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Welcome to the Corbeil Research Group

 

The research of our group is  centred on the investigation of host-pathogen relationships and the integration of omics sciences. We have utilized many approaches to carry out these investigations with a constant of using new technologies coupled to the power of bioinformatics and more specifically machine learning to gain insight into biological processes. We focus on HIV/AIDS, Leishmania, respiratory viruses and more recently on Malaria, Tuberculosis and emerging pathogens. We are also interested in the metagenomic aspects of microbes in diverse environments and the effect of drugs on the composition of the human gut microbiome. Recognizing that the bottleneck in most studies was the extraction of pertinent information, we developed software applications and bioinformatics processes to assist in deciphering the data. Our bioinformatics efforts are implemented at Université Laval with funds provided by the Canadian Foundation for Innovation and the Compute Canada infrastructure. We are utilizing system biology approaches and kernel-based algorithms to assist with the massive amount of data coming out of the new sequencing and mass spectrometry technologies, including metabolomic profiling.

We also continue to work extensively in the cancer and diagnostic fields.  We use novel instrumentation to monitor molecular interactions (protein-protein, DNA-protein and small molecules) using porous silicate and interferometry to assist in system biology model reconstruction.  My Chair is focused in translating our research discoveries to the market. We identify problems at the bedside and try to solve them at the bench.

For more information, see our research projects in the project section.

Our team members

Principal investigator

JACQUES CORBEIL

Principal investigator


CAREER SUMMARY

Dr. Jacques Corbeil, Canada Research Chair in Medical Genomics, focuses on deciphering the interactions between agents such as HIV-1, respiratory viruses and other microorganisms and the human host. He uses new algorithms, machine learning and bioinformatics approaches to sort out these complex host-pathogen systems.

 

RECENT PUBLICATIONS (see all here)

Scientific coordinator

LYNDA ROBITAILLE

Project manager


CAREER SUMMARY

My academic training coupled with over 25 years of scientific experience in different areas always interesting and challenging one than the other led me to excel. So I got an advanced degree, the pharmaceutical management specialist M.B.A.. This graduate level training just supports my growing experience in managing large projects and will be more beneficial for the rest of my management career. I work in the field of high technology or the medical genomics and big data, and in the field of rapid diagnosis. I contributed to the installation of a platform of non-human primates at Laval University and I actively participated in the first scientific protocol with the first cohort of monkeys. Recently, I was entrusted with the coordination of the new Big Data Research Center of Université Laval (BDRC), I’m a executive member of the this new center. The BDRC has 36 researchers, includes four faculties and 11 departments.

FORMATION
Biologist/M.B.A Pharmaceutical management

 

PUBLICATIONS

  • Moukambi Félicien1, Rabezanahary Henintsoa1, Rodrigues Vasco2, Racine Gina1, Robitaille Lynda1, Krust Bernard2, Andreani Guadalupe1, Soundaramourty Calayselvy2, Silvestre Ricardo3, Laforge Mireille 2,*, Estaquier Jérôme1,2,* . Early loss of splenic Tfh cells in SIV-infected rhesus macaques. PLoS Pathog. 2015 Dec 7;11(12):e1005287. doi: 10.1371/journal.ppat.1005287. eCollection 2015 Dec. PMID: 26640894
  • Foster MW, Gerhardt G, Robitaille L, Plante PL, Boivin G, Corbeil J, Moseley MA. Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures. Anal Chem. 2015 Oct 20;87(20):10247-54. doi: 10.1021/acs.analchem.5b01544. Epub 2015 Sep 29. PMID: 26376123
  • Frédéric Raymond, Nancy Boucher, Robin Allary, Lynda Robitaille, Brigitte Lefebvre, Cécile Tremblay, Jacques Corbeil, Alain Gervaix. Serotyping of Streptococcus pneumoniae Based on Capsular Genes Polymorphisms. PLoS ONE 8(9): e76197. doi:10.1371/journal.pone.0076197 Received June 27, 2013; Accepted August 20, 2013; Published September 24, 2013
  • Chappuy H, Keitel K, Gehri M, Tabin R, Robitaille L, Raymond F, Corbeil J, Maspoli V, Bouazza N, Alcoba G, Lacroix L, Manzano S, Galetto-Lacour A, Gervaix A. Nasopharyngeal carriage of individual Streptococcus pneumoniae serotypes during pediatric radiologically confirmed community acquired pneumonia following PCV7 introduction in Switzerland. BMC Infect Dis. 2013 Jul 31;13:357. doi: 10.1186/1471-2334-13-357.
  • Papenburg J, Hamelin MÈ, Ouhoummane N, Carbonneau J, Ouakki M, Raymond F, Robitaille L, Corbeil J, Caouette G, Frenette L, De Serres G, Boivin G. Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children. J Infect Dis. 2012 Jul 15;206(2):178-89. Epub 2012 May 2.
  • Sirois M, Robitaille L, Allary R, Shah M, Woelk CH, Estaquier J, Corbeil J. TRAF6 and IRF7 control HIV replication in macrophages. PLoS One. 2011;6(11):e28125. Epub 2011 Nov 28.
  • Raymond F, Carbonneau J, Boucher N, Robitaille L, Boisvert S, Wu WK, De Serres G, Boivin G, Corbeil J. J Clin Microbiol. 2009 Mar;47(3):743-50. Epub 2009 Jan 21. Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. Sperandio S, Fortin J, Sasik R, Robitaille L, Corbeil J, de Belle I. The transcription factor Egr1 regulates the HIF-1alpha gene during hypoxia. Mol Carcinog. 2009 Jan;48(1):38-44. Sirois M, Robitaille L, Sasik R, Estaquier J, Fortin J, Corbeil J. R5 and X4 HIV viruses differentially modulate host gene expression in resting CD4+ T cells. AIDS Res Hum Retroviruses. 2008 Mar;24(3):485-93. Morin S, Pozzulo G, Robitaille L, Cross J, Nemer M. MEF2-dependent recruitment of the HAND1 transcription factor results in synergistic activation of target promoters. J Biol Chem. 2005 Sep 16;280(37):32272-8. Epub 2005 Jul 25.
  • Charron F, Tsimiklis G, Arcand M, Robitaille L, Liang Q, Molkentin JD, Meloche S, Nemer M. Tissue specific GATA factors are transcriptional effectors of the small GTPase RhoA. Genes Dev 2001 Oct 15 :15(20) : 2702-19
  • Bruneau BG, Nemer G, Schmitt JP, Charron F, Robitaille L, Caron S, Conner DA, Gessler M, Nemer M, Seidman CE, Seidman JG. A murine model of Holt-Oram syndrome defines roles of the T-box transcription factor Tbx5 in cardiogenesis and disease. Cell. 2001 Sep 21; 106(6) :709-21
  • Bhalla SS, Robitaille L, Nemer M. Cooperative activation by GATA-4 and YY1 of the cardiac B-type natriuretic peptide promoter. J. Biol Chem. 2001 Apr 6;276(14) : 11439-45
  • Morin S, Charron F, Robitaille L, Nemer M. GATA-dependant recruitment of MEF2 proteins to target promoters. EMBO J 2000 May 2;19(9) :2046-55
  • Grépin C, Robitaille L, Antakly T, Nemer M. Inhibition of transcription factor GATA-4 expression blocks in vitro cardiac muscle differentiation. Mol Cell Biol 1995,15 : 4095-4102
  • Grépin C, Dagnino L, Robitaille L, Haberstroh L, Antakly T, Nemer M. A hormone coding gene identifies a pathway for cardiac but not skeletal muscle gene transcription. Mol Cell Biol 1994, 14 :3115-3129
  • Argentin S, Ardati A, Tremblay S, Lihrmann I, Robitaille L, Drouin J, Nemer M. Developmental stage-specific regulation of ANF gene transcription in cardiac cells. Mol Cell Biol 1994, 14 :777-790
  • McBride K, Robitaille L, Tremblay S, Argentin S, Nemer M. Fos/jun repression of cardiac-specific transcription in quiescent and growth-stimulated myocytes is targeted at a tissue-specific cis element. Mol Cell Biol 1993, 13 : 600-612
  • Claude Labrecque, Johny Huard, Guy Dansereau, Lynda Robitaille, and Jacques P. Tremblay. Labelling with BrdU and new technic to hybridization.
  • Claude Labrecque, Johny Huard, Guy Dansereau, Lynda Robitaille, and Jacques P. Tremblay. A new technique to identify hybrid myotubes in vitro without culture fixation. The Journal of Histochemistry and Cytochemistry 1991, vol. 39, 1 :139-14
  • Johny Huard, Claude Labrecque, Guy Dansereau, Lynda Robitaille, and Jacques P. Tremblay. Dystrophin expression in myotubes formed by the fusion of normal and dystrophic myoblasts. Muscle & Nerve 1991, 14 :178-182
Project manager

FRÉDÉRIC RAYMOND

Post-doctoral fellow


 

CAREER SUMMARY

My long time interest for genomics and informatics have led me to study microbiology using bioinformatics. Specifically, I am interested in molecular diagnostics of infectious diseases, large scale comparative genomics and microbiome research. My main research objective is to efficiently analyze complex genomic or metagenomic datasets to better understand clinically relevant problems, such as antibiotic resistance or microbial virulence, in order to improve health.

 

FINANCING

2011-2013       Bourse MITACS Accelerate
2006-2009       CIHR Frederick Banting and Charles Best Canada Graduate Scholarships – Doctoral Award
2004-2005       Bourse de l’Ambassade de France au Canada

 

