Sébastien Rodrigue

Publications

Articles

• Mirco Plante, Antoine Champie, François Michaud, Sébastien Rodrigue. (2026). Toward full automation in synthetic biology: A progressive conceptual framework integrating robotics and intelligent agents. SLAS Technology. DOI
• Frédéric Grenier, Vincent Baby, Sarah Allard, Simon Lévesque, François Papale, Richard Sullivan, Hannah L. Landecker, Paul G. Higgins, Sébastien Rodrigue, Louis-Patrick Haraoui, Nana Ama Amissah. (2024). Isolation of a bla NDM-1 -positive strain in Israel predating the earliest observations from India. Microbiology Spectrum. DOI
• Frédéric Grenier, Simon Lévesque, Sébastien Rodrigue, Louis-Patrick Haraoui, Nabil Karah, Benno H. Ter Kuile. (2024). Earliest observation of the tetracycline destructase tet(X3 ). Microbiology Spectrum. DOI
• Maude Pomerleau, Vincent Charron-Lamoureux, Lucille Léonard, Frédéric Grenier, Sébastien Rodrigue, Pascale B. Beauregard, Ákos T. Kovács, Yunrong Chai. (2024). Adaptive laboratory evolution reveals regulators involved in repressing biofilm development as key players in Bacillus subtilis root colonization. mSystems. DOI
• Thomas A. Hamilton, Benjamin R. Joris, Arina Shrestha, Tyler S. Browne, Sébastien Rodrigue, Bogumil J. Karas, Gregory B. Gloor, David R. Edgell. (2023). De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials. ACS Synthetic Biology. DOI
• Dominick Matteau, Antoine Champie, Frédéric Grenier, Sébastien Rodrigue. (2023). Complete sequence of the genome-reduced Escherichia coli DGF-298. Microbiology Resource Announcements. DOI
• Nancy Allard, Arianne Collette, Josianne Paquette, Sébastien Rodrigue, Jean-Philippe Côté. (2023). Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids. Communications Biology. DOI
• Champie, A., De Grandmaison, A., Jeanneau, S., Grenier, F., Jacques, P.-É., Rodrigue, S. (2023). Enabling low-cost and robust essentiality studies with high-throughput transposon mutagenesis (HTTM). PLoS ONE. DOI
• Allard, N., Neil, K., Grenier, F., Rodrigue, S. (2022). The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota. Microbiology Spectrum. DOI
• Matteau, D., Rodrigue, S. (2021). An engineered Mycoplasma pneumoniae to fight Staphylococcus aureus. Molecular Systems Biology. DOI
• Durand, R., Huguet, K.T., Rivard, N., Carraro, N., Rodrigue, S., Burrus, V. (2021). Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids. Nucleic Acids Research. DOI
• Lachance, J.-C., Matteau, D., Brodeur, J., Lloyd, C.J., Mih, N., King, Z.A., Knight, T.F., Feist, A.M., Monk, J.M., Palsson, B.O., Jacques, P.-É., Rodrigue, S. (2021). Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular Systems Biology. DOI
• Neil, K., Allard, N., Roy, P., Grenier, F., Menendez, A., Burrus, V., Rodrigue, S. (2021). High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. Molecular Systems Biology. DOI
• Neil, K., Allard, N., Rodrigue, S. (2021). Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota. Frontiers in Microbiology. DOI
• Demontier, E., Dubé-Duquette, A., Brouillette, E., Larose, A., Ster, C., Lucier, J.-F., Rodrigue, S., Park, S., Jung, D., Ruffini, J., Ronholm, J., Dufour, S., Roy, J.-P., Ramanathan, S., Malouin, F. (2021). Relative virulence of Staphylococcus aureus bovine mastitis strains representing the main Canadian spa types and clonal complexes as determined using in vitro and in vivo mastitis models. Journal of Dairy Science. DOI
