Portrait de Jacques Corbeil

Jacques Corbeil

Membre affilié
Professeur titulaire, Université Laval
Linearis Venture and Labs
Sujets de recherche
Apprentissage automatique appliqué
Biologie computationnelle
IA et santé
Site web
Google Scholar
LinkedIn

Biographie

Le Dr Jacques Corbeil se concentre sur l'utilisation des dernières techniques de bio-informatique et d'apprentissage automatique pour faciliter le diagnostic, le pronostic et la réponse au traitement. Les techniques modernes de génomique et de métabolomique génèrent un déluge de données qui doivent être interprétées à l'aide de nouvelles approches informatiques. Le Dr Corbeil utilise des instruments et des méthodologies de pointe pour faciliter l'interprétation de données complexes, y compris la spectrométrie de masse à haut débit, en particulier la métabolomique et le séquençage next-gen.

Les recherches du Dr Corbeil portent notamment sur la manière dont les micro-organismes infectieux interagissent avec leur hôte, sur les effets des antibiotiques sur notre flore microbienne et sur l'environnement, et sur la manière de concevoir de petites molécules et des médicaments pour interférer avec des fonctions microbiennes spécifiques et avec la progression du cancer. Travaillant à l'interface de l'apprentissage automatique et des sciences omiques, il possède une expertise dans l'intégration des données omiques et se spécialise dans l'analyse de données massives appliquée aux maladies infectieuses et au cancer. Le Dr Corbeil collabore avec de nombreuses industries pour améliorer leurs processus et mettre en œuvre des stratégies d'intelligence artificielle. Depuis 2004, le Dr Corbeil est titulaire de la Chaire de recherche du Canada en génomique médicale (niveau 1).

