize Paper--A5 NON-INVASIVE PEPTIDOMIC SIGNATURE DISTINGUISHING ACTIVE AND REMISSIVE IBD USING A NESTED CROSS-VALIDATED MACHINE-LEARNING STUDY. Journal of the Canadian Association of Gastroenterology.
• Wacholder, Aaron, Deutsch, Eric W, Kok, Leron W, van Dinter, Jip T, Lee, Jiwon, Wright, James C, Leblanc, Sebastien, Jayatissa, Ayodya H, Jiang, Kevin, Arefiev, Ihor, others. (2026). Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics. Nature Communications.
• Deutsch, Eric W, Kok, Leron W, Mudge, Jonathan M, Valls, Cristian F, Jungreis, Irwin, Ruiz-Orera, Jorge, Sun, Zhi, Kusebauch, Ulrike, Fierro-Monti, Ivo, Abelin, Jennifer G, others. (2026). Expanding the human proteome with microproteins and peptideins. Nature.
• Gagné, David, Shajari, Elmira, Malick, Mandy, Roy, Patricia, Noël, Jean-François, Gagnon, Hugo, Brunet, Marie A, Carrier, Julie C, Boisvert, François-Michel, Beaulieu, Jean-François. (2026). Exploring an Intermediate Colorectal Cancer Screening Test Based on Stool Proteomics and Machine Learning for Optimizing the Selection of Patients for Colonoscopy Identified From FIT. Molecular & Cellular Proteomics.
• Shajari, Elmira, Gagné, David, Malick, Mandy, Roy, Patricia, Noël, Jean-François, Gagnon, Hugo, Delisle, Maxime, Boisvert, François-Michel, Brunet, Marie A, Beaulieu, Jean-François. (2026). Non-Invasive Assessment of Inflammatory Bowel Disease Activity Using a DIA-Derived Stool Peptidomic Signature and Machine Learning. Frontiers in Molecular Biosciences.
• Véronique Gaudreault, Benoit Marchand, Raphaëlle Larcher, Sonya Nassari, Francis Bourassa, Mathilde Moreau, Dominique Jean, François-Michel Boisvert, Marie A. Brunet, Steve Jean. (2025). A proximity map of RAB GTPases delineates roles for RAB14 in EARP complex and UHRF1BP1 endosomal recruitments. Communications Biology. DOI
• Gagnon, Anthony, Gillet, Virginie, Desautels, Anne-Sandrine, Lepage, Jean-François, Baccarelli, Andrea A, Posner, Jonathan, Descoteaux, Maxime, Brunet, Marie A, Takser, Larissa. (2025). 366. Modeling Cognition and Behavior as a Fuzzy Network: Findings From 3 Independent Pediatric Cohorts. Biological Psychiatry.
• Shajari, E, Malick, M, Roy, P, Delisle, M, Brunet, M, Boisvert, F, Beaulieu, J, others. (2025). A155 STOOL-BASED PROTEIN SIGNATURES FOR NON-INVASIVE ACCURATE DIAGNOSIS AND SUBTYPING OF INFLAMMATORY BOWEL DISEASE THROUGH HIGH-THROUGHPUT PROTEOMICS AND MACHINE LEARNING APPROACHES. Journal of the Canadian Association of Gastroenterology.
• Umut Çakır, Noujoud Gabed, Yunus Emre Köroğlu, Selen Kaya, Senjuti Sinharoy, Vagner A. Benedito, Marie Brunet, Xavier Roucou, Igor S. Kryvoruchko. (2025). Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis. Computational and Structural Biotechnology Journal. DOI
• Sachsenberg, Timo, Pino, Lindsay K, Brunet, Marie, Bludau, Isabell, Kohlbacher, Oliver, Vizcaino, Juan Antonio, Bittremieux, Wout. (2025). Perspectives in computational mass spectrometry: recent developments and key challenges. Bioinformatics advances.
• Shajari, Elmira, Gagné, David, Bourassa, Francis, Malick, Mandy, Roy, Patricia, Noël, Jean-François, Gagnon, Hugo, Delisle, Maxime, Boisvert, François-Michel, Brunet, Marie, others. (2025). Stool-Based Proteomic Signature for the Non-Invasive Classification of Crohn’s Disease and Ulcerative Colitis Using Machine Learning. Clinical and Translational Gastroenterology.
• ́Swirski, Michał I, Tierney, Jack AS, Albà, M Mar, Andreev, Dmitry E, Aspden, Julie L, Atkins, John F, Bassani-Sternberg, Michal, Berry, Marla J, Biffo, Stefano, Boris-Lawrie, Kathleen, others. (2025). Translon: a single term for translated regions. Nature methods.
• Valeriia Vasylieva, Ihor Arefiev, Francis Bourassa, Félix-Antoine Trifiro, Marie A. Brunet. (2024). Proteomics Can Rise to the Challenge of Pseudogenes’ Coding Nature. Journal of Proteome Research. DOI