• Langlois, J.-P., Millette, G., Guay, I., Dubé-Duquette, A., Chamberland, S., Jacques, P.-É., Rodrigue, S., Bouarab, K., Marsault, É., Malouin, F. (2020). Bactericidal Activity of the Bacterial ATP Synthase Inhibitor Tomatidine and the Combination of Tomatidine and Aminoglycoside Against Persistent and Virulent Forms of Staphylococcus aureus. Frontiers in Microbiology. DOI
• Neil, K., Allard, N., Grenier, F., Burrus, V., Rodrigue, S. (2020). Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl₂ conjugative plasmid TP114. Communications Biology. DOI
• Matteau, D., Lachance, J.-C., Grenier, F., Gauthier, S., Daubenspeck, J.M., Dybvig, K., Garneau, D., Knight, T.F., Jacques, P.-É., Rodrigue, S. (2020). Integrative characterization of the near-minimal bacterium Mesoplasma florum. Molecular Systems Biology. DOI
• Neil, K., Allard, N., Jordan, D., Rodrigue, S. (2019). Assembly of large mobilizable genetic cargo by double recombinase operated insertion of DNA (DROID). Plasmid. DOI
• Lachance, J.-C., Lloyd, C.J., Monk, J.M., Yang, L., Sastry, A.V., Seif, Y., Palsson, B.O., Rodrigue, S., Feist, A.M., King, Z.A., Jacques, P.-É. (2019). BOFDAT: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Computational Biology. DOI
• Lachance, J.-C., Rodrigue, S., Palsson, B.O. (2019). Minimal cells, maximal knowledge: Modeling all the chemical reactions that take place in a minimal cell will help us understand the fundamental interactions that power life. eLife. DOI
• Baby, V., Labroussaa, F., Lartigue, C., Rodrigue, S. (2019). Synthetic chromosomes: Rewriting the code of life,Chromosomes synthétiques: Réécrire le code de la vie. Medecine/Sciences. DOI
• Labroussaa, F., Baby, V., Rodrigue, S., Lartigue, C. (2019). Whole genome transplantation: Bringing natural or synthetic bacterial genomes back to life,La transplantation de génomes: Redonner vie à des génomes bactériens naturels ou synthétiques. Medecine/Sciences. DOI
• Baby, V., Labroussaa, F., Brodeur, J., Matteau, D., Gourgues, G., Lartigue, C., Rodrigue, S. (2018). Cloning and Transplantation of the Mesoplasma florum Genome. ACS Synthetic Biology. DOI
• Larochelle, M., Robert, M.-A., Hébert, J.-N., Liu, X., Matteau, D., Rodrigue, S., Tian, B., Jacques, P.-É., Bachand, F. (2018). Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nature Communications. DOI
• Meteignier, L.-V., El Oirdi, M., Cohen, M., Barff, T., Matteau, D., Lucier, J.-F., Rodrigue, S., Jacques, P.-E., Yoshioka, K., Moffett, P. (2018). Corrigendum: Translatome analysis of an NB-LRR immune response identifies important contributors to plant immunity in Arabidopsis (Journal of Experimental Botany (2017) 68:9 (2333-2344) DOI: 10.1093/jxb/erx078). Journal of Experimental Botany. DOI
• Baby, V., Lachance, J.-C., Gagnon, J., Lucier, J.-F., Matteau, D., Knight, T., Rodrigue, S. (2018). Inferring the minimal genome of mesoplasma florum by comparative genomics and transposon mutagenesis. mSystems. DOI
