Jacques Corbeil

Affiliate Member

Full Professor, Université Laval

General Partner et CSO, Linearis Venture and Labs

Research Topics

AI and Healthcare

Applied Machine Learning

Computational Biology

Website

Google Scholar

Biography

Dr. Jacques Corbeil focuses on using the latest techniques in bioinformatics and machine learning to assist diagnostic, prognostic and response to treatment. Modern genomics and metabolomics techniques generate a deluge of data that needs to be interpreted using novel informatics approaches. Dr. Corbeil uses state-of-the-art instrumentation and methodologies to facilitate the interpretation of complex data, including high throughput mass spectrometry, in particular, metabolomics and next-gen sequencing.

Dr. Corbeil’s research includes investigating how infectious microorganisms interact with their host, the effects of antibiotics on our microbial flora and the environment, and exploring how to design small molecules and drugs to interfere with specific microbial functions and cancer progression. Operating at the interface of machine learning and omics sciences, he specializes in big data analytics applied to infectious diseases and cancer and he has expertise in the integration of omics data. Dr. Corbeil collaborates with many industries to ameliorate their process and implement artificial intelligence strategies. Since 2004, Dr. Corbeil holds the Canada Research Chair in Medical Genomics (Tier 1).

Publications

Comparative genomics of Pseudomonas paraeruginosa.

Maxime Déraspe

Lori L. Burrows

R. 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 … (see more)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 (published)

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… (see more)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 (published)

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… (see more)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 (published)

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 (published)

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… (see more)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 (preprint)

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 (published)

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