• Elmira Shajari, David Gagné, Mandy Malick, Patricia Roy, Jean-François Noël, Hugo Gagnon, Marie A. Brunet, Maxime Delisle, François-Michel Boisvert, Jean-François Beaulieu. (2024). Application of SWATH Mass Spectrometry and Machine Learning in the Diagnosis of Inflammatory Bowel Disease Based on the Stool Proteome. Biomedicines. DOI
• Roy M, Mbous Nguimbus L, Badiane PY, Goguen-Couture V, Degrandmaison J, Parent JL, Brunet MA, Roux S. (2024). Galectin-8 modulates human osteoclast activity partly through isoform-specific interactions. Life science alliance. DOI
• Leblanc S, Yala F, Provencher N, Lucier JF, Levesque M, Lapointe X, Jacques JF, Fournier I, Salzet M, Ouangraoua A, Scott MS, Boisvert FM, Brunet MA, Roucou X. (2024). OpenProt 2.0 builds a path to the functional characterization of alternative proteins. Nucleic acids research. DOI
• Shajari, E, Gagné, D, Malick, M, Brunet, M, Delisle, M, Boisvert, F, Beaulieu, J. (2024). A260 Advancing inflammatory bowel disease diagnosis through stool proteomic signatures obtained via DIA-MASS spectrometry and machine learning. Journal of the Canadian Association of Gastroenterology.
• Roy, Michèle, Mbous Nguimbus, Léopold, Badiane, Papa Yaya, Goguen-Couture, Victor, Degrandmaison, Jade, Parent, Jean-Luc, Brunet, Marie A, Roux, Sophie. (2024). Galectin-8 modulates human osteoclast activity partly through isoform-specific interactions. Life Science Alliance.
• Leblanc, Sébastien, Yala, Feriel, Provencher, Nicolas, Lucier, Jean-François, Levesque, Maxime, Lapointe, Xavier, Jacques, Jean-Francois, Fournier, Isabelle, Salzet, Michel, Ouangraoua, Äıda, others. (2024). OpenProt 2.0 builds a path to the functional characterization of alternative proteins. Nucleic Acids Research.
• Laura Kienzle, Stefano Bettinazzi, Thierry Choquette, Marie Brunet, Hajar Hosseini Khorami, Jean-François Jacques, Mathilde Moreau, Xavier Roucou, Christian R. Landry, Annie Angers, Sophie Breton. (2023). A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics. BMC Biology. DOI
• Guilloy N, Brunet MA, Leblanc S, Jacques JF, Hardy MP, Ehx G, Lanoix J, Thibault P, Perreault C, Roucou X. (2023). OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases. Journal of proteome research. DOI
• Çakır, Umut, Gabed, Noujoud, Brunet, Marie, Roucou, Xavier, Kryvoruchko, Igor. (2023). Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability. The FEBS Journal.
• Guilloy, Noe, Brunet, Marie A, Leblanc, Sébastien, Jacques, Jean-François, Hardy, Marie-Pierre, Ehx, Gregory, Lanoix, Joël, Thibault, Pierre, Perreault, Claude, Roucou, Xavier. (2023). OpenCustomDB: integration of unannotated open reading frames and genetic variants to generate more comprehensive customized protein databases. Journal of proteome research.
• David Gagné, Elmira Shajari, Marie-Pier Thibault, Jean-François Noël, François-Michel Boisvert, Corentin Babakissa, Emile Levy, Hugo Gagnon, Marie A. Brunet, David Grynspan, Emanuela Ferretti, Valérie Bertelle, Jean-François Beaulieu. (2022). Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis. International Journal of Molecular Sciences. DOI
• Jonathan M. Mudge, Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Thomas F. Martinez, Jana Felicitas Schulz, Yucheng T. Yang, M. Mar Albà, Julie L. Aspden, Pavel V. Baranov, Ariel A. Bazzini, Elspeth Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, ... Sebastiaan van Heesch. (2022). Standardized annotation of translated open reading frames. Nature Biotechnology. DOI
• Liu W, He QY, Brunet MA. (2022). Editorial: Emerging Proteins and Polypeptides Expressed by "Non-Coding RNAs". Frontiers in cell and developmental biology. DOI
• Hamelin Morrissette J, Tremblay D, Marcotte-Chénard A, Lizotte F, Brunet MA, Laurent B, Riesco E, Geraldes P. (2022). Transcriptomic modulation in response to high-intensity interval training in monocytes of older women with type 2 diabetes. European journal of applied physiology. DOI
