Ha, Kam Pou, Etornam Kofi Kumeko, and Philippe Bouloc. 2025. “A Small Regulatory RNA Controls Antibiotic Adaptation in Staphylococcus Aureus by Modulating Efflux Pump Expression.” Antimicrobial Agents and Chemotherapy, April, e0117624. https://doi.org/10.1128/aac.01176-24.

Delaleau, Mildred, Nara Figueroa-Bossi, Thuy Duong Do, Patricia Kerboriou, Eric Eveno, Lionello Bossi, and Marc Boudvillain. 2024. “Rho-Dependent Transcriptional Switches Regulate the Bacterial Response to Cold Shock.” Molecular Cell, August, S1097-2765(24)00632-4. https://doi.org/10.1016/j.molcel.2024.07.034.

Barrault, Maxime, Elise Leclair, Etornam Kofi Kumeko, Eric Jacquet, and Philippe Bouloc. 2024. “Staphylococcal SRNA IsrR Downregulates Methylthiotransferase MiaB under Iron-Deficient Conditions.” Microbiology Spectrum, August, e0388823. https://doi.org/10.1128/spectrum.03888-23.

Barrault, Maxime, Svetlana Chabelskaya, Rodrigo H Coronel-Tellez, Claire Toffano-Nioche, Eric Jacquet, and Philippe Bouloc. 2024. “Staphylococcal Aconitase Expression during Iron Deficiency Is Controlled by an SRNA-Driven Feedforward Loop and Moonlighting Activity.” Nucleic Acids Research 52 (14): 8241–53. https://doi.org/10.1093/nar/gkae506.

Figueroa-Bossi, Nara, Rocío Fernández-Fernández, Patricia Kerboriou, Philippe Bouloc, Josep Casadesús, María Antonia Sánchez-Romero, and Lionello Bossi. 2024. “Transcription-Driven DNA Supercoiling Counteracts H-NS-Mediated Gene Silencing in Bacterial Chromatin.” Nature Communications 15 (1): 2787. https://doi.org/10.1038/s41467-024-47114-w.

Leiba, Jade, Tamara Sipka, Christina Begon-Pescia, Matteo Bernardello, Sofiane Tairi, Lionello Bossi, Anne-Alicia Gonzalez, et al. 2024. “Dynamics of Macrophage Polarization Support Salmonella Persistence in a Whole Living Organism.” ELife 13 (January):e89828. https://doi.org/10.7554/eLife.89828.

Braetz, Sebastian, Peter Schwerk, Nara Figueroa-Bossi, Karsten Tedin, and Marcus Fulde. 2023. “Prophage Gifsy-1 Induction in Salmonella Enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure.” Microbiology Spectrum, June, e0187423. https://doi.org/10.1128/spectrum.01874-23.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Mapping Transposon Insertion Sites by Inverse Polymerase Chain Reaction and Sanger Sequencing.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.prot108197.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Use of Transposable Reporters in the Analysis of Bacterial Regulatory Networks.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.top108327.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Generating Libraries of Random LacZY or GFP Gene Fusions in the Bacterial Chromosome: Screening for Differentially Expressed Fusions.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.prot108196.

Clerissi, Camille, Xing Luo, Aude Lucasson, Shogofa Mortaza, Julien de Lorgeril, Eve Toulza, Bruno Petton, et al. 2023. “A Core of Functional Complementary Bacteria Infects Oysters in Pacific Oyster Mortality Syndrome.” Animal Microbiome 5 (1): 26. https://doi.org/10.1186/s42523-023-00246-8.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Scarless DNA Recombineering.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107857.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Recombineering 101: Making an in-Frame Deletion Mutant.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107856.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “DNA Recombineering Applications.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.top107855.

Balbontín, Roberto, Mathilde Ratel, Nara Figueroa-Bossi, and Lionello Bossi. 2023. “Converting an FRT-Tagged Gene into a Fluorescent Protein Gene Fusion by Flp-Mediated Site-Specific Recombination.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107951.

Balbontín, Roberto, Nara Figueroa-Bossi, and Lionello Bossi. 2023. “Construction of Single-Copy Fluorescent Protein Fusions by One-Step Recombineering.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107950.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Preparing Plasmid DNA from Bacteria.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107852.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Preparing Bacterial Genomic DNA.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107853.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Quick Transformation with Plasmid DNA.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107854.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Basic Bacteriological Routines.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107849.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Working with Bacteria, Phage, and Plasmids.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.top107848.

Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Working with Phage P22.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107850.

Coronel-Tellez, Rodrigo H, Mateusz Pospiech, Maxime Barrault, Wenfeng Liu, Valérie Bordeau, Christelle Vasnier, Brice Felden, Bruno Sargueil, and Philippe Bouloc. 2022. “SRNA-Controlled Iron Sparing Response in Staphylococci.” Nucleic Acids Research, July, gkac648. https://doi.org/10.1093/nar/gkac648.