SELECTED PUBLICATIONS

  • Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J. 2015 Sep 11. doi: 10.1038/ismej.2015.148.
  • Ubeda J.-M.*, Raymond F.*, Mukherjee A.*, Plourde M., Gingras H., Roy G., Lapointe A., Leprohon P., Papadopoulou B., Corbeil J., Ouellette M. Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania. PLoS Biol. 2014 May 20;12(5):e1001868. doi: 10.1371/journal.pbio.1001868. eCollection 2014. (*Premier auteur partagé)
  • Raymond F., Boucher N., Allary R., Robitaille L., Lefebvre B, et al. (2013) Serotyping of Streptococcus pneumoniae Based on Capsular Genes Polymorphisms. PLoS ONE 8(9): e76197. doi:10.1371/journal.pone.0076197
  • Boisvert S., F. Raymond, E. Godzaridis, F. Laviolette et J. Corbeil. « Ray Meta: scalable de novo metagenome assembly and profiling. » Genome Biol. 2012 Dec 22;13(12):R122.
  • Raymond F., S. Boisvert, G. Roy, J.-F. Ritt, D. Légaré, A. Isnard, M. Stanke, M. Olivier, M. Tremblay, B. Papadopoulou, M. Ouellette et J. Corbeil. 2011. « Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species ». Nucl. Acids Res. First published online October 13, 2011.
  • Raymond F., J. Carbonneau, N. Boucher, L. Robitaille, S. Boisvert, W. K. Wu, G. De Serres, G. Boivin et J. Corbeil. 2009. « Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children ». J. Clin. Microbiol. 47:743-750.

 

ALL PUBLICATIONS

  • Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J. 2015 Sep 11. doi: 10.1038/ismej.2015.148.
  • Vilacoba E., C. Quiroga, M. Pistorio, A. Famiglietti, H. Rodríguez, J. Kovensky, M. Déraspe, F. Raymond, P. Roy et D. Centron. 2014. « A blaVIM-2 plasmid disseminating in extensively drug-resistant cliniCIHR Frederick Banting and Charles Best Canada Graduate Scholarships – Doctoral Awardcal Pseudomonas aeruginosa and Serratia marcescens isolates ». Antimicrob Agents Chemother. 2014 Nov;58(11):7017-8.
  • Lévesque S., P.-L. Plante, N. Mendis, P. Cantin, G. Marchand, H. Charest, F. Raymond, C. Huot, I. Goupil-Sormany, F. Desbiens, S. P. Faucher, J. Corbeil et C. Tremblay. 2014. « Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012 ». PLoS One. 10.1371/journal.pone.0103852.
  • Ubeda J.-M.*, Raymond F.*, Mukherjee A.*, Plourde M., Gingras H., Roy G., Lapointe A., Leprohon P., Papadopoulou B., Corbeil J., Ouellette M. Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania. PLoS Biol. 2014 May 20;12(5):e1001868. doi: 10.1371/journal.pbio.1001868. eCollection 2014. (*Premier auteur partagé)
  • Raymond F., Boucher N., Allary R., Robitaille L., Lefebvre B, et al. (2013) Serotyping of Streptococcus pneumoniae Based on Capsular Genes Polymorphisms. PLoS ONE 8(9): e76197. doi:10.1371/journal.pone.0076197
  • Ritt J.-F., Raymond F., Leprohon P., Légaré D., Corbeil J. et Ouellette M. Gene Amplification and Point Mutations in Pyrimidine Metabolic Genes in 5-Fluorouracil Resistant Leishmania infantum. PLoS Negl Trop Dis. 2013 Nov 21;7(11):e2564. doi: 10.1371/journal.pntd.0002564.
  • Dionne L.-L., Raymond F., Corbeil J., Longtin J., Gervais P., Longtin Y. Correlation between Clostridium difficile Bacterial Load, Commercial Real-time PCR Cycle Thresholds, and Results of Diagnostic Tests Based on Enzyme Immunoassay and Cell-Culture Cytotoxicity Assay. J Clin Microbiol. 2013 Aug 21.
  • Chappuy H., Keitel K., Gehri M., Tabin R., CIHR Frederick Banting and Charles Best Canada Graduate Scholarships – Doctoral AwardRobitaille L., Raymond F., Corbeil J., Maspoli V., Bouazza N., Alcoba G., Lacroix L., Manzano S., Galetto-Lacour A., Gervaix A. Nasopharyngeal carriage of individual Streptococcus pneumoniae serotypes during pediatric radiologically confirmed community acquired pneumonia following PCV7 introduction in Switzerland. BMC Infect Dis. 2013 Jul 31;13:357.
  • Kumar P., Lodge R., Raymond F., Ritt J.-F., Jalaguier P., Corbeil J., Ouellette M., Tremblay M.J. Gene expression modulation and the molecular mechanisms involved in Nelfinavir resistance in Leishmania donovani axenic amastigotes. Mol Microbiol. 2013 Aug;89(3):565-82.
  • Mukherjee A., S. Boisvert, R. L. Monte-Neto, A. C. Coelho, F. Raymond, R. Mukhopadhyay, J. Corbeil et M. Ouellette. « Telomeric gene deletion and intrachromosomal amplification in antimony-resistant Leishmania. » Mol Microbiol. 2013 Apr;88(1):189-202.<
  • Boisvert S., F. Raymond, E. Godzaridis, F. Laviolette et J. Corbeil. « Ray Meta: scalable de novo metagenome assembly and profiling. » Genome Biol. 2012 Dec 22;13(12):R122.
  • Gervaix A., J. Taguebue, B. N. Bescher, J. Corbeil, F. Raymond, G. Alcoba, M. Kobela et E. Tetanye. « Bacterial meningitis and pneumococcal serotype distribution in children in cameroon. » Pediatr Infect Dis J. 2012 Oct;31(10):1084-7.
  • Papenburg J., M.-È. Hamelin, N. Ouhoummane, J. Carbonneau, M. Ouakki, F. Raymond, L. Robitaille, J. Corbeil, G. Caouette, L. Frenette, G. De Serres et G. Boivin. « Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children. » J Infect Dis. 2012 Jul 15;206(2):178-89.
  • Raymond F., S. Boisvert, G. Roy, J.-F. Ritt, D. Légaré, A. Isnard, M. Stanke, M. Olivier, M. Tremblay, B. Papadopoulou, M. Ouellette et J. Corbeil. 2011. « Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species ». Nucl. Acids Res. First published online October 13, 2011.
  • Raymond F., J. Carbonneau, N. Boucher, L. Robitaille, S. Boisvert, W. K. Wu, G. De Serres, G. Boivin et J. Corbeil. 2009. « Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children ». J. Clin. Microbiol. 47:743-750.
  • Do Monte Neto R. L., A. C. Coelho, F. Raymond, M. N. Melo, F. J. G. Frézard, M. Ouellette. « Gene expression profilinf and molecular characterization of antimony resistance in Leishmania amazonensis ». PLoS Neglected Tropical Diseases. 5:e1167. doi:10.1371/journal.pntd.0001167.
  • Leprohon P., D. Légaré, F.Raymond, E. Madore, G. Hardiman, J. Corbeil et M. Ouellette. 2009. « Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum ». Nucleic Acids Res. 37:1387-1399.
  • Rochette A., F.Raymond, J. Corbeil, M. Ouellette et B. Papadopoulou. 2009. « Whole-genome comparative RNA expression profiling of axenic and intracellular amastigote forms of Leishmania infantum ». Mol. Biochem. Parasitol. 165:32-47.
  • Raymond F., W. K. Wu et J. Corbeil. 2009. « Development of an integrated molecular diagnostic test to identify respiratory viruses ». In Hardiman, G. (Éd.), Microarray innovations: Technology and experimentation. 1re édition, CRC Press, Boca Raton, États-Unis, p. 259-270.
  • Rochette A., F.Raymond, J. M. Ubeda, M. Smith, N. Messier, S. Boisvert, P. Rigault, J. Corbeil, M. Ouellette et B. Papadopoulou. 2008. « Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species ». BMC Genomics. 9:255.
  • Ubeda J. M., D. Légaré, F.Raymond, A. A. Ouameur, S. Boisvert, P. Rigault, J. Corbeil, M. J. Tremblay, M. Olivier, B. Papadopoulou et M. Ouellette. 2008. « Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy ». Genome. Biol. 9:R115.
  • Hivin P., J. Basbous, F. Raymond, D. Henaff, C. Arpin-André, V. Robert-Hebmann, B. Barbeau et J. M. Mesnard. 2007. « The HBZ-SP1 isoform of human T-cell leukemia virus type I represses JunB activity by sequestration into nuclear bodies ». Retrovirology. 4:14.
  • Peytavi R., F. Raymond, D. Gagné, F. J. Picard, G. Jia, J. Zoval, M. Madou, K. Boissinot, M. Boissinot, L. Bissonnette, M. Ouellette et M. G. Bergeron. 2005. « Microfluidic device for rapid (
  • Peytavi R., L. Y. Tang, F. Raymond, K. Boissinot, L. Bissonnette, M. Boissinot, F. J. Picard, A. Huletsky, M. Ouellette et M. G. Bergeron. 2005. « Correlation between microarray DNA hybridisation efficiency and the position of short capture probe on the target nucleic acid ». Biotechniques. 39:89-96.
  • Raymond F., H. A. Ho, R. Peytavi, L. Bissonnette, M. Boissinot, F. J. Picard, M. Leclerc et M. G. Bergeron. 2005. « Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support ». BMC Biotechnology. 5:10.

FORMATION

2011-               Stage post-doctoral en bio-informatique
Université Laval, Québec, Canada

Directeur : Dr Jacques Corbeil
Titre du projet : Étude de l’impact des antibiotiques sur le microbiome humain

2005-2011       Doctorat en physiologie-endocrinologie
Université Laval, Québec, Canada
Directeur : Dr Jacques Corbeil
Titre du projet : Bio-informatique pour la génomique et le diagnostic des maladies infectieuses

2004-2005       Stage en biologie-santé
Université Montpellier I, Montpellier, France
Directeur : Dr Jean-Michel Mesnard
Titre du projet : Caractérisation du domaine activateur de la protéine HBZ du virus de la leucémie T humaine de type I (HTLV-I) et étude de l’effet de cette protéine sur la prolifération cellulaire

2002-2004       Maîtrise en microbiologie-immunologie
Université Laval, Québec, Canada
Directeur : Dr Michel G. Bergeron
Titre du projet : Développement d’une plate-forme de biopuce compatible avec le diagnostic moléculaire des maladies infectieuses

1999-2002       Baccalauréat en microbiologie
Université Laval, Québec, Canada

Ph.D, Mol. Medicine

PIER-LUC PLANTE

Ph.D Molecular Medicine


  • Boursier MITACS-Converge
Ph.D, Mol. Medicine

MAXIME DÉRASPE

Ph.D, Molecular Medicine


 

CAREER SUMMARY

After completing a formation in computer sciences, I wanted to gain more domain knowledge in biology, which led me to study bioinformatics.
So far, I have been involved in research projects regarding bacterial resistances, genomics, metagenomics as well as machine learning methods applied to different omics.
Throughout the years, I have developed a lot of interests in data engineering methods for large scale applications and different database technologies (SQL, NoSQL, Semantic Web and graph databases).

