• 2025
  Darracq B, Littner E, Brunie M, Bos J, Kaminski PA, Depardieu F, Slesak W, Debatisse K, Touchon M, Bernheim A, Bikard D, Le Roux F, Mazel D, Rocha EPC, Loot C, Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems., Science, 2025 May; 388(6747): eads0768.
• 2025
  Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH, Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons., Nat Microbiol 2025 Jan; (): .
• 2025
  Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont, Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series, The International Society of Microbiologial Ecology Journal, 2025, 19 (1), ⟨10.1093/ismejo/wrae245⟩.
• 2024
  Tesson F, Huiting E, Wei L, Ren J, Johnson M, Planel R, Cury J, Feng Y, Bondy-Denomy J, Bernheim A, Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements., Nucleic Acids Res 2024 Dec; (): .
• 2024
  Gaborieau B, Vaysset H, Tesson F, Charachon I, Dib N, Bernier J, Dequidt T, Georjon H, Clermont O, Hersen P, Debarbieux L, Ricard JD, Denamur E, Bernheim A, Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information., Nat Microbiol 2024 Nov; 9(11): 2847-2861.
• 2024
  Jean Cury, Matthieu Haudiquet, Veronica Hernandez Trejo, Ernest Mordret, Anael Hanouna, Maxime Rotival, Florian Tesson, Delphine Bonhomme, Gal Ofir, Lluis Quintana-Murci, Philippe Benaroch, Enzo Z Poirier, Aude Bernheim, Conservation of antiviral systems across domains of life reveals immune genes in humans, Cell Host & Microbe, 2024, 32 (9), pp.1594-1607.e5. ⟨10.1016/j.chom.2024.08.002⟩.
• 2024
  Nathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce Wilkinson, Mikhail Skutel, Andrew Santiago-Frangos, Ava Graham, Alexei Livenskyi, Anna Chechenina, Natalia Morozova, Trevor Zahl, William Henriques, Murat Buyukyoruk, Christophe Rouillon, Baptiste Saudemont, Lena Shyrokova, Tatsuaki Kurata, Vasili Hauryliuk, Konstantin Severinov, Justine Groseille, Agnès Thierry, Romain Koszul, Florian Tesson, Aude Bernheim, David Bikard, Blake Wiedenheft, Artem Isaev, A virally encoded tRNA neutralizes the PARIS antiviral defence system, Nature, 2024, 634 (8033), pp.424-431. ⟨10.1038/s41586-024-07874-3⟩.
• 2024
  Helena Shomar, Héloïse Georjon, Yanlei Feng, Bismarck Olympio, Marie Guillaume, Florian Tesson, Jean Cury, Fabai Wu, Aude Bernheim, Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold, Nature Ecology & Evolution, 2024, 8 (9), pp.667-1679. ⟨10.1038/s41559-024-02463-z⟩.
• 2024
  Bernheim A, Cury J, Poirier EZ, The immune modules conserved across the tree of life: Towards a definition of ancestral immunity., PLoS Biol 2024 Jul; 22(7): e3002717.
• 2024
  F. Tesson, R. Planel, A. Egorov, H. Georjon, H. Vaysset, B. Brancotte, B. Néron, E. Mordret, G. Atkinson, A Bernheim, J. Cury, A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases, 2024.
• 2023
  Aël Hardy, Helena Shomar, Aude Bernheim, Immunité bactérienne : à la découverte d’un nouveau monde [Bacterial immunity: Uncovering a new world], Médecine/Sciences, 2023, 39 (11), pp.862-868. ⟨10.1051/medsci/2023163⟩.
• 2023
  Georjon H, Bernheim A, The highly diverse antiphage defence systems of bacteria., Nat Rev Microbiol 2023 Oct; 21(10): 686-700.
• 2023
  Georjon H, Tesson F, Shomar H, Bernheim A, Genomic characterization of the antiviral arsenal of Actinobacteria., Microbiology (Reading) 2023 Aug; 169(8): .
• 2023
  Tesson F, Bernheim A, Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?, Curr Opin Microbiol 2023 Feb; 71(): 102238.
• 2022
  Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, Ofir G, Hochhauser D, Stokar-Avihail A, Tal N, Sharir S, Voichek M, Erez Z, Ferrer JLM, Dar D, Kacen A, Amitai G, Sorek R, An expanded arsenal of immune systems that protect bacteria from phages., Cell Host Microbe 2022 Nov; 30(11): 1556-1569.e5.
• 2022
  Garb J, Lopatina A, Bernheim A, Zaremba M, Siksnys V, Melamed S, Leavitt A, Millman A, Amitai G, Sorek R, , Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion., Nat Microbiol 2022 Nov; 7(11): 1849-1856.
• 2022
  Cury J, Bernheim A, CRISPR-Cas and restriction-modification team up to achieve long-term immunity., Trends Microbiol 2022 Jun; 30(6): 513-514.
• 2022
  François Rousset, Florence Depardieu, Solange Miele, Julien Dowding, Anne-Laure Laval, Erica Lieberman, Daniel Garry, Eduardo P. C. Rocha, Aude Bernheim, David Bikard, Phages and their satellites encode hotspots of antiviral systems, Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩.
• 2022
  Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, Bernheim A, Systematic and quantitative view of the antiviral arsenal of prokaryotes., Nat Commun 2022 May; 13(1): 2561.
• 2022
  Klompe SE, Jaber N, Beh LY, Mohabir JT, Bernheim A, Sternberg SH, Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons., Mol Cell 2022 Feb; 82(3): 616-628.e5.
• 2022
  Florian Tesson, Alexandre Hervé, Ernest Mordret, Marie Touchon, Camille D’humières, Jean Cury, Aude Bernheim, Systematic and quantitative view of the antiviral arsenal of prokaryotes, Nature Communications, 2022, 13 (1), pp.2561. ⟨10.1038/s41467-022-30269-9⟩.
• 2021
  Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R, , Prokaryotic viperins produce diverse antiviral molecules., Nature 2021 Jan; 589(7840): 120-124.
• 2020
  Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R, , Bacterial Retrons Function In Anti-Phage Defense., Cell 2020 Dec; 183(6): 1551-1561.e12.
• 2020
  Bernheim A, Sorek R, , The pan-immune system of bacteria: antiviral defence as a community resource., Nat Rev Microbiol 2020 Feb; 18(2): 113-119.
• 2020
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo Rocha, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩.
• 2019
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩.
• 2018
  David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel, CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩.
• 2018
  Bernheim A, Sorek R, , Viruses cooperate to defeat bacteria., Nature 2018 Jul; 559(7715): 482-484.
• 2017
  Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P C Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩.