Frédéric Raymond

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