 

FINANCING

2015-2018 FRQNT
2013-2014 MITACS
2012-2013 CQDM

 

PUBLICATIONS

  • Drouin, A., Giguère, S., Déraspe, M., Marchand, M., Tyers, M., Loo, V. G., … Corbeil, J. (2016). Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons. bioRxiv, 45153.
  • Drouin, A., Giguère, S., Déraspe, M., Marchand, M., Corbeil, J., & Laviolette, F. (2016). Set Covering Machines and Reference-Free Genome Comparisons Uncover Predictive Biomarkers of Antibiotic Resistance.
  • Raymond, F., Ouameur, A. a, Déraspe, M., Iqbal, N., Gingras, H., Dridi, B., … Corbeil, J. (2015). The initial state of the human gut microbiome determines its reshaping by antibiotics. The ISME Journal, 1–14. http://doi.org/10.1038/ismej.2015.148
  • Kos, V. N., Déraspe, M., McLaughlin, R. E., Whiteaker, J. D., Roy, P. H., Alm, R. A., … Gardner, H. (2015). The resistome of Pseudomonas seudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrobial Agents and Chemotherapy, 59(1), 427–436. http://doi.org/10.1128/AAC.03954-14
  • Drouin, A., Giguère, S., Déraspe, M., Laviolette, F., Marchand, M., & Corbeil, J. (2015). Greedy Biomarker Discovery in the Genome with Applications to Antimicrobial Resistance. arXiv Preprint arXiv:1505.06249.
  • Vilacoba, E., Quiroga, C., Pistorio, M., Famiglietti, A., Rodríguez, H., Kovensky, J., Déraspe, M., …, Centrón, D. (2014). A blaVIM-2 plasmid disseminating in extensively drug-resistant clinical Pseudomonas aeruginosa and Serratia marcescens isolates. Antimicrobial Agents and Chemotherapy. http://doi.org/10.1128/AAC.02934-14
  • Vilacoba, E., Déraspe, M., Traglia, G. M., Roy, P. H., Ramírez, M. S., & Centrón, D. (2014). Draft Genome Sequence of an International Clonal Lineage 1 Acinetobacter baumannii Strain from Argentina. Genome Announcements, 2(6). http://doi.org/10.1128/genomeA.01190-14
  • Déraspe, M., Alexander, D. C., Xiong, J., Ma, J. H., Low, D. E., Jamieson, F. B., & Roy, P. H. (2014). Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176. FEMS Microbiology Letters, 356(2), 212–216.
  • Drouin, A., Giguère, S., Sagatovich, V., Déraspe, M., Laviolette, F., Marchand, M., & Corbeil, J. (2014). Learning interpretable models of phenotypes from whole genome sequences with the Set Covering Machine. arXiv Preprint arXiv:1412.1074.
  • Xiong, J., Alexander, D. C., Ma, J. H., Déraspe, M., Low, D. E., Jamieson, F. B., & Roy, P. H. (2013). Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrobial Agents and Chemotherapy, 57(8), 3775–3782.

 

FORMATION

2015 – 2018 PhD in Molecular medicine
Université Laval, Québec, Canada
Director: Jacques Corbeil, Codirector: François Laviolette and Paul H. Roy

2015 – MSc in Bioinformatics
Université Laval, Québec, Canada
Director: Jacques Corbeil, Codirector: Paul H. Roy

2012 BSc in Bioinformatics
Université Laval, Québec, Canada

2010 BSc in Informatics
Université Laval, Québec, Canada

Research Professional

NANCY BOUCHER

Research professional



CAREER SUMMARY

Since 2014, my career profile as a reseach professional has revolved around the fascinating field of mass spectrometry. This science allow to dissect cellular mechanisms using innovative and advanced analysis methods. Our studies using LDTD-MS allow to identify and develop metabolomic signatures for specific clinical or industrial aspects. We also develop quantitative metabolomic methods applied to infectious diseases using LC-MRM. Our SYNAPT G2-Si is versatile and allow us to work on varied projects.

 

PUBLICATIONS

  • Raymond F, Boucher N, Allary R, Robitaille L, Lefebvre B, Tremblay C, Corbeil J, Gervaix A.Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms.
    PLoS One. 2013 Sep 24. doi: 10.1371/journal.pone.0076197.
  • Raymond F, Carbonneau J, Boucher N, Robitaille L, Boisvert S, Wu WK, De Serres G, Boivin G, Corbeil J.Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children.
    J Clin Microbiol. 2009 Mar. doi: 10.1128/JCM.01297-08
  • Lemieux AM, Paré ME, Audet B, Legault E, Lefort S, Boucher N, Landry S, van Opijnen T, Berkhout B, Naghavi MH, Tremblay MJ, Barbeau B.T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region.
    J Biol Chem. 2004 Dec 17.