• Boulet, M.L., Isabelle, C., Guay, I., Brouillette, E., Langlois, J.-P., Jacques, P.-É., Rodrigue, S., Brzezinski, R., Beauregard, P.B., Bouarab, K., Boyapelly, K., Boudreault, P.-L., Marsault, É., Malouin, F. (2018). Tomatidine is a lead antibiotic molecule that targets staphylococcus aureus ATP Synthase subunit C. Antimicrobial Agents and Chemotherapy. DOI
• Matteau, D., Pepin, M.-E., Baby, V., Gauthier, S., Giraldo, M.A., Knight, T.F., Rodrigue, S. (2017). Development of oriC-based plasmids for Mesoplasma florum. Applied and Environmental Microbiology. DOI
• Meteignier, L.-V., El-Oirdi, M., Cohen, M., Barff, T., Matteau, D., Lucier, J.-F., Rodrigue, S., Jacques, P.-E., Yoshioka, K., Moffett, P. (2017). Translatome analysis of an NB-LRR immune response identifies important contributors to plant immunity in Arabidopsis. Journal of Experimental Botany. DOI
• Blondeau, A., Lucier, J.-F., Matteau, D., Dumont, L., Rodrigue, S., Jacques, Blouin, R. (2016). Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells. Neural Development. DOI
• Labroussaa, F., Lebaudy, A., Baby, V., Gourgues, G., Matteau, D., Vashee, S., Sirand-Pugnet, P., Rodrigue, S., Lartigue, C. (2016). Impact of donor-recipient phylogenetic distance on bacterial genome transplantation. Nucleic Acids Research. DOI
• Matteau, D., Baby, V., Pelletier, S., Rodrigue, S. (2015). A small-volume, low-cost, and versatile continuous culture device. PLoS ONE. DOI
• Brunelle, M., Nordell Markovits, A., Rodrigue, S., Lupien, M., Jacques, P.-E., Gévry, N. (2015). The histone variant H2A.Z is an important regulator of enhancer activity. Nucleic Acids Research. DOI
• Poulin-Laprade, D., Matteau, D., Jacques, P.-E., Rodrigue, S., Burrus, V. (2015). Transfer activation of SXT/R391 integrative and conjugative elements: Unraveling the SetCD regulon. Nucleic Acids Research. DOI
• Carraro, N., Matteau, D., Burrus, V., Rodrigue, S. (2015). Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements. Mobile Genetic Elements. DOI
• Grenier, F., Matteau, D., Baby, V., Rodrigue, S. (2014). Complete genome sequence of Escherichia coli BW25113. Genome Announcements. DOI
• Carraro, N., Sauvé, M., Matteau, D., Lauzon, G., Rodrigue, S., Burrus, V. (2014). Development of pVCR94ΔX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Frontiers in Microbiology. DOI
• Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R., Follows, M.J., Stepanauskas, R., Chisholm, S.W. (2014). Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. DOI
• Carraro, N., Matteau, D., Luo, P., Rodrigue, S., Burrus, V. (2014). The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination. PLoS Genetics. DOI
• Zitouni, M., Fortin, M., Scheerle, R.K., Letzel, T., Matteau, D., Rodrigue, S., Brzezinski, R. (2013). Biochemical and molecular characterization of a thermostable chitosanase produced by the strain Paenibacillus sp. 1794 newly isolated from compost. Applied Microbiology and Biotechnology. DOI
• Daccord, A., Ceccarelli, D., Rodrigue, S., Burrus, V. (2013). Comparative analysis of mobilizable Genomic Islands. Journal of Bacteriology. DOI
• Baby, V., Matteau, D., Knight, T.F., Rodrigue, S. (2013). Complete genome sequence of the Mesoplasma florum W37 strain. Genome Announcements. DOI
• Malmstrom, R.R., Rodrigue, S., Huang, K.H., Kelly, L., Kern, S.E., Thompson, A., Roggensack, S., Berube, P.M., Henn, M.R., Chisholm, S.W. (2013). Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME Journal. DOI
