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Marie Brunet

Professeure, Faculté de médecine et des sciences de la santé
FMSS Département de pédiatrie

Présentation

Sujet de recherche

Bioinformatique, Gènes, Génomique, Maladies neurodégénératives, Protéines, Protéomique

Disciplines de recherche

Biochimie, Biologie cellulaire, Biologie moléculaire, Génétique, Médecine vétérinaire, Pharmacologie, Statistiques

Mots-clés

biochemistry, bioinformatics, biostatistics, cellular biology, machine learning, molecular evolution, Proteogenomique

Intérêts de recherche

Développement de méthodes analytiques et modèles afin de mieux explorer et comprendre les relations génotype-phénotype, en particulier dans le cadre de maladies rares et cancers pédiatriques.

Langues parlées et écrites

Anglais, Espagnol (castillan), Français

Diplômes

(2016). Reconstruction of P2X7R molecular evolution: insights onto its carboxyl tail function (Doctorat, PhD). University of Cambridge - Christ's College.

(2011). Action de la génistéine sur le Cystic Fibrosis Transmembrane Regulator (CFTR) : étude sur la muqueuse colique chez la souris (Équivalent du doctorat, Doctorat de Médecine Vétérinaire). Ecole Nationale Vétérinaire d'Alfort.

Titres de compétence

(2020) Certificate of expertise in Machine Learning (theory, mathematics and code).

Expérience académique

Professeur Adjoint / Assistant Professor. (2021-). Université de Sherbrooke. Canada.

Chercheure en Emergence / Early Career Researcher. (2021-2021). Centre Hospitalier Univ. de Sherbrooke. Canada.

Associée de Recherche / Research Associate. (2019-2021). Université de Sherbrooke. Canada.

Postdoctorat / Postdoctoral Fellow. (2016-2018). Université de Sherbrooke. Canada.

Prix et distinctions

  • (2019) Award Jean-Marie Beauregard. FRQS / Université de Sherbrooke. (Prix).
  • (2019) CNPN 2019 Best Presentation Award. Canadian National Proteomics Network. (Prix).
  • (2018) HUPO World Congress 2018 Best Presentation Award. HUPO. (Prix).
  • (2018) Proteomeus Annual Symposium 2018 Best Presentation Award. Proteomeus. (Prix).
  • (2018) Genome Canada Travel Award. Genome Canada. (Prix).
  • (2018) PROTEO Travel Award. PROTEO. (Prix).
  • (2017) CNPN 2017 Best Talk Award. Canadian National Proteomics Network. (Prix).
  • (2017) Genome Canada Travel Award. Genome Canada. (Prix).
  • (2017) Proteomeus Annual Symposium 2017 Best Talk Award. Proteomeus. (Prix).
  • (2015) Gates Cambridge Scholarship. University of Cambridge. (Distinction).
  • (2012) Silver Medal for Outstanding Veterinary Medicine Thesis. Ecole Nationale Vétérinaire d'Alfort. (Distinction).
  • (2011) Erasmus Research Abroad Scholarship. Ecole Nationale Vétérinaire d'Alfort. (Distinction).

Financement

  • Subvention. (Obtenu). Cocandidat. Challenging the dogmas of monocistronic genes and pseudogenes using proteogenomics and systems biology approaches to better define the human proteome in health and diseases. Instituts de Recherche en Santé du Canada (IRSC). Genomics. 1 166 625 $. (2021-2026)
  • Bourse de recherche. (Obtenu). Candidat principal. FRQS Junior 1 - Intelligence Artificielle appliquée aux Sciences de la Santé. Fonds de recherche du Québec - Santé (FRQS). 80 000 $. (2021-2025)
  • Subvention. (Obtenu). Candidat principal. University Start-up Funds. Université de Sherbrooke. 140 000 $. (2021-2024)
  • Subvention. (Obtenu). Cocandidat. Assessing the clinical stages of Alzheimer's disease: identification of molecular biomarkers in blood cells.. Centre de Recherche sur le Vieillissement de l'Université de Sherbrooke (CdRV). Initiatives Stratégiques. 20 000 $. (2021-2022)
  • Subvention. (Obtenu). Cocandidat. ALS Canada Project Grant "Cracking the FUS code in ALS: From the dual-coding gene FUS, AltFUS engages too in the pathology". ALS Canada. Project Grant. 125 000 $. (2018-2021)
  • Bourse d’études. (Terminé). Candidat principal. Gates Cambridge Scholarship. Bill and Melinda Gates Foundation. Gates Cambridge. 130 000 $. (2011-2015)