Figueroa-Bossi, Nara, María Antonia Sánchez-Romero, Patricia Kerboriou, Delphine Naquin, Clara Mendes, Philippe Bouloc, Josep Casadesús, and Lionello Bossi. 2022. “Pervasive Transcription Enhances the Accessibility of H-NS–Silenced Promoters and Generates Bistability in Salmonella Virulence Gene Expression.” Proceedings of the National Academy of Sciences 119 (30): e2203011119. https://doi.org/10.1073/pnas.2203011119.

García-Del Portillo, Francisco, Nara Figueroa-Bossi, and Lionello Bossi. 2022. “Remembering Pepe Casadesús.” MicroLife 3:uqac016. https://doi.org/10.1093/femsml/uqac016.

Le Huyen, Kim Boi, Cintia Daniela Gonzalez, Gaëtan Pascreau, Valérie Bordeau, Vincent Cattoir, Wenfeng Liu, Philippe Bouloc, Brice Felden, and Svetlana Chabelskaya. 2021. “A Small Regulatory RNA Alters Staphylococcus Aureus Virulence by Titrating RNAIII Activity.” Nucleic Acids Research, September, gkab782. https://doi.org/10.1093/nar/gkab782.

Ha, Kam Pou, and Andrew M. Edwards. 2021. “DNA Repair in Staphylococcus Aureus.” Microbiology and Molecular Biology Reviews: MMBR, September, e0009121. https://doi.org/10.1128/MMBR.00091-21.

Zaworski, Julie, Oyut Dagva, Anthony W. Kingston, Alexey Fomenkov, Richard D. Morgan, Lionello Bossi, and Elisabeth A. Raleigh. 2021. “Genome Archaeology of Two Laboratory Salmonella Enterica Enterica Sv Typhimurium.” G3 (Bethesda, Md.) 11 (9): jkab226. https://doi.org/10.1093/g3journal/jkab226.

Bossi, Lionello, Nara Figueroa-Bossi, Philippe Bouloc, and Marc Boudvillain. 2020. “Regulatory Interplay between Small RNAs and Transcription Termination Factor Rho.” Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1863 (7): 194546. https://doi.org/10.1016/j.bbagrm.2020.194546.

Lacoux, Caroline, Aymeric Fouquier d’Hérouël, Françoise Wessner-Le Bohec, Nicolas Innocenti, Chantal Bohn, Sean P. Kennedy, Tatiana Rochat, et al. 2020. “Dynamic Insights on Transcription Initiation and RNA Processing during Bacterial Adaptation.” RNA (New York, N.Y.) 26 (4): 382–95. https://doi.org/10.1261/rna.073288.119.

Liu, Wenfeng, Pierre Boudry, Chantal Bohn, and Philippe Bouloc. 2020. “Staphylococcus Aureus Pigmentation Is Not Controlled by Hfq.” BMC Research Notes 13 (1): 63. https://doi.org/10.1186/s13104-020-4934-4.

Deng, Yiqin, Xing Luo, Mei Xie, Philippe Bouloc, Chang Chen, and Annick Jacq. 2019. “The IlvGMEDA Operon Is Regulated by Transcription Attenuation in Vibrio Alginolyticus ZJ-T.” Applied and Environmental Microbiology 85 (19): e00880-19. https://doi.org/10.1128/AEM.00880-19.

Rubio, Tristan, Daniel Oyanedel, Yannick Labreuche, Eve Toulza, Xing Luo, Maxime Bruto, Cristian Chaparro, et al. 2019. “Species-Specific Mechanisms of Cytotoxicity toward Immune Cells Determine the Successful Outcome of Vibrio Infections.” Proceedings of the National Academy of Sciences of the United States of America 116 (28): 14238–47. https://doi.org/10.1073/pnas.1905747116.

Briand, William, Ousmane Dao, Guillaume Garnier, Raphaël Guegan, Britany Marta, Clémence Maupu, Julie Miesch, et al. 2018. “Dégradation d’un anticancéreux dans les eaux usées - Une médaille d’or pour l’équipe GO Paris-Saclay.” Medecine Sciences: M/S 34 (12): 1111–14. https://doi.org/10.1051/medsci/2018304.

Nguyen, An Ngoc, Elena Disconzi, Guillaume M. Charriere, Delphine Destoumieux-Garzon, Philippe Bouloc, Frederique Le Roux, and Annick Jacq. 2018. “CsrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio Tasmaniensis LGP32.” Msphere 3 (6): e00582-18. https://doi.org/10.1128/mSphere.00582-18.

Rochat, Tatiana, Chantal Bohn, Claire Morvan, Thao Nguyen Le Lam, Fareha Razvi, Adrien Pain, Claire Toffano-Nioche, et al. 2018. “The Conserved Regulatory RNA RsaE Down-Regulates the Arginine Degradation Pathway in Staphylococcus Aureus.” Nucleic Acids Research 46 (17): 8803–16. https://doi.org/10.1093/nar/gky584.

Raghunathan, Nalini, Rajvardhan M Kapshikar, Jakku K Leela, Jillella Mallikarjun, Philippe Bouloc, and Jayaraman Gowrishankar. 2018. “Genome-Wide Relationship between R-Loop Formation and Antisense Transcription in Escherichia Coli.” Nucleic Acids Research 46 (7): 3400–3411. https://doi.org/10.1093/nar/gky118.