Publications

Comparative genomics of Pseudomonas paraeruginosa
Maxime Déraspe
Lori L. Burrows
Romé Voulhoux
Daniela Centrón
Jacques Corbeil
Paul H Roy
ABSTRACT The PA7-clade (or group 3) of Pseudomonas aeruginosa is now recognized as a distinct species, Pseudomonas paraeruginosa. We report … (voir plus)here the genomic sequences of six new strains of P. paraeruginosa: Zw26 (the first complete genome of a cystic fibrosis isolate of P. paraeruginosa), draft genomes of four burn and wound strains from Argentina very closely related to PA7, and of Pa5196, the strain in which arabinosylation of type IV pili was documented. We compared the genomes of 82 strains of P. paraeruginosa and confirmed that the species is divided into two sub-clades. Core genomes are very similar, while most differences are found in “regions of genomic plasticity” (RGPs). Several genomic deletions were identified, and most are common to the CR1 sub-clade that includes Zw26 and Pa5196. All strains lack the type 3 secretion system (T3SS) and instead use an alternative virulence strategy involving an exolysin, a characteristic shared with group 5 P. aeruginosa. All strains tend to be multiresistant like PA7, with a significant proportion of carbapenem-resistant strains, either oprD mutants or carrying carbapenemase genes. Although P. paraeruginosa is still relatively rare, it has a worldwide distribution. Its multiresistance and its alternative virulence strategy need to be considered in future therapeutic development. IMPORTANCE Pseudomonas aeruginosa is an important opportunistic pathogen causing respiratory infections, notably in cystic fibrosis, and burn and wound infections. Our study reports six new genomes of Pseudomonas paraeruginosa, a new species recently reported as distinct from P. aeruginosa. The number of sequenced genomes of P. paraeruginosa is only about 1% that of P. aeruginosa. We compare the genomic content of nearly all strains of P. paraeruginosa in GenBank, highlighting the differences in core and accessory genomes, antimicrobial resistance genes, and virulence factors. This novel species is very similar in environmental spectrum to P. aeruginosa but is notably resistant to last-line antibiotics and uses an alternative virulence strategy based on exolysin—this strategy being shared with some P. aeruginosa outliers.
2025-07-25
Journal of Bacteriology (publié)
doi.org
Comparative genomics of
<i>Pseudomonas paraeruginosa</i>
Maxime Déraspe
Lori L. Burrows
Romé Voulhoux
Daniela Centrón
Jacques Corbeil
Paul H Roy
2025-07-25
Journal of Bacteriology (publié)
doi.org
Comparative genomics of Pseudomonas paraeruginosa.
Maxime Déraspe
Lori L. Burrows
Romé Voulhoux
D. Centrón
Jacques Corbeil
Paul H Roy
The PA7-clade (or group 3) of Pseudomonas aeruginosa is now recognized as a distinct species, Pseudomonas paraeruginosa. We report here the … (voir plus)genomic sequences of six new strains of P. paraeruginosa: Zw26 (the first complete genome of a cystic fibrosis isolate of P. paraeruginosa), draft genomes of four burn and wound strains from Argentina very closely related to PA7, and of Pa5196, the strain in which arabinosylation of type IV pili was documented. We compared the genomes of 82 strains of P. paraeruginosa and confirmed that the species is divided into two sub-clades. Core genomes are very similar, while most differences are found in "regions of genomic plasticity" (RGPs). Several genomic deletions were identified, and most are common to the CR1 sub-clade that includes Zw26 and Pa5196. All strains lack the type 3 secretion system (T3SS) and instead use an alternative virulence strategy involving an exolysin, a characteristic shared with group 5 P. aeruginosa. All strains tend to be multiresistant like PA7, with a significant proportion of carbapenem-resistant strains, either oprD mutants or carrying carbapenemase genes. Although P. paraeruginosa is still relatively rare, it has a worldwide distribution. Its multiresistance and its alternative virulence strategy need to be considered in future therapeutic development.IMPORTANCEPseudomonas aeruginosa is an important opportunistic pathogen causing respiratory infections, notably in cystic fibrosis, and burn and wound infections. Our study reports six new genomes of Pseudomonas paraeruginosa, a new species recently reported as distinct from P. aeruginosa. The number of sequenced genomes of P. paraeruginosa is only about 1% that of P. aeruginosa. We compare the genomic content of nearly all strains of P. paraeruginosa in GenBank, highlighting the differences in core and accessory genomes, antimicrobial resistance genes, and virulence factors. This novel species is very similar in environmental spectrum to P. aeruginosa but is notably resistant to last-line antibiotics and uses an alternative virulence strategy based on exolysin-this strategy being shared with some P. aeruginosa outliers.
2025-07-25
Journal of Bacteriology (publié)
doi.org
Pharmaco-nutraceutical improvement of the response to obeticholic acid with omega-3 polyunsaturated fatty acids
Audrey-Anne Lavoie
Ariane Thérien
Anisia Silva
Emanuel Paré
Anna Ciešlak
William Gagnon
Clémence Desjardins
Mélanie Verreault
Jocelyn Trottier
Marie-Claude Vohl
Jean-Philippe Drouin-Chartier
Jacques Corbeil
Alexandre Caron
Olivier Barbier
2025-07-22
Biochemical Journal (publié)
doi.org
Pharmaco-nutraceutical improvement of the response to obeticholic acid with omega-3 polyunsaturated fatty acids.
Audrey-Anne Lavoie
Ariane Thérien
Anisia Silva
Emanuel Paré
Anna Ciešlak
William Gagnon
Clémence Desjardins
Mélanie Verreault
J. Trottier
Marie-Claude Vohl
Jean-Philippe Drouin-Chartier
Jacques Corbeil
Alexandre Caron
Olivier Barbier
Obeticholic acid (OCA) is the second line therapy for primary biliary cholangitis. While efficient in promoting BA detoxification and limiti… (voir plus)ng liver fibrosis, its clinical use is restricted by severe dose-dependent side effects. We tested the hypothesis that adding n-3 polyunsaturated fatty acids, eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids to OCA may improve the therapeutic effect of the low drug dosage. Several liver cell lines were exposed to vehicle, low or high OCA dose (1-20μM) in the presence or absence of EPA/DHA for 24H. To induce ER stress, apoptosis, and fibrosis, HepG2 cells were exposed to a 400μM BA mixture or to 2ng/mL TGF-β. For inflammation analyses, THP-1 cells were activated with 100ng/mL LPS. The impact OCA+EPA/DHA was assessed using transcriptomic (qRT-PCR), proteomic (ELISA, caspase-3), and metabolomic (LC-MS/MS) approaches. The addition of EPA/DHA reinforced the ability of low OCA dose to down-regulate the expression of genes involved in BA synthesis (CYP7A1, CYP8B1) and uptake (NTCP) and to up-regulate MRP2 & 3 genes expression. EPA/DHA also enhanced the anti-inflammatory response of the drug by reducing the expression of the LPS-induced cytokines: TNFα, IL-6, IL-1β and MCP-1 in THP-1 macrophages. OCA+EPA/DHA decreased the expression of BIP, CHOP and COL1A1 genes and the caspase-3 activity. EPA+DHA potentiate the response to low OCA doses on BA toxicity, and provide additional benefits on ER stress, apoptosis, inflammation and fibrosis. These observations support the idea that adding n-3 polyunsaturated fatty acids to the drug may reduce the risk of dose-related side effects in patients treated with OCA.
2025-07-22
Biochemical Journal (publié)
doi.org
On Selecting Robust Approaches for Learning Predictive Biomarkers in Metabolomics Data Sets.
Thibaud Godon
Pier-Luc Plante
Jacques Corbeil
Pascal Germain
Alexandre Drouin
Metabolomics, the study of small molecules within biological systems, offers insights into metabolic processes and, consequently, holds grea… (voir plus)t promise for advancing health outcomes. Biomarker discovery in metabolomics represents a significant challenge, notably due to the high dimensionality of the data. Recent work has addressed this problem by analyzing the most important variables in machine learning models. Unfortunately, this approach relies on prior hypotheses about the structure of the data and may overlook simple patterns. To assess the true usefulness of machine learning methods, we evaluate them on a collection of 835 metabolomics data sets. This effort provides valuable insights for metabolomics researchers regarding where and when to use machine learning. It also establishes a benchmark for the evaluation of future methods. Nonetheless, the results emphasize the high diversity of data sets in metabolomics and the complexity of finding biologically relevant biomarkers. As a result, we propose a novel approach applicable across all data sets, offering guidance for future analyses. This method involves directly comparing univariate and multivariate models. We demonstrate through selected examples how this approach can guide data analysis across diverse data set structures, representative of the observed variability. Code and data are available for research purposes.
2025-06-12
Analytical Chemistry (publié)
doi.org
Associations between circulating amino acids and metabolic dysfunction‐associated steatotic liver disease in individuals living with severe obesity
Ina Maltais‐Payette
Jérôme Bourgault
Marie‐Frédérique Gauthier
Laurent Biertho
Simon Marceau
François Julien
Patricia L. Mitchell
Christian Couture
Francis Brière
Jacques Corbeil
Benoît J. Arsenault
André Tchernof
2025-01-27
Physiological Reports (publié)
doi.org
Turncoat antibodies unmasked in a model of autoimmune demyelination: from biology to therapy
Reza Taghipour-Mirakmahaleh
Françoise Morin
Yu Zhang
Louis Bourhoven
Louis-Charles Béland
Qun Zhou
Julie Jaworski
Anna Park
Juan Manuel Dominguez
Jacques Corbeil
Eoin P Flanagan
Romain Marignier
Catherine Larochelle
Steven Kerfoot
Luc Vallières
Autoantibodies contribute to many autoimmune diseases, yet there is no approved therapy to neutralize them selectively. A popular mouse mode… (voir plus)l, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. Here we report the discovery of autoantibody-secreting extrafollicular plasmablasts in EAE induced with specific myelin oligodendrocyte glycoprotein (MOG) antigens. Single-cell RNA sequencing reveals that these cells produce non-affinity-matured IgG antibodies. These include pathogenic antibodies competing for shared binding space on MOG’s extracellular domain. Interestingly, the synthetic anti-MOG antibody 8-18C5 can prevent the binding of pathogenic antibodies from either EAE mice or people with MOG antibody disease (MOGAD). Moreover, an 8-18C5 variant carrying the NNAS mutation, which inactivates its effector functions, can reduce EAE severity and promote functional recovery. In brief, this study provides not only a comprehensive characterization of the humoral response in EAE models, but also a proof of concept for a novel therapy to antagonize pathogenic anti-MOG antibodies.
2024-12-06
bioRxiv (prépublication)
doi.org
Substitution of dietary monounsaturated fatty acids from olive oil for saturated fatty acids from lard increases LDL apolipoprotein B-100 fractional catabolic rate in subjects with dyslipidemia associated with insulin resistance: a randomized controlled trial.
Louis-Charles Desjardins
Francis Brière
André J Tremblay
Maryka Rancourt-Bouchard
Jean-Philippe Drouin-Chartier
Jacques Corbeil
Valéry Lemelin
Amélie Charest
Ernst J Schaefer
Benoit Lamarche
Patrick Couture
2024-03-01
American Journal of Clinical Nutrition (publié)
doi.org
Substitution of dietary monounsaturated fatty acids from olive oil for saturated fatty acids from lard increases LDL apolipoprotein B-100 fractional catabolic rate in subjects with dyslipidemia associated with insulin resistance: a randomized controlled trial.
Louis-Charles Desjardins
Francis Brière
André J Tremblay
Maryka Rancourt-Bouchard
Jean-Philippe Drouin-Chartier
Jacques Corbeil
Valéry Lemelin
Amélie Charest
Ernst J Schaefer
Benoit Lamarche
Patrick Couture
2024-03-01
American Journal of Clinical Nutrition (publié)
doi.org
Substitution of dietary monounsaturated fatty acids from olive oil for saturated fatty acids from lard increases low-density lipoprotein apolipoprotein B-100 fractional catabolic rate in subjects with dyslipidemia associated with insulin resistance: a randomized controlled trial
Louis-Charles Desjardins
Francis Brière
André J Tremblay
Maryka Rancourt-Bouchard
Jean-Philippe Drouin-Chartier
Jacques Corbeil
Valéry Lemelin
Amélie Charest
Ernst J Schaefer
Benoit Lamarche
Patrick Couture
2024-03-01
American Journal of Clinical Nutrition (publié)
doi.org
Learning self-supervised molecular representations for drug–drug interaction prediction
Rogia Kpanou
Patrick Dallaire
Elsa Rousseau
Jacques Corbeil
2024-01-30
BMC Bioinformatics (publié)
doi.org