Publications

Articles de revue

  • Leblanc, S*; Brunet, MA; Jacques, JF; Lekehal, AM*; Duclos, A*; Tremblay, A*; Bruggeman-Gascon, A*; Samandi, S; Brunelle, M; Cohen, AA; Scott MS; Roucou, X. (2021). Newfound coding potential of transcripts unveils missing members of human protein communities. eLife (Article soumis).
  • Brunet, MA; Lucier, JF; Levesque, M; Leblanc, S*; Jacques, JF; Al-Saedi, H*; Guilloy, N*; Grenier, F*; Avino, M*; Fournier, I; Salzet, M; Ouangraoua, A; Scott, M; Boisvert, FM; Roucou, X. (2021). OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acid Research Database Issue gkaa1036. (Article publié).
  • Brunet, MA; Leblanc, S*; Roucou, X. (2021). OpenVar: Exploring alternative ORFs to bridge genotypes and phenotypes. Nature Genetics (Article soumis).
  • Brunet, MA*; Jacques, JF; Nassari, S*; Tyzack, GE*; McGoldrick, P*; Zinman, L; Jean, S; Robertson, J; Patani, R; Roucou, X. (2020). FUS gene is dual-coding with both proteins united in FUS-mediated toxicity. EMBO Reports e202050640 e202050640. (Article publié).
  • Brunet, MA; Lekehal, AM*; Roucou, X. (2020). How to illuminate the dark proteome using the multi-omic OpenProt resource. Current Protocols in Bioinformatics 71 (1), e103. (Article publié).
  • Leblanc, S*; Brunet, MA. (2020). Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses. Computational and Structural Biotechnology Journal 18 2836-2850. (Article publié).
  • Roucou, X; Brunet, MA. (2020). Multiomic study supports polycistronic annotations of genomes. Science e-Letter online. (Article publié).
  • Brunet MA, Leblanc S*, Roucou X. (2020). Reconsidering Proteomic Diversity with Functional Investigation of Small ORFs and Alternative ORFs. Experimental Cell Research 393 (1), 112057. (Article publié).
  • Dubois M-L*, Samandi S*, Brunelle M, Frion J*, Toupin A*, Brunet MA*, Jacques JF, Lévesque D, Scott MS, Lavigne P, Roucou X co-corresponding, Boisvert FM co-corresponding. (2020). UBB Pseudogene 4 Encodes Functional Ubiquitin Variants. Nature Communications 11 (1), 1306. (Article publié).
  • Cohen, AA; Wey, TW*; Dansereau, G*; Roberge E; Legault, V; Brunet, MA*; Kemnitz, JW; Ferrucci, L. (2019). Conservation of integrative physiological aging mechanisms across primates. Innovation in Aging 3 S8. (Article publié).
  • Dansereau D*, Wey TW*, Legault V, Brunet MA*, Kemnitz JW, Ferrucci L, Cohen AA. (2019). Conservation of physiological dysregulation signatures of aging across primates. Aging Cell e12925 e12925. (Article publié).
  • Brunet MA*, Roucou X. (2019). Mass Spectrometry-Based Proteomics Analyses Using the Openprot Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. J. Vis. Exp. e59589 e59589. (Article publié).
  • Brunet MA*, Brunelle M, Lucier JF, Delcourt V*, Levesque M, Grenier F, Samandi S*, Leblanc S*, Aguilar JD*, Dufour P*, Jacques JF, Fournier I, Ouangraoua A, Scott MS, Boisvert FM, Roucou X. (2018). OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Research Database issue Online. (Article publié).
  • Brunet MA*, Levesque SA, Hunting DJ, Cohen AA, Roucou X. (2018). Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Research 28 609-624. (Article publié).

Livres

  • Kirpensteijn J, Gert ter Haar. (2015). (Book Translation) Chirurgie de reconstruction et gestion des blessures du chien et chat. France : MED'COM. DOI. (Article publié).
  • Sturgess K. (2015). (Book Translation) Médecine Interne Féline. France : MED'COM. DOI. (Article publié).

