Jacques Corbeil

Guillaume Bachelot

Claudia Carpentier

Riikka Huusaari

Maxime Déraspe

Juho Rousu

Caroline Quach

2025-09-22

Frontiers in Bioinformatics (published)

www.ncbi.nlm.nih.gov

Extracting a COVID-19 signature from a multi-omic dataset

Baptiste Bauvin

Guillaume Bachelot

Claudia Carpentier

Riikka Huusaari

Maxime Déraspe

Juho Rousu

Caroline Quach

The complexity of COVID-19 requires approaches that extend beyond symptom-based descriptors. Multi-omic data, combining clinical, proteomic,… (see more) and metabolomic information, offer a more detailed view of disease mechanisms and biomarker discovery.As part of a large-scale Quebec initiative, we collected extensive datasets from COVID-19 positive and negative patient samples. Using a multi-view machine learning framework with ensemble methods, we integrated thousands of features across clinical, proteomic, and metabolomic domains to classify COVID-19 status. We further applied a novel feature relevance methodology to identify condensed signatures.Our models achieved a balanced accuracy of 89% ± 5% despite the high-dimensional nature of the data. Feature selection yielded 12- and 50-feature signatures that improved classification accuracy by at least 3% compared to the full feature set. These signatures were both accurate and interpretable.This work demonstrates that multi-omic integration, combined with advanced machine learning, enables the extraction of robust COVID-19 signatures from complex datasets. The condensed biomarker sets provide a practical path toward improved diagnosis and precision medicine, representing a significant advancement in COVID-19 biomarker discovery.

2025-09-22

Frontiers in Bioinformatics (published)

Extracting a COVID-19 signature from a multi-omic dataset

Baptiste Bauvin

Guillaume Bachelot

Claudia Carpentier

Riikka Huusaari

Maxime Déraspe

Juho Rousu

Caroline Quach

Introduction The complexity of COVID-19 requires approaches that extend beyond symptom-based descriptors. Multi-omic data, combining clinica… (see more)l, proteomic, and metabolomic information, offer a more detailed view of disease mechanisms and biomarker discovery. Methods As part of a large-scale Quebec initiative, we collected extensive datasets from COVID-19 positive and negative patient samples. Using a multi-view machine learning framework with ensemble methods, we integrated thousands of features across clinical, proteomic, and metabolomic domains to classify COVID-19 status. We further applied a novel feature relevance methodology to identify condensed signatures. Results Our models achieved a balanced accuracy of 89% ± 5% despite the high-dimensional nature of the data. Feature selection yielded 12- and 50-feature signatures that improved classification accuracy by at least 3% compared to the full feature set. These signatures were both accurate and interpretable. Discussion This work demonstrates that multi-omic integration, combined with advanced machine learning, enables the extraction of robust COVID-19 signatures from complex datasets. The condensed biomarker sets provide a practical path toward improved diagnosis and precision medicine, representing a significant advancement in COVID-19 biomarker discovery.

2025-09-22

Frontiers in Bioinformatics (published)

Extracting a COVID-19 signature from a multi-omic dataset

Baptiste Bauvin

Guillaume Bachelot

Claudia Carpentier

Riikka Huusaari

Maxime Déraspe

Juho Rousu

Caroline Quach

Introduction The complexity of COVID-19 requires approaches that extend beyond symptom-based descriptors. Multi-omic data, combining clinica… (see more)l, proteomic, and metabolomic information, offer a more detailed view of disease mechanisms and biomarker discovery. Methods As part of a large-scale Quebec initiative, we collected extensive datasets from COVID-19 positive and negative patient samples. Using a multi-view machine learning framework with ensemble methods, we integrated thousands of features across clinical, proteomic, and metabolomic domains to classify COVID-19 status. We further applied a novel feature relevance methodology to identify condensed signatures. Results Our models achieved a balanced accuracy of 89% ± 5% despite the high-dimensional nature of the data. Feature selection yielded 12- and 50-feature signatures that improved classification accuracy by at least 3% compared to the full feature set. These signatures were both accurate and interpretable. Discussion This work demonstrates that multi-omic integration, combined with advanced machine learning, enables the extraction of robust COVID-19 signatures from complex datasets. The condensed biomarker sets provide a practical path toward improved diagnosis and precision medicine, representing a significant advancement in COVID-19 biomarker discovery.

2025-09-22

Frontiers in Bioinformatics (published)

Extracting a COVID-19 signature from a multi-omic dataset

Baptiste Bauvin

Guillaume Bachelot

Claudia Carpentier

Riikka Huusaari

Maxime Déraspe

Juho Rousu

Caroline Quach

2025-09-22

Frontiers in Bioinformatics (published)

Using machine learning to predict the consumption of a Mediterranean diet with untargeted metabolomics data from controlled feeding studies.

Mélina Côté

Didier Brassard

Pier-Luc Plante

Francis Brière

P. Couture

Simone Lemieux

B. Lamarche

2025-09-01

Nutrition, Metabolism and Cardiovascular Diseases (published)

Comparative genomics of Pseudomonas paraeruginosa

Maxime Déraspe

Lori L. Burrows

Romé Voulhoux

Daniela Centrón

Paul H Roy

ABSTRACT The PA7-clade (or group 3) of Pseudomonas aeruginosa is now recognized as a distinct species, Pseudomonas paraeruginosa. We report … (see more)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 (published)

Comparative genomics of
<i>Pseudomonas paraeruginosa</i>

Maxime Déraspe

Lori L. Burrows

Romé Voulhoux

Daniela Centrón

Paul H Roy

2025-07-25

Journal of Bacteriology (published)

Comparative genomics of Pseudomonas paraeruginosa

Maxime Déraspe

Lori L. Burrows

Romé Voulhoux

Daniela Centrón

Paul H Roy

ABSTRACT The PA7-clade (or group 3) of Pseudomonas aeruginosa is now recognized as a distinct species, Pseudomonas paraeruginosa. We report … (see more)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 (published)

Comparative genomics of Pseudomonas paraeruginosa.

Maxime Déraspe

Lori L. Burrows

Romé Voulhoux

D. Centrón

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)

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

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)

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

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)