44. Neil K*, Allard N*, Jordan D*, Rodrigue S. (2019) Assembly of Large Mobilizable Genetic Cargo by Double Recombinase Operated Insertion of DNA (Droid). Plasmid 104: 102419.

43. Lachance JC*, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PE. (2019) Bofdat: Generating Biomass Objective Functions for Genome-Scale Metabolic Models from Experimental Data. PLoS Comput Biol 15, no. 4: e1006971.

42. Lachance JC*, Rodrigue S, Palsson BO. (2019). Synthetic Biology: Minimal cells, maximal knowledge. eLife. 8: e45379.

41. Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D*, Rodrigue S, Tian B, Jacques PE, Bachand F. (2018). Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nature Communications. 9(1): 4364.

40. Lamontagne Boulet M, Isabelle C, Guay I, Brouillette E, Langlois JP, Jacques PE, Rodrigue S, et al. (2018) Tomatidine, a lead antibiotic molecule that targets Staphylococcus aureus ATP synthase subunit C. Antimicrob. Agents Chemother. 62:1-32.

39. Baby V*, Lachance JC*, Gagnon J, Lucier JF, Matteau D*, Knight TK, Rodrigue S. (2018) Inferring the minimal genome of Mesoplasma florum by comparative genomics and transposon mutagenesis. mSystems 3:1-12.

38. Baby V*, Labroussaa F, Brodeur J*, Matteau D*, Gourgues G, Lartigue C, Rodrigue S. (2017) Cloning and Transplantation of the Mesoplasma florum Genome. ACS Synth Biol. 7(1):209-17.37.

37. Meteignier LV, El Oirdi M, Cohen M, Barff T, Matteau D*, Lucier JF, Rodrigue S, Jacques PE, Yoshioka K, Moffett P. (2017) Translatome analysis of an NB-LRR immune response identifies important contributors to plant immunity in Arabidopsis. J Exp Bot. 68(9):2333-44.

36. Matteau D*, Pepin ME*, Baby V*, Gauthier S*, Arango Giraldo M*, Knight TF, Rodrigue S. (2017) Development of oriC-Based Plasmids for Mesoplasma florum. Appl Environ Microbiol. Mar 17;83(7).

35. Brunelle M, Rodrigue S, Jacques PE, Gévry N. (2017) High-Resolution Genome-Wide Mapping of Nucleosome Positioning and Occupancy Level Using Paired-End Sequencing Technology. Methods Mol Biol. 1528:229-243.

34. 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 Res. 44(17):8501-11.

33. Blondeau A, Lucier JF, Matteau D*, Dumont L, Rodrigue S, Jacques PE, Blouin R. (2016). Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells. Neural Dev. 11(1):13.

32. Carraro N, Matteau D*, Burrus V, Rodrigue S. (2015). Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements. Mob Genet Elements. 5(3):1-5.

31. Bianco S, Rodrigue S, Murphy BD, Gévry N. (2015) Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq). Methods Mol Biol. vol. 1334:261-72.

30. Grenier F*, Lucier JF, Rodrigue S. (2015) Selection and Validation of Spacer Sequences for CRISPR-Cas9 Genome Editing and Transcription Regulation in Bacteria. Methods Mol Biol. vol. 1334:233-44.

29. Matteau D*, Rodrigue S. (2015) Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo). Methods Mol Biol. vol. 1334:173-93.

28. 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 Mol Biol. vol. 1334:143-59.

27. Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques PE, Gévry N. (2015) The histone variant H2A.Z is an important regulator of enhancer activity. Nucleic Acids Res. 2015 Aug 28. pii: gkv825.

26. Methods in Molecular Biology: DNA-protein interactions, vol. 1334, 4th edition (2015) Editeurs Leblanc B. & Rodrigue S.

25. Matteau D*, Baby V*, Pelletier S, Rodrigue S. (2015). A Small-Volume, Low-Cost, and Versatile Continuous Culture Device. PLoS ONE 10(7): e0133384. doi: 10.1371/journal.pone.0133384.

24. 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. 5(3), 1-5. doi: 10.1080/2159256X.2015.1045116.

23. Poulin-Laprade D, Matteau D*, Jacques PE, Rodrigue S, Burrus V. (2015) Transfer Activation of SXT/R391 Integrative and Conjugative Elements: Unraveling the SetCD Regulon. Nucleic Acids Research, doi: 10.1093/nar/gkv071.