• Waldbauer, J.R., Rodrigue, S., Coleman, M.L., Chisholm, S.W. (2012). Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle. PLoS ONE. DOI
• Rodrigue, S., Materna, A.C., Timberlake, S.C., Blackburn, M.C., Malmstrom, R.R., Alm, E.J., Chisholm, S.W. (2010). Unlocking short read sequencing for metagenomics. PLoS ONE. DOI
• Wu, S., Barnes, P.F., Samten, B., Pang, X., Rodrigue, S., Ghanny, S., Soteropoulos, P., Gaudreau, L., Howard, S.T. (2009). Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth. Microbiology. DOI
• Rodrigue, S., Malmstrom, R.R., Berlin, A.M., Birren, B.W., Henn, M.R., Chisholm, S.W. (2009). Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE. DOI
• Donà, V., Rodrigue, S., Dainese, E., Palù, G., Gaudreau, L., Manganelli, R., Provvedi, R. (2008). Evidence of complex transcriptional, translational, and posttranslational regulation of the extracytoplasmic function sigma factor σ^E in Mycobacterium tuberculosis. Journal of Bacteriology. DOI
• Rodrigue, S., Brodeur, J., Jacques, P.-É., Gervais, A.L., Brzezinski, R., Gaudreau, L. (2007). Identification of mycobacterial σ factor binding sites by chromatin immunoprecipitation assays. Journal of Bacteriology. DOI
• Kettler, G.C., Martiny, A.C., Huang, K., Zucker, J., Coleman, M.L., Rodrigue, S., Chen, F., Lapidus, A., Ferriera, S., Johnson, J., Steglich, C., Church, G.M., Richardson, P., Chisholm, S.W. (2007). Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genetics. DOI
• Sureka, K., Dey, S., Datta, P., Singh, A.K., Dasgupta, A., Rodrigue, S., Basu, J., Kundu, M. (2007). Polyphosphate kinase is involved in stress-induced mprAB-sigE-rel signalling in mycobacteria. Molecular Microbiology. DOI
• Jacques, J.-F., Rodrigue, S., Brzezinski, R., Gaudreau, L. (2006). A recombinant Mycobacterium tuberculosis in vitro transcription system. FEMS Microbiology Letters. DOI
• Jacques, P.-É., Rodrigue, S., Gaudreau, L., Goulet, J., Brzezinski, R. (2006). Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. BMC Bioinformatics. DOI
• Dainese, E., Rodrigue, S., Delogu, G., Provvedi, R., Laflamme, L., Brzezinski, R., Fadda, G., Smith, I., Gaudreau, L., Palù, G., Manganelli, R. (2006). Posttranslational regulation of Mycobacterium tuberculosis extracytoplasmic-function sigma factor σ^L and roles in virulence and in global regulation of gene expression. Infection and Immunity. DOI
• Rodrigue, S., Provvedi, R., Jacques, P.-É., Gaudreau, L., Manganelli, R. (2006). The σ factors of Mycobacterium tuberculosis. FEMS Microbiology Reviews. DOI
• Manganelli, R., Provvedi, R., Rodrigue, S., Beaucher, J., Gaudreau, L., Smith, I. (2004). Erratum: σ Factors and Global Gene Regulation in Mycobacterium tuberculosis (Journal of Bacteriology (2004) 186, 4 (895-902)). Journal of Bacteriology. DOI
• Manganelli, R., Proveddi, R., Rodrigue, S., Beaucher, J., Gaudreau, L., Smith, I. (2004). σ Factors and Global Gene Regulation in Mycobacterium tuberculosis. Journal of Bacteriology. DOI
• Beaucher, J., Rodrigue, S., Jacques, P.-É., Smith, I., Brzezinski, R., Gaudreau, L. (2002). Novel Mycobacterium tuberculosis anti-σ factor antagonists controls σ^F activity by distinct mechanisms. Molecular Microbiology. DOI