• Hamelin Morrissette, Jovane, Tremblay, Dominic, Marcotte-Chénard, Alexis, Lizotte, Farah, Brunet, Marie A, Laurent, Benoit, Riesco, Eléonor, Geraldes, Pedro. (2022). Transcriptomic modulation in response to high-intensity interval training in monocytes of older women with type 2 diabetes. European Journal of Applied Physiology.
• Çakır U, Gabed N, Brunet M, Roucou X, Kryvoruchko I. (2021). Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability. The FEBS journal. DOI
• Marie A Brunet, Jean-Francois Jacques, Sonya Nassari, Giulia E Tyzack, Philip McGoldrick, Lorne Zinman, Steve Jean, Janice Robertson, Rickie Patani, Xavier Roucou. (2021). The FUS gene is dual-coding with both proteins contributing to FUS-mediated toxicity. The EMBO Reports. DOI
• (2021). OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic acids research. DOI
• Brunet, Marie A, Lucier, Jean-Francois, Levesque, Maxime, Leblanc, Sébastien, Jacques, Jean-Francois, Al-Saedi, Hassan RH, Guilloy, Noé, Grenier, Frederic, Avino, Mariano, Fournier, Isabelle, others. (2021). OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Research.
• (2020). Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses. Computational and structural biotechnology journal. DOI
• (2020). How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. Current protocols in bioinformatics. DOI
• (2020). Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs. Experimental cell research. DOI
• (2020). UBB pseudogene 4 encodes functional ubiquitin variants. Nature communications. DOI
• Brunet, Marie A, Lekehal, Amina M, Roucou, Xavier. (2020). How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. Current Protocols in Bioinformatics.
• Leblanc, Sebastien, Brunet, Marie A. (2020). Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses.
• Brunet, Marie A, Leblanc, Sebastien, Roucou, Xavier. (2020). Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs. Experimental cell research.
• Dubois, Marie-Line, Meller, Anna, Samandi, Sondos, Brunelle, Mylène, Frion, Julie, Brunet, Marie A, Toupin, Amanda, Beaudoin, Maxime C, Jacques, Jean-François, Lévesque, Dominique, others. (2020). UBB pseudogene 4 encodes functional ubiquitin variants. Nature communications.
• (2019). Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. Journal of visualized experiments : JoVE. DOI
• (2019). Conservation of physiological dysregulation signatures of aging across primates. Aging cell. DOI
• (2019). OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic acids research. DOI
• Cohen, Alan A, Wey, Tina W, Dansereau, Gabriel, Roberge, Emy, Legault, Véronique, Brunet, Marie, Kemnitz, Joseph W, Ferrucci, Luigi. (2019). CONSERVATION OF INTEGRATIVE PHYSIOLOGICAL AGING MECHANISMS ACROSS PRIMATES. Innovation in Aging.
• Dansereau, Gabriel, Wey, Tina W, Legault, Véronique, Brunet, Marie A, Kemnitz, Joseph W, Ferrucci, Luigi, Cohen, Alan A. (2019). Conservation of physiological dysregulation signatures of aging across primates. Aging cell.
• Brunet, Marie A, Roucou, Xavier. (2019). Mass spectrometry-based proteomics analyses using the OpenProt database to unveil novel proteins translated from non-canonical open reading frames. JoVE (Journal of Visualized Experiments).
• Brunet, Marie A, Brunelle, Mylene, Lucier, Jean-Francois, Delcourt, Vivian, Levesque, Maxime, Grenier, Frédéric, Samandi, Sondos, Leblanc, Sébastien, Aguilar, Jean-David, Dufour, Pascal, others. (2019). OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic acids research.
• (2018). Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome research. DOI
• Brunet, Marie A, Levesque, Sébastien A, Hunting, Darel J, Cohen, Alan A, Roucou, Xavier. (2018). Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome research.