22. 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 10(10): e1004714. doi: 10.1371/journal.pgen.1004714.

21. Grenier F*, Matteau D*, Baby V*, Rodrigue S. (2014) Complete genome sequence of Escherichia coli BW25113. GenomeA 2(5), e01038-14.

20. Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. (2014) Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus. Science 344 (6182), 416-420.

19. 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 5: 256.

18. Baby V*, Matteau D*, Knight TF, Rodrigue S. (2013) Complete genome sequence of the Mesoplasma florum W37 strain. GenomeA 1 (6), e00879-13

17. Daccord A, Ceccarelli D, Rodrigue S, Burrus V. (2013) Comparative analysis of mobilizable genomic islands. Journal of Bacteriology 195 (3), 606-614.

16. Zitouni M, Fortin M, Scheerle RK, 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 97 (13), 5801-5813.

15. Waldbauer JR, *Rodrigue S, Coleman ML, Chisholm SW. (2012) Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle. PLoS One 7(8): e43432.

14. Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. (2012) Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J; doi:10.1038/ismej.2012.89

13. Rodrigue S,  Materna AC,  Timberlake SC,  Blackburn MC,  Malmstrom RR, Alm EJ, Chisholm SW. (2010). Unlocking Short Read Sequencing for Metagenomics. PLoS ONE 5: e11840.

12. Rodrigue S, Malmstrom RM, Berlin AM, Birren BW, Henn MR, Chisholm SW. (2009). Whole-Genome Amplification and De novo Assembly of Single-Bacterial Cells. PLoS One. 4:e6864.

11. Wu S, Barnes PF, Samten B, Pang X, Rodrigue S, Ghanny S, Soteropoulos P, Gaudreau L, Howard ST. (2009). Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth. Microbiology, 155:1272-81.

10. Dona V, Rodrigue S, Dainese E, Palu G, Gaudreau L, Manganelli R, Provvedi R. (2008) Evidence of complex transcriptional, translational & posttranslational regulation of the ECF σ factor σE in Mycobacterium tuberculosisJ Bacteriol., 190: 5963-5971.

9. Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW. (2007) Patterns & implications of gene gain & loss in the evolution of Prochlorococcus. PLoS Genet 3: e231.

8. Sureka K, Dey S, Datta P, Singh AK, Dasgupta A, Rodrigue S, Basu J, Kundu M. (2007) Polyphosphate kinase is involved in stress-induced MprAB-σE-Rel signalling in mycobacteria. Mol Microbiol 65: 261-276.

7. Rodrigue S, Brodeur J, Jacques PE, Gervais AL, Brzezinski R, Gaudreau L. (2007) Identification of mycobacterial σ factor binding sites by chromatin immunoprecipitation assays. J Bacteriol 189: 1505-1513.

6. Rodrigue S, Provvedi R, Jacques PE, Gaudreau L, Manganelli R. (2006) The σ factors of Mycobacterium tuberculosis. FEMS Microbiol Rev 30: 926-941.

5. Dainese E, Rodrigue S*, Delogu G, Provvedi R, Laflamme L, Brzezinski R, Fadda G, Smith I, Gaudreau L, Palu G, Manganelli R. (2006) Posttranslational regulation of Mycobacterium tuberculosis extracytoplasmic-function σ factor σL & roles in virulence & in global regulation of gene expression. Infect Immun 74: 2457-2461.

4. Jacques JF, Rodrigue S*, Brzezinski R, Gaudreau L. (2006) A recombinant Mycobacterium tuberculosis in vitro transcription system. FEMS Microbiol Lett 255: 140-147.

3. Jacques PE, Rodrigue S, Gaudreau L, Goulet J, Brzezinski R. (2006) Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. BMC Bioinformatics 7: 423.

2. Manganelli R, Provvedi R, Rodrigue S, Beaucher J, Gaudreau L, Smith I. (2004) σ factors & global gene regulation in Mycobacterium tuberculosis. J Bacteriol 186: 895-902.

1. Beaucher J, Rodrigue S, Jacques PE, Smith I, Brzezinski R, Gaudreau L. (2002) Novel Mycobacterium tuberculosis anti-σ factor antagonists control σF activity by distinct mechanisms. Mol Microbiol 45: 1527-1540.

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