Livres

• Leblanc, B.P., Rodrigue, S. (2015). DNA-protein interactions: Principles and protocols: Fourth Edition. DNA-Protein Interactions: Principles and Protocols: Fourth Edition. DOI
• Leblanc, B.P., Rodrigue, S. (2015). Preface. DNA-Protein Interactions: Principles and Protocols: Fourth Edition. DOI

Chapitres de livre

• Lachance, J.-C., Rodrigue, S., Palsson, B.O. (2019). The use of in silico genome-scale models for the rational design of minimal cells. Minimal Cells: Design, Construction, Biotechnological Applications. DOI
• Brunelle, M., Rodrigue, S., Jacques, P.-É., Gévry, N. (2017). High-resolution genome-wide mapping of nucleosome positioning and occupancy level using paired-end sequencing technology. Methods in Molecular Biology. DOI
• Bianco, S., Rodrigue, S., Murphy, B.D., Gévry, N. (2015). Global mapping of open chromatin regulatory elements by formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Methods in Molecular Biology. DOI
• Matteau, D., Rodrigue, S. (2015). Precise identification of DNA-binding proteins genomic location by exonuclease coupled chromatin immunoprecipitation (ChIP-exo). Methods in Molecular Biology. DOI
• Matteau, D., Rodrigue, S. (2015). Precise identification of genome-wide transcription start sites in bacteria by 5’-rapid amplification of cDNA ends (5’-RACE). Methods in Molecular Biology. DOI
• Grenier, F., Lucier, J.-F., Rodrigue, S. (2015). Selection and validation of spacer sequences for CRISPR-Cas9 genome editing and transcription regulation in bacteria. Methods in Molecular Biology. DOI

Autres contributions

Cours enseignés à l'UdeS

• MCB519 - Projet en génétique expérimentale. (2025-2026). (2CR).
• OMP700 - Projet de spécialité en sciences omiques appliquées. (2026). (9CR).
• OMP701 - Projet expérimental I en sciences omiques appliquées. (2025-2026). (3CR).
• OMP702 - Projet expérimental II en sciences omiques appliquées. (2025-2026). (3CR).
• OMP704 - Sujets spéciaux en sciences omiques appliquées. (2025-2026). (3CR).
• OMX701 - Méthodes transcriptomiques. (2026). (3CR).
• OMX702 - Approches épigénomiques - protéines. (2026). (3CR).
• OMX703 - Approches métagénomiques. (2026). (3CR).
• OMX704 - Méthodes protéomiques. (2026). (3CR).
• OMX760 - Initiation à la mutagénèse par insertion de transposons. (2024, 2026). (3CR).
• BCM319 - Laboratoire de génétique moléculaire. (2025). (2CR).
• BFT708 - Introduction aux méthodes et aux données génomiques. (2023-2025). (1CR).
• MCB631 - Initiation à la recherche en microbiologie I. (2023-2025). (2CR).
• MCB633 - Initiation à la recherche en microbiologie II. (2023-2025). (4CR).
• MCB635 - Initiation à la recherche en microbiologie III. (2023-2025). (4CR).
• OMX700 - Technologies de séquençage à haut débit pour les sciences omiques appliquées. (2025). (3CR).
• OMX762 - Méthodes avancées d’assemblage de fragments d’ADN. (2024-2025). (3CR).
• OMX862 - Méthodes avancées d’assemblage de fragments d’ADN. (2024-2025). (3CR).
• TSB703 - Principes des techniques en biologie moléculaire. (2025). (3CR).
• BCM315 - Biologie moléculaire - Travaux pratiques. (2023-2024). (2CR).
• OMX860 - Initiation à la mutagénèse par insertion de transposons. (2024). (3CR).

Divers

• Grenier, F., Baby, V., Allard, S., Heynemand, F., Lévesque, S., Sullivan, R., Landecker, H.L., Higgins, P.G., Rodrigue, S., Haraoui, L.-P. (2022). Molecular epidemiology of carbapenemase-producing Acinetobacter spp. from Israel, 2001-2006: earliest report of bla_NDM predating the oldest known bla_NDM-positive strains. bioRxiv.
• Durand, R., Huguet, K.T., Rivard, N., Carraro, N., Rodrigue, S., Burrus, V. (2020). Crucial role of Salmonella genomic island 1 master activator in parasitism of IncC plasmids. bioRxiv.
• Lachance, J.-C., Monk, J.M., Lloyd, C.J., Seif, Y., Palsson, B.O., Rodrigue, S., Feist, A.M., King, Z.A., Jacques, P.-É. (2018). BOFdat: Generating biomass objective function stoichiometric coefficients from experimental data. bioRxiv.