 

RESEARCH EXPERIENCE

2014 Research professionnal
CHU research center, Jacques Corbeil et Marc Ouellet, Québec, Canada

2011 Laboratory technician -Technological Innovation and Analytical Support
Médicago, Québec, Canada

2005-2010 Research professionnal
Molecular Endocrinology Research Center, CHUL, Jacques Corbeil, Québec, Canada

2002 Research professionnal
Infectious Disease Research Center, CHUL , Benoît Barbeau, Québec, Canada

 

FORMATION

2003-2005 Masters in Microbiology – Immunology
Université Laval, Québec
Director : Dr Benoît Barbeau
Project’s title : Implications des membres de la famille NFAT dans la modulation transcriptionnelle chez le VIH-1

2000-2003 Bachelor of Biotechnology ( cooperative scheme )
Sherbrooke University, Sherbrooke, Québec

1997-2000 College degree in chemistry – biology techniques
Cégep de Lévis-Lauzon, Lévis, Québec

Research Professional
Ph.D Student

Mazid Abiodoun Osseni

Ph.D Candidate Informatics



CAREER SUMMARY

Since highschool, I’ve always wanted to work in biological sciences without staying in wet lab. This is why i pursue a carrer in Bioinformatics field. By doing so, i grow a strong interest into computer sciences too. I did a master into computational neuroscience modeling. 
By working with the Groupe de Recherche en Apprentissage Automatique de l’université Laval (GRAAL) and the Corbeil Lab, i want to apply machine learning methods to biological data, in particular to cancer data and to apply the learning methods to systems biology aspect of biological question. 

FINANCING
2010 – 2013: Scholaship of Benin Republic

 

PUBLICATIONS

  • Freschi, Luca, Mazid Osseni, and Christian R. Landry. “Functional divergence and evolutionary turnover in mammalian phosphoproteomes.” PLoS Genet 10.1 (2014): e1004062.

 

MEMOIR

Osseni,PUBLICATIONSMazid Abiodoun. Modélisation électrophysiologique et biochimique d’un neurone: CA1 cellule de l’hippocampe. Diss. Université Laval, 2015.


FORMATION
2016 – PhD in Computer Sciences
Université Laval, Québec, Canada
Director: François Laviolette, Codirector: Jacques Corbeil
2013-2015 Masters in Computer Sciences
Université Laval, Québec, Canada
Director: Simon Hardy, Codirector: Nicolas Doyon
Project title: Modélisation électrophysiologique et biochimique d’un neurone: CA1 cellule de l’hippocampe
2010-2013  Bachelor’s Degree in Bioinformatics
Ph.D, Computer Science

FRANCIS BROCHU

Ph.D Informatics



CAREER SUMMARY

Originally a student in biological sciences, I have discovered a growing interest for computer sciences, especially, during my Master’s, an interest for machine learning. I now work with the Corbeil lab and lthe Groupe de Recherche en Apprentissage Automatique de l’université Laval (GRAAL) in order to apply machine learning methods to biological data, in particular to metabolomics data.

 

FINANCING

2014 – 2015 Bourse MITACS accelerate
2013 Bourse de recrutement à la maîtrise des Fonds Wilbrod-Bhérer
2011 – 2012 Bourse de Recherche du Premier Cycle du CRSNG

 

PUBLICATIONS

  • Brochu F, Plante PL, Drouin A, Robitaille LÉ, Laviolette F, Marchand M and Corbeil J. Virtual Lock Masses: an algorithmic method to enable mass spectra comparison in untargeted studies. Présenté à la 64th Conference on Mass Spectrometry and Allied Topics de l’American Society of Mass Spectrometry. San Antonio, Texas, USA. Juin 2016.
  • Emond-Rheault JG, Vincent AT, Trudel MV, Brochu F, Boyle B, Tanaka KH, Attéré SA, Jubinville É, Loch TP, Winters AD, Faisal M, Frenette M, Derome N, Charette SJ. Variants of a genomic island in Aeromonas salmonicida subsp. Salmonicida link isolates with their geographical origins. Vet. Microbiol. 2015 Jan 30; 175(1):68-76. DOI : 10.1016/j.vetmic.2014.11.014.
  • Cheiab B, Leboulch M, Delgado M, Brochu F, Mercier PL, Boutin S, Gauthier J, Derome N. Lake Meta-Community Adaptation to Heavy Metal Contamination : Thresholds, Sweeps and Switches in Short-Term Evolution. Présenté au American Fisheries Society 144th Annual Meeting, Août 2014.
  • Charrette SJ, Brochu F, Boyle B, Filion G, Tanaka KH, Derome N. Draft Genome Sequence of the Virulent Strain 01-B526 of the Fish Pathogen Aeromonas salmonicida. J. Bacteriol. 2012, 194(3):722. DOI:10.1128/JB.06276-11.