Liu, Wenfeng, Tatiana Rochat, Claire Toffano-Nioche, Thao Nguyen Le Lam, Philippe Bouloc, and Claire Morvan. 2018. “Assessment of Bona Fide SRNAs in Staphylococcus Aureus.” Frontiers in Microbiology 9:228. https://doi.org/10.3389/fmicb.2018.00228.

Dias, Graciela M., Adeline Bidault, Patrick Le Chevalier, Gwenaëlle Choquet, Clio Der Sarkissian, Ludovic Orlando, Claudine Medigue, et al. 2018. “Vibrio Tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.” Frontiers in Microbiology 9:227. https://doi.org/10.3389/fmicb.2018.00227.

Richarme, Gilbert, Cailing Liu, Mouadh Mihoub, Jad Abdallah, Thibaut Leger, Nicolas Joly, Jean-Claude Liebart, et al. 2017. “Guanine Glycation Repair by DJ-1/Park7 and Its Bacterial Homologs.” Science 357 (6347): 208–11. https://doi.org/10.1126/science.aag1095.

Le Lam, Thao Nguyen, Claire Morvan, Wenfeng Liu, Chantal Bohn, Yan Jaszczyszyn, and Philippe Bouloc. 2017. “Finding SRNA-Associated Phenotypes by Competition Assays: An Example with Staphylococcus Aureus.” Methods 117:21–27. https://doi.org/10.1016/j.ymeth.2016.11.018.

Felden, Brice, and Philippe Bouloc. 2017. “Regulatory RNAs in Bacteria: From Identification to Function.” Methods 117:1–2. https://doi.org/10.1016/j.ymeth.2017.03.018.

Bouloc, Philippe, and Francis Repoila. 2016. “Fresh Layers of RNA-Mediated Regulation in Gram-Positive Bacteria.” Current Opinion in Microbiology 30 (April):30–35. https://doi.org/10.1016/j.mib.2015.12.008.

Vanhove, Audrey S., Tristan P. Rubio, An N. Nguyen, Astrid Lemire, David Roche, Julie Nicod, Agnès Vergnes, et al. 2016. “Copper Homeostasis at the Host Vibrio Interface: Lessons from Intracellular Vibrio Transcriptomics.” Environmental Microbiology 18 (3): 875–88. https://doi.org/10.1111/1462-2920.13083.

Vingadassalon, Audrey, Philippe Bouloc, and Sylvie Rimsky. 2016. “Removing Nucleic Acids from Nucleoid-Associated Proteins Purified by Affinity Column.” Journal of Biological Methods 3 (1): e35. https://doi.org/10.14440/jbm.2016.98.

Deng, Yiqin, Chang Chen, Zhe Zhao, Jingjing Zhao, Annick Jacq, Xiaochun Huang, and Yiying Yang. 2016. “The RNA Chaperone Hfq Is Involved in Colony Morphology, Nutrient Utilization and Oxidative and Envelope Stress Response in Vibrio Alginolyticus.” PloS One 11 (9): e0163689. https://doi.org/10.1371/journal.pone.0163689.

Messaoudi, Nadia, Valérie Gautier, Julien Dairou, Mouhad Mihoub, Gaëlle Lelandais, Philippe Bouloc, Ahmed Landoulsi, and Gilbert Richarme. 2015. “Fermentation and Alternative Respiration Compensate for NADH Dehydrogenase Deficiency in a Prokaryotic Model of DJ-1-Associated Parkinsonism.” Microbiology (Reading, England) 161 (11): 2220–31. https://doi.org/10.1099/mic.0.000181.

Goudenège, David, Marie Agnès Travers, Astrid Lemire, Bruno Petton, Philippe Haffner, Yannick Labreuche, Delphine Tourbiez, et al. 2015. “A Single Regulatory Gene Is Sufficient to Alter Vibrio Aestuarianus Pathogenicity in Oysters.” Environmental Microbiology 17 (11): 4189–99. https://doi.org/10.1111/1462-2920.12699.

Rosinski-Chupin, Isabelle, Elisabeth Sauvage, Odile Sismeiro, Adrien Villain, Violette Da Cunha, Marie-Elise Caliot, Marie-Agnès Dillies, et al. 2015. “Single Nucleotide Resolution RNA-Seq Uncovers New Regulatory Mechanisms in the Opportunistic Pathogen Streptococcus Agalactiae.” BMC Genomics 16 (May):419. https://doi.org/10.1186/s12864-015-1583-4.

Innocenti, Nicolas, Monica Golumbeanu, Aymeric Fouquier d’Hérouël, Caroline Lacoux, Rémy A. Bonnin, Sean P. Kennedy, Françoise Wessner, et al. 2015. “Whole-Genome Mapping of 5’ RNA Ends in Bacteria by Tagged Sequencing: A Comprehensive View in Enterococcus Faecalis.” RNA (New York, N.Y.) 21 (5): 1018–30. https://doi.org/10.1261/rna.048470.114.