In bold are me or my trainees, while an asterisk (*) indicates a corresponding authorship, and an underline indicates a first author.

• Fatima R, MacNeil LT, Hynes AP*. 2024. Temperate phages increase antibiotic effectiveness in a Caenorhabditis elegans infection model . BiorXiv [Preprint]

• Fatima R, Hynes AP*. 2024. Temperate phage-antibiotic synergy is widespread, but varies by phage, host, and antibiotic pairing. mBio in press, link to BiorXiv Pre-Print

• Nair G, Chavez-Carbajal A, di Tullio R, French S, Maddiboina D, Harvey H, Dizzel S, Brown ED, Hosseinidoust Z, Surette MG, Burrows LL, Hynes AP*. 2024. Micro-plaque assays: A High-throughput method to detect, isolate, and characterize bacteriophages. BiorXiv {Preprint]

• Croteau FC, Tran J, Hynes AP*. 2024. CRISPR adaptation in Streptococcus thermophilus can be driven by phage environmental DNA. BiorXiv [Preprint]

• Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP*. 2024. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 15(6): e00504-24

• Al-Anany AM, Hooey PB, Cook JB, Burrows LL, Martinyuik J, Hynes AP, German GJ. 2023. Phage Therapy in the Management of of Urinary Tract Infections: A Comprehensive Systematic Review. PHAGE Sept2023: 112-127

• Champagne-Jorgensen K, Jose TA, Stanisz AM, Mian MF, Hynes AP*, Bienenstock J*. 2021. Bacterial membrane vesicles and phages in blood after consumption of Lacticaseibacillus rhamnosus JB-1. Gut Microbes 13:1

• Gomez-Garcia J, Chavez-Carbajal A, Segundo-Arizmendi N, Baron-Pichardo MG, Mendoza-Elvira SE, Hernandez-Baltazar E, Hynes AP*, Torres-Angeles O*. 2021. Efficacy of Salmonella bacteriophage S1 delivered and released by alginate beads in a chicken model of infection. Viruses 13(10):1932

• Al-Anany AM, Fatima R, Hynes AP*. 2021. Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell Reports 35(8):109172

• Sutcliffe SG, Shamash M, Hynes AP, Maurice CF*. 2021. Common oral medications lead to prophage induction in bacterial isolates from the human gut. Viruses 13(3):455

• Shareefdeen H, Hynes AP*. 2021. Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut?. Anaerobe 68:102319

• Croteau FR, Hynes AP*. 2020. In the anti-CRISPR jungle, only the Weak thrive?. Cell Host & Microbe 27(2):157-159

• (International Patent, Inventor) Novel anti-CRISPR genes and proteins and methods of use, WO 2018/197495 A1

• (International Patent, Inventor) Methods and compositions of anti-CRISPR proteins for use in plants , WO 2018/197520

• Hynes AP, Rousseau GM, Agudelo D, Goulet A, Amigues B, Loehr J, Romero DA, Fremaux C, Horvath P, Doyon Y, Cambillau C & Moineau S*. 2018. Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nature Communications. 9: 2919

• Hynes AP, Rousseau GM, Lemay M-L, Horvath P, Romero DA, Fremaux C & Moineau S*. 2017. An anti-CRISPR from a virulent streptococcal phage inhibits SpCas9. Nature Microbiology. 2(10):1374-1380

• Hynes AP & Moineau S*. 2017. Phagebook: The Social Network. Molecular Cell. 65(6):963-964

• Hynes AP, Lemay M-L, Trudel L, Deveau H, Frenette M, Tremblay DM, & Moineau S*. 2017. Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings. Nature Protocols; 12:547-565

• Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E., Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O*, & Lang AS*. 2016. Functional and evolutionary characterization of a gene transfer agent's multi-locus 'genome'. Molecular Biology and Evolution; 33(10):2530-2543

• Hynes AP, Lemay M-L & Moineau S*. 2016. Applications of CRISPR-Cas in its natural habitat. Current Opinion in Chemical Biology; 34:30-36

• Hynes AP, Labrie SJ & Moineau S*. 2016. Programming native CRISPR arrays for the generation of targeted immunity. mBIO; 7(3):e00202-16

• Hynes AP, Villion M, & Moineau S*. 2014. Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages. Nature Communications; 5:4399

• Hynes AP & Moineau S*. 2014. Making the cut. Microbe; 9:204-210

• Hynes AP & Lang AS*. 2013. Rhodobacter capsulatus gene transfer agent (RcGTA) activity bioassays. www.bio-protocol.org

• Hynes AP, Mercer RG, Watton DE, Buckley CB & Lang AS*. 2012. DNA packaging bias and differential expression of gene transfer gene genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. Molecular Microbiology; 85(2):314-325

• Fogg PCM, Hynes AP, Digby E, Lang AS & Beatty JT*. 2011. Characterization of a newly discovered Mu-like bacteriophage, RcapMu, in Rhodobacter capsulatus strain SB1003. Virology; 421(2):211-321

• Op den en Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A & Dunfield PF*. 2009. Environmental, genomic, and taxonomic perspectives on methanotrophic Verrucomicrobia. Environmental Microbiology Reports; 1(5):293-306

• Tremaroli V, Workentine ML, Weljie AM, Vogel HJ, Ceri H, Viti C, Tatti E, Zhang P, Hynes AP, Turner RJ & Zannoni D*. 2009. Metabolomic investigation of the bacterial response to a metal challenge. Applied and Environmental Microbiology; 75(3): 719–728