Articles de journaux

  • (2013). Die Another Day – When Biology Becomes a Crime Hunt. Huffington Post, [online].

Ressources en ligne

  • Brunet, MA; Roucou, X. (2021). OpenVar website: Exploring unannotated ORFs to bridge genotypes and phenotypes. Site Web.
  • Brunet, MA; Lucier, JF; Levesque, M; Roucou, X. (2019). OpenProt website: deeper functional annotation of the coding potential of eukaryotic genomes. Site Web.
  • (2015). You Only Live Twice – Molecular Evolution of P2X7 Receptor. Site Web.

Articles de conférence

  • Brunet, MA; Roucou, X. (2021). ORAL:. The Festival of Genomics and BioData. (Article publié).
  • Leblanc, S*; Brunet, MA; Jacques, JF; Lekehal, AM*; Duclos, A*; Tremblay, A*; Bruggeman-Gascon, A*; Samandi, S; Brunelle, M; Cohen, AA; Scott MS; Roucou, X. (2021). ORAL:. US HUPO 2021. (Article publié).
  • Guilloy, N*; Leblanc, S*; Jacques, JF; Brunet, MA; Roucou, X. (2021). OpenCMS: personalized proteogenomics databases using deep annotations for functional proteomics. US HUPO 2021. (Article publié).
  • Rocha J*, Brunet MA*, St-Germain J, Avila Lopez J*, Miard S, Picard F, Plourde M, Laurent B. (2020). Age-related changes in the transcriptomic signature of the adult mouse choroid plexus. "Cerebral Fluid Flow and Function: Lymphatics, Glymphatics and the Choroid Plexus". (Article publié).
  • Brunet, MA; Jacques, JF; Nassari, S; Tyzack, GE; McGoldrick, P; Zinman, L; Jean, S; Robertson, J; Patani, R; Roucou, X. (2020). FUS gene is dual-coding with both proteins united in FUS-mediated toxicity. Virtual 31st International Symposium on ALS/MND. (Article publié).
  • Brunet MA*, Jacques JF, Lekehal AM*, Roucou X. (2020). Proteogenomic analysis reveals FUS gene as dual-coding with both proteins united in molecular hallmarks of amyotrophic lateral sclerosisORAL:. US HUPO 2020: From Genes to Function. (Article publié).
  • Rocha J*, Brunet MA*, St-Germain J, Avila Lopez J*, Miard S, Picard F, Plourde M, Laurent B. (2019). Age-related changes in the transcriptomic signature of the adult mouse choroid plexus. International Symposium “Biology of Aging: Understanding aging to better intervene”. (Article publié).
  • Rocha J*, Brunet MA*, Avila Lopez J*, Miard S, Picard F, Plourde M, Laurent B. (2019). Age-related changes in the transcriptomic signature of the adult mouse choroid plexus. 2019 RiboClub Annual Meeting. (Article publié).
  • Leblanc, S*; Jacques, JF; Samandi, S; Brunelle, M; Brunet, MA; Scott, MS; Roucou, X. (2019). ORAL:. CNPN 2019 Annual Meeting. (Article publié).
  • Brunet MA*, Jacques JF, Roucou X. (2019). The noise of silence: ALS-linked FUS synonymous mutations alter an overlapping open reading frame, which is responsible for pathological hallmarks. FMSS Annual Day. (Article publié).
  • Brunet MA*, Jacques JF, Roucou X. (2019). The noise of silence: ALS-linked FUS synonymous mutations alter an overlapping open reading frame, which is responsible for pathological hallmarks. CNPN 2019 Annual Meeting. (Article publié).
  • Leblanc, S*; Brunet, MA; Jacques, JF; Samandi, S; Scott, MS; Roucou, X. (2018). Discovering novel proteins in interaction networks. HUPO 2018 World Congress. (Article publié).
  • Brunet MA*, Jacques JF, Nassari S*, Jean S, Roucou X. (2018). FUS is a dual-coding gene: both proteins cooperate for the worst in Amyotrophic Lateral Sclerosis (ALS). FMSS Annual Day 2018. (Article publié).
  • Brunet MA*, Raisch J*, Rivard N, Roucou X. (2018). FZD1 gene encodes a second small protein, which, too, activates the ?-catenin pathway. Proteomeus Annual Symposium 2018. (Article publié).
  • Brunet MA*, Jacques JF, Raisch J*, Dubois ML*, Rivard N, Boisvert FM, Roucou X. (2018). Large-scale proteomic analysis of alternative ORFs using OpenProt reveals important novel proteins, from ubiquitinylation to the Wnt signaling pathway. CNPN 2018 Annual Meeting. (Article publié).
  • Brunet MA*, Raisch J*, Dubois ML*, Jacques JF, Brunelle M, Rivard N, Boisvert FM, Roucou X. (2018). Large-scale proteomic analysis of alternative ORFs using OpenProt reveals important novel proteins,from ubiquitinylation to the Wnt signaling pathwayORAL:. CNPN 2018 Annual Meeting. (Article publié).
  • Brunet MA*, Jacques JF, Nassari S*, Jean S, Roucou X. (2018). Large-scale proteomic analysis of alternative open reading frames reveals novel pivotal proteins in neurodegenerative diseases such as ALSORAL:. HUman Proteome Organization 2018 World Congress. (Article publié).
  • Leblanc, S; Brunet, MA; Jacques, JF; Samandi, S; Scott, MS; Roucou, X. (2018). ORAL:. Proteomeus Annual Symposium 2018. (Article publié).
  • Brunet MA*, Roucou X. (2018). OpenProt enables non-canonical open reading frames detection in ALS-associated genes. ALS Canada Annual Symposium 2018. (Article publié).
  • Dubois, ML*; Delattre, P*; Jacques, JF; Levesque, D; Delcourt, V*; Beaudoin, MC; Brunelle, M; Samandi, S; Brunet, MA; Lavigne, P; Roucou, X.; Boisvert, FM. (2018). UbKEKS: A novel ubiquitin variant expressed from a pseudogene. HUPO 2018 World Congress. (Article publié).
  • Brunet MA*, Delcourt V*, Jacques JF, Roucou X. (2017). ALS-linked FUS gene encodes for a second small protein altFUS that regulates FUS localization and macro-autophagy. Gordon Research Conference Series: Amyotrophic Lateral Sclerosis (ALS) & Related Motor Neuron Diseases. (Article publié).
  • Brunet MA*, Delcourt V*, Jacques JF, Roucou X. (2017). AltFUS: a novel mitochondrial protein encoded in an alternative ORF of FUS gene that regulates FUS localisation and macro-autophagyORAL:. Proteomeus Annual Symposium 2017. (Article publié).
  • Brunet MA*, Delcourt V*, Jacques JF, Roucou X. (2017). Discovery of A Novel Protein Encoded in an Alternative Open Reading Frame of FUS Gene and itsImportance in ALS. Keystone Symposia: OMICS Strategies to Study the Proteome. (Article publié).
  • Brunet MA*, Delcourt V*, Jacques JF, Roucou X. (2017). Discovery of A Novel Protein Encoded in an Alternative Open Reading Frame of FUS Gene and itsImportance in ALSORAL:. Keystone Symposia: OMICS Strategies to Study the Proteome. (Article publié).
  • Brunet MA*, Delcourt V*, Jacques JF, Roucou X. (2017). Large-scale proteomic analysis of alternative open reading frames reveals a new player in ALS, altFUS encoded within FUS geneORAL:. CNPN 2017 Annual Meeting. (Article publié).
  • Brunet MA*, Murrell-Lagnado R. (2014). Genetic Analysis of the P2X7 Receptor: Insights into its Structure and Function. Purines 2014 International Conference. (Article publié).
  • Brunet MA*, Robinson L*, Murrell-Lagnado R. (2013). A Comparison of the Expression, Degradation, and Subcellular Distribution of Rodent versus Human P2X7 Receptors. 5th UK Purine Club Meeting. (Article publié).
  • Brunet MA*, Murrell-Lagnado R. (2013). Genetic Analysis of P2X7 Receptor: What Evolution Tells Us?. 5th UK Purine Club Meeting. (Article publié).
  • Brunet MA*, Robinson L*, Murrell-Lagnado R. (2013). The role of the P2X7 Receptor C-terminal in Trafficking and Targeting to the Plasma Membrane. 37th Congress of the International Union of Physiological Sciences. (Article publié).
  • Brunet MA*, Robinson L*, Murrell-Lagnado R. (2013). The role of the P2X7 Receptor C-terminal in Trafficking and Targeting to the Plasma Membrane. Cambridge Ion Channel Forum. (Article publié).
  • Brunet MA*, Murrell-Lagnado R. (2012). P2X7 Receptor Expression, Trafficking and Targeting in Fibroblasts. Pharmacology Departmental Away Day 2012. (Article publié).
  • Brunet MA*, Murrell-Lagnado R. (2012). The Role of the P2X7 Receptor C-terminal Domain in Targeting and Trafficking to the Plasma Membrane. 4th UK Purine Club Meeting. (Article publié).

Autres contributions

Gestion d'évènements

  • Co-organisateur. (2019) Canadian National Proteomics Network Pre-Symposium. (Conférence).

Activités de collaboration internationale

  • Investigateur. Royaume-Uni. Collaboration: exploration of the dual-coding nature of the FUS gene in iPSC-derived motor neurons from ALS patients.
  • Co-investigateur. Turquie. Collaboration: exploration of the mosaic translation hypothesis through ribosomal frameshifting.
  • Co-investigateur. France. Collaboration: identification of novel targets for the development of a glioblastoma-specific immunotherapy strategy using chimeric antigen receptor macrophages.
  • Co-investigateur. Royaume-Uni. International Consortium led by GENCODE looking at the insertion of novel coding sequences within current genome annotations.

Présentations

  • (2021). Analyse intelligente des données multi-omiques. ACFAS international congress - colloque 114: Génomique Fonctionnelle, vers la découverte du plein potentiel codant versus non-codant du génome. Sherbrooke, Canada
  • (2021). Deep proteomics reveal hidden treasures in our genome. PostDoc Day Université de Sherbrooke. Sherbrooke, Canada
  • (2021). Newfound coding potential of transcripts unveils missing members of human protein communities. Invitation to Dr. Edward Marcotte's group lab meeting (virtual event). Austin, États-Unis
  • (2021). The noise of silence: exploring the deep proteome reveals hidden treasures in our genome. The Festival of Genomics and Biodata. London, Royaume-Uni
  • (2020). Proteogenomic analysis reveals FUS gene as dual-coding with both proteins united in molecular hallmarks of amyotrophic lateral sclerosis. US HUman Proteome Organization: From Genes to Function. États-Unis
  • (2019). Human genes are polycistronic: the example of the ALS-linked FUS gene. Francis Crick Institute Internal Seminar. Royaume-Uni
  • (2018). FUS is a dual-coding gene: implications for ALS. ALS Canada Annual Symposium 2018. Canada
  • (2018). Large-scale proteomic analysis of alternative ORFs using OpenProt reveals important novel proteins, from ubiquitinylation to the Wnt signaling pathway. CNPN 2018 Annual Meeting. Canada
  • (2018). Large-scale proteomic analysis of alternative open reading frames reveals novel pivotal proteins in neurodegenerative diseases such as ALS. HUPO 2018 World Congress. États-Unis
  • (2018). OpenProt: Deeper proteomic annotations shed new light in ALS and Colorectal Cancer mechanisms. Biochemistry Departmental Research Seminar. Canada
  • (2017). ALS-linked FUS gene encodes for a second small protein, altFUS, which regulates FUS localization and macro-autophagy. Biochemistry Departmental Research Seminar. Canada
  • (2017). AltFUS: a novel mitochondrial protein encoded in an alternative ORF of FUS gene that regulates FUS localisation and macro-autophagy. Proteomeus Annual Symposium 2017. Canada
  • (2017). Discovery of a Novel Protein Encoded in an Alternative Open Reading Frame of FUS gene and its importance in ALS. Keystone Symposia: OMICS Strategies to Study the Proteome. Breckenridge, États-Unis
  • (2017). Large scale proteomic analysis of alternative open reading frames reveals a new player in ALS: altFUS encoded within FUS gene. Canadian National Proteomic Network Annual Meeting. Toronto, Canada
  • (2016). Eukaryotic mRNAs can code for more than one protein: the end of a dogma. Pharmacology Departmental Invited Seminar. Royaume-Uni
  • (2014). Genetic Analysis of P2X7 Receptor: Evolutionary Insights into its Structure and Function. Pharmacology Departmental Seminar Series. Royaume-Uni