 

FORMATION

2016 – PhD in Computer Sciences
Université Laval, Québec, Canada
Director: François Laviolette, Codirector: Jacques Corbeil

2013 – 2015 Masters in Microbiology-Immunology
Université Laval, Québec, Canada
Director:Jacques Corbeil
Project title: Amélioration du contrôle de qualité de produits sanguins utilisant la spectrométrie de masse à haut-débit et l’apprentissage automatique

2010 – 2012 Bachelor’s Degree in Bioinformatics
Université Laval, Québec, Canada

Research Professional

Katy Cantin

Research Professional


Ph.D, Mol. Medicine

CHARLES JOLY BEAUPARLANT

Ph.D Molecular Medicine


CAREER SUMMARY

The principal theme of my academic research is genetics and genomics. I completed my Master’s degree on the genetic risk factor of breast cancer in high risk family. Before starting my PhD, I received a Certificate in informatic.

The main goal of my research is to develop new tools to help with the analysis of epigenomic data. I especially interested in the analysis of transcription factors enrichment profiles. I’m trying to find new ways to compare profiles that are efficient and robust to facilitate the study of the dynamic of transcription factors recruitment.

During my PhD, I also had the opportunity to work in transcriptomic (RNA-Seq), metagenomics and exome sequencing.

I also teach the Computational Genomics (BIF-4004/BIF-7004) course and the sections on Next-Generation Sequencing, Epigenomics and Transcriptomics in the Bioinformatic I course (BIF-7900).

 

FUNDING

2013-2016 Doctoral Award – FRQS
2012-2013 Doctoral Award – CREMOGH
2008-2009 Master Degree Award – IRSC
2007-2008 Genomic Formation Award – IRSC

 

PUBLICATIONS

  • Le Luyer J., Deschamps M-H., Proulx E., Poirier Stewart N., Joly Beauparlant
    C., Droit A., Robert C., Vandenberg G. W. Establishment of a comprehensive
    reference transcriptome for vertebral bone tissue to study the impacts of
    nutritional phosphorus deficiency in rainbow trout (Oncorhynchus mykiss,
    Walbaum), Marine genomics 2014, accepted.
  • Fournier F, Beauparlant CJ, Paradis R, Droit A. rTANDEM, an R/Bioconductor
    package for MS/MS protein identification. Bioinformatics 2014, btu178.
  • Bélanger S, Plourde KV, Beauparlant CJ, St-Laurent Pedneault C, Bouffard F,
    Ouellette G, Labrie Y, Durocher F. Impaired Effects of a FANCC Splicing
    Isoform in FANC-BRCA DNA Repair Pathway. J Genet Syndr Gene Ther 2013;4:5.
  • Markovitz AN, Beauparlant CJ, Toupin D, Wang S, Droit A, Gevry N. NGS++:
    a library for rapid prototyping of epigenomics software tools. Bioinformatics
    2013;29(15):1893-4.
  • Desjardins S, Beauparlant JC, Labrie Y, Ouellette G, Durocher F. Variations in
    the NBN/NBS1 gene and the risk of breast cancer in non-BRCA1/2 French Canadian
    families with high risk of breast cancer. BMC Cancer 2009;9:181.
  • Guénard F, Labrie Y, Ouellette G, Beauparlant CJ, Durocher F. Genetic sequence
    variations of BRCA1-interacting genes AURKA, BAP1, BARD1 and DHX9 in French
    Canadian families with high risk of breast cancer. J. Hum. Genet 2009
    Mar;54(3):152-161.
  • Guénard F, Labrie Y, Ouellette G, Joly Beauparlant C, Simard J, Durocher F.
    Mutational analysis of the breast cancer susceptibility gene BRIP1
    /BACH1/FANCJ in high-risk non-BRCA1/BRCA2 breast cancer families. J. Hum. Genet
    2008;53(7):579-591.
  • Guénard F, Labrie Y, Ouellette G, Beauparlant CJ, Bessette P, Chiquette J,
    Laframboise R, Lépine J, Lespérance B, Pichette R, Plante M, Durocher F.
    Germline mutations in the breast cancer susceptibility gene PTEN are rare in
    high-risk non-BRCA1/2 French Canadian breast cancer families. Fam. Cancer
    2007;6(4):483-490.

 

FORMATION

2012- PhD bio-informatique
Université Laval, Québec
Director: Arnaud Droit
Codirector: Jacques Corbeil
Thesis title: Development of new tools for next-generation sequencing applied
to ChIP-Seq and microbiome

2011-2012 Informatic certificate.
Université Laval, Québec

2008-2011 Master degree in Physiologie-Endocrinologie
Université Laval, Québec
Director: Francine Durocher
FÉS roll of honor.
Subject: Breast cancer genetic susceptibility.

2008-2009 Microprogram in Génomique Fonctionnelle
Université Laval, Québec

2004-2007 Baccalaureate in Biotechnology
Concentration in Molecular Biology
Université de Sherbrooke, Sherbrooke

2001-2004 Techniques in Chemistry-Biology
Cégep de Lévis-Lauzon, Lévis

Ph.D Student

ALEXANDRE DROUIN

Ph.D Student


CAREER RESUME

My main fields of interest are machine learning and computational biology. I enjoy analyzing biological problems and designing algorithmic solutions to address them. In the context of my PhD, I am developing machine learning approaches to predict phenotypes from multiomics data (genomics, transcriptomics, metabolomic, etc.). I am particularly interested in making the most out of the vast amount of publicly available data through supervised and semi-supervised machine learning. Recently, I have been working on predicting antibiotic resistance in bacteria, a major public health concern. 

 
FINANCING
 
2014-2017       NSERC Alexander Graham Bell Canada Graduate Scholarship – Doctoral
2013-2014       FRQ Graduate Masters Scholarship (B1)
2012-2013       NSERC Alexander Graham Bell Canada Graduate Scholarship – Master’s     
2012-2012       NSERC Undergraduate Student Research Award
 
 
PUBLICATIONS
  • Drouin, A., Giguère, S., Déraspe, M., Marchand, M., Tyers, M., Loo, V.G., Bourgault, A.-M., Laviolette, F. & Corbeil, J. (2016). Predictive Computational Phenotyping and Biomarker Discovery Using Reference-Free Genome Comparisons. Submitted. [ pdf ]
  • Drouin, A., Giguère, S., Déraspe, M., Laviolette, F., Marchand, M. & Corbeil, J. (2015, July). Greedy Biomarker Discovery in the Genome with Applications to Antimicrobial Resistance. Greed is Great Workshop, ICML, Lille, France. [ pdf ]
  • Drouin, A., Giguère, S., Sagatovich, V., Déraspe, M., Laviolette, F., Marchand, M. & Corbeil, J. (2014, December). Learning interpretable models of phenotypes from whole genome sequences with the Set Covering Machine. Machine Learning in Computational Biology Workshop, NIPS, Montréal, Canada. [ pdf ]
  • Giguère, S., Drouin, A., Lacoste, A., Marchand, M., Corbeil, J., & Laviolette, F. (2013). MHC-NP: Predicting peptides naturally processed by the MHC. Journal of immunological methods, 400, 30-36. [ pdf ]
  • Latulippe, M., Drouin, A., Giguère, P., & Laviolette, F. (2013, August). Accelerated robust point cloud registration in natural environments through positive and unlabeled learning. In Proceedings of the Twenty-Third international joint conference on Artificial Intelligence (pp. 2480-2487). AAAI Press. [ pdf ]
  • Giguère, S., Marchand, M., Laviolette, F., Drouin, A., & Corbeil, J. (2013). Learning a peptide-protein binding affinity predictor with kernel ridge regression. BMC bioinformatics, 14(1), 82. [pdf ]

FORMATION

2014 –      Ph.D degree in computer science

Université Laval, Québec, Canada

Director : Dr François Laviolette

Project title : L’apprentissage automatique et les sciences “omiques”

2012-2014      Master’s degree in computer science

Université Laval, Québec, Canada

Director : Dr François Laviolette

Project title : Algorithmes d’apprentissage automatique à grande échelle pour l’élaboration de nouveaux composés pharmaceutiques

2010–2012      Bachelor’s degree in computer science

Université Laval, Québec, Canada

Research Professional

FAIZA TEBBJI

Research Professional


PUBLICATIONS

See all Faiza’s publication here.

M. Sc, Computer science

PRUDENCIO TOSSOU

Master’s degree in informatics


 CAREER SUMMARY

I was always interested in Computer sciences and biology.
Since I wanted to explore both, I started my career with a Bachelor’s degree in Bioinformatics.
Pursing the goal to solve hard problems in biology using artificial intelligence, I started a Master in machine learning.
So far, my coworkers and I, have tried to develop a new approach to find an inhibitor for a pharmaceutical target.
This work can greatly improve the discovery of new drugs.
I am also working to improve proteins’ structure prediction using the new algorithms in machine learning.

 

PUBLICATIONS

Macaulay, A. D., Gilbert, I., Caballero, J., Barreto, R., Fournier, E., Tossou, P., … & Hyttel, P. (2014). The gametic synapse: RNA transfer to the bovine oocyte. Biology of reproduction, 91(4), 90.
Grant, J. R. Fournier, E., Tossou, P. (2014). ELMA: A Platform for Transcriptional and Epigenetic Microarray Studies of Livestock Embryos. In Plant and Animal Genome XXII Conference. Plant and Animal Genome.

 

FINANCING

2011-2015 Scholarship of Répubique du Bénin

 

FORMATION

2014-2016 Master in Computer Science
Université Laval, Québec, Canada
Advisor : Mario Marchand and Jacques Corbeil
Project’s title : New approch in drug discovery based in machine learning algorithms

2011-2014 Bachelor’s degree in Bioinformatics
Université Laval, Québec, Canada

 


Alumni


Sébastien Boisvert, Ph.D.
Sébastien Giguère, Ph.D.
David Paladini, M.Sc.
Miguel Retamal, Ph.D.
Mélissa Sirois, Ph.D.
Thibault Varin, Ph.D.


 

Affiliations

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