Articles de conférence

• Mudge, Jonathan M, Deutsch, Eric, Kok, Leron, Moritz, Robert, Choudhary, Jyoti, Vizcaino, Juan Antonio, Brunet, Marie, Prensner, John, van Heesch, Sebastiaan, Frankish, Adam. (2025). Progress in the annotation of the dark proteome. EUROPEAN JOURNAL OF HUMAN GENETICS.
• Larcher, R, Marchand, B, Gaudreault, V, Nassari, S, Bourassa, F, Brunet, M, Jean, S. (2024). A PROXIMITY INTERACTION MAP OF RAB GTPASES IDENTIFIES RAB14 AS A REGULATOR OF THE EARP COMPLEX IN ENDOSOMAL SORTING. MOLECULAR BIOLOGY OF THE CELL.
• Nguimbus, Leopold Mbous, Roy, Michele, Brunet, Marie A, Roux, Sophie. (2023). Interactome of Galectin-8 Isoforms to Dissect their Impact on Human Osteoclasts. JOURNAL OF BONE AND MINERAL RESEARCH.
• Brunet, Marie. (2023). The coding potential of pseudogenes: between relics and new beginnings. PROTEIN SCIENCE.

Autres contributions

Cours enseignés ou supervisés à l'UdeS

• BCM513 - Analyse de données en biochimie avec Python. (2023-2026). (2CR).
• BCH724 - Python pour l’analyse de données en biochimie. (2023-2025). (2CR).

Activités professionnelles

• TransCODE. Executive member. Sherbrooke, Canada. (2025-2028).
• Canadian National Proteomics Network. VP Communications. Montreal, Canada. (2024-2028).

Divers

• Bellavance, Caroline, Raufaste-Cazavieille, Virgile, Trifiro, Felix-Antoine, Droit, Arnaud, Langlois, Sylvie, Sontag, Thomas, Cellot, Sonia, Sinnett, Daniel, Lavallée, Vincent-Philippe, Tran, Thai Hoa, others. (2025). Multi-omics evaluation of relapsed pediatric cancers: What information do these sequential analyses yield?.
• Liu, Wanting, He, Qing-Yu, Brunet, Marie A. (2022). Emerging Proteins and Polypeptides Expressed by “Non-Coding RNAs”. Frontiers in Cell and Developmental Biology.
• Jonathan M. Mudge, Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Jose Manuel Gonzalez, Michele Magrane, Thomas Martinez, Jana Felicitas Schulz, Yucheng T. Yang, M. Mar Albà, Pavel V. Baranov, Ariel Bazzini, Elspeth Bruford, Maria Jesus Martin, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Paul Flicek, Adam Frankish, ... Sebastiaan van Heesch. (2021). A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq.