Marie Brunet

Financement

• 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 $. (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. 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

• 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
• 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
• 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
• Sébastien Leblanc, Marie A. Brunet, Jean-François Jacques, Amina M. Lekehal, Andréa Duclos, Alexia Tremblay, Alexis Bruggeman-Gascon, Sondos Samandi, Mylène Brunelle, Alan A. Cohen, Michelle S. Scott, Xavier Roucou. (2023). Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. Genomics, Proteomics & Bioinformatics. DOI
• 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
• Inès Khatir, Marie A. Brunet, Anna Meller, Florent Amiot, Tushar Patel, Xavier Lapointe, Jessica Avila Lopez, Noé Guilloy, Anne Castonguay, Mohammed Amir Husain, Joannie St. Germain, François-Michel Boisvert, Mélanie Plourde, Xavier Roucou, Benoit Laurent. (2023). Decoupling of mRNA and Protein Expression in Aging Brains Reveals the Age-Dependent Adaptation of Specific Gene Subsets. Cells. DOI
• Joannie St-Germain, Muhammad Riaz Khan, Viktoriia Bavykina, Rebecka Desmarais, Micah Scott, Guylain Boissonneault, Marie A. Brunet, Benoit Laurent. (2023). Functional Characterization of a Phf8 Processed Pseudogene in the Mouse Genome. Genes. DOI
• 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
• Marie A. Brunet, Sébastien Leblanc, Xavier Roucou. (2022). OpenVar: functional annotation of variants in non-canonical open reading frames. Cell & Bioscience. 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
• 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. EMBO reports. DOI
• (2021). OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic acids research. DOI
• (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
• (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
• (2018). Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome research. DOI

Autres contributions

Cours enseignés à l'UdeS

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

Divers

• 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.