A human homolog of SIR2 antiphage proteins mediates immunity via the TLR pathway
Bonhomme D*, Vaysset H*, Ednacot E., Rodrigues V., Cury J., Salloum Y, Wang A, Benchetrit A., Affaticati P., Hernandez Trejo V., Vittot P., Bories C., Cornec A., Levreaud J., Hernandez P., Benaroch P., Morehouse B, Bernheim A.*, Poirier E.*
Science ,389, eadr8536

Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons
Vaysset H*, Meers C*, Cury J, Bernheim A*, Sternberg S*
Nature Microbiology, doi.org/10.1038/s41564-024-01889-2

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements
Tesson F* , Huiting E* , Wei L , Ren J , Johnson M , Planel R , Cury J , Feng Y , Bondy-Denomy J* , Bernheim A*
Nucleic Acid Research, /10.1093/nar/gkae1171

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery
Haudiquet M*, Chakravarti A*, Zhang Z*, Ramirez J, Herrero del Valle A, Olinares P, Lavenir R, Aït Ahmed M, Cruz M, Chait B, Sternberg S, Bernheim A*, Dinshaw Patel*
bioRxiv, 2025.04. 02.646746

Protein and genomic language models chart a vast landscape of antiphage defenses
Mordret E., Hervé A. , Vaysset H., Clabby T., Tesson F., Shomar H., Lavenir R., Cury J, Bernheim A.
bioRxiv, 2025.01. 08.631966

Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Darracq B, Littner E, Brunie M, Bos J, Kaminski P, Depardieu F, Slesak W, Debatisse K, Touchon M, Bernheim A, Bikard D, Le Roux F, Mazel D, Rocha EPC, Loot C
Science , 388 (6747), eads0768

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information
Gaborieau B*, Vaysset H*., Tesson H*., Charachon I., Dib N., Bernier J., Dequidt T., Georjon H., Clermont O., Hersen P., Debarbieux L, Ricard JD, Denamur E., Bernheim A
Nature Microbiology, 10.1038/s41564-024-01832-5 (2024)
Scientific Commentary: Nature Reviews Microbiology

Conservation of antiviral systems across domains of life reveals immune genes in humans
Cury J.*, Haudiquet M.*, Hernandez-Trejo V., Mordret E*., Hanouna A., Rotival M, Tesson F.,Bonhmme, D. Ofir G., Quintana-Murci L., Benaroch P., Poirier Z. P*., Bernheim A.*
Cell Host and Microbes, 10.1016/j.chom.2024.08.002
Scientific Commentary: Cell Host and Microbes

Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold
Shomar H*.,Georjon H.*, Feng Y, Olympio B, Cury J, Tesson F., Wu F*., Bernheim A*.
Nature Ecology and Evolution, 10.1038/s41559-024-02463-z, https://hal.science/hal-04690206
Scientific Commentary: Nature Research Briefing

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.
Tesson F., Planel R., Egorov A., Georjon H., Vaysset H., Brancotte B., Neron B., Mordret E., Atkinson G., Bernheim A*, Cury J*
Peer Community Journal, 10.1101/2024.01.25.577194

The immune modules conserved across the tree of life: Towards a definition of ancestral immunity
Bernheim A.*, Cury J, Poirier Z. E*.
Plos Biology, 10.1371/journal.pbio.3002717 (2024) (Essay)

A virally-encoded tRNA neutralizes the PARIS antiviral defence system
Burman N.*, Belukhina S.* , Depardieu F.*, Wilkinson R.*, Skutel M., Santiago-Frangos A., Graham A., Livenskyi A., Chechenina A., Morozova N, Zahl T., Henriques W., Buyukyoruk M., Rouillon C., Shyrokova L, Kurata, T Hauryliuk V, Severinov K, Groseille J, Thierry A, Koszul R., Tesson F., Bernheim A, Bikard D., Wiedenheft B, Isaev A.
Nature, 0.1038/s41586-024-07874-3

Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a twenty-year human gut time series
Condamine B, Morel-Journel T., Tesson F., Magnan M., Bernheim A., Denamur E., Blanquart F. , Clermont O.
ISME Journal, 10.1093/ismejo/wrae245

A family of lanthipeptides with anti-phage function
Shomar H., Tesson F., Guillaume M., Ongenae V., Le Bot ., Georjon H., Mordret E., Zhang L., van Wezel G., Rozen D., Briegel A., Zirah S., Claessen D., Li Y., Bernheim A.
bioRxiv, 10.1101/2024.06.26.600839

The highly diverse antiphage defence systems of bacteria
Georjon H, Bernheim A.
Nature Reviews Microbiology, 1/-15 (Review)
Chosen for Nature Reviews Microbiology 20th Anniversary collection.

Genomic characterization of the antiviral arsenal of Actinobacteria
Georjon H., Tesson F., Shomar H*., Bernheim A*.
Microbiology Aug;169(8):001374

Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?
Tesson F., Bernheim A.
Curr Opinion in Microbiology Feb:71:102238 (Review)

Immunité bactérienne: à la découverte d’un nouveau monde
A Hardy, H Shomar, A Bernheim
médecine/sciences 39 (11), 862-868 (Review)

Systematic and quantitative view of the anti-viral arsenal of prokaryotes
Tesson F., Hervé A., Touchon M., Mordret E., d’Humières C., Cury J., Bernheim A.
Nature Communications, 13:256
Scientific Commentary: Nature Reviews Microbiology

CRISPR-Cas and restriction-modification team up to achieve long-term immunity
Cury J, Bernheim A
Trends in Microbiology, S0966-842X(22)00091-9. (Comment)

An expanding arsenal of immune systems that protect bacteria from phages
Millman A., Melamed S., Leavitt A., Doron S., Bernheim A, Hör J., Lopatina A., Ofir G., Hochhauser D., Stokar-Avihail A., Tal N., Sharir S., Voichek M., Erez Z., Lorenzo M Ferrer J., Dar D., Kacen A., Amitai G., Sorek R.
Cell Host and Microbes, 30,1556-1569

Phages and their satellites encode hotspots of antiviral systems
Rousset F., Depardieu F., Miele S., Dowding J., Liebermann E., Garry D., Rocha E.P.C, Bernheim A, Bikard D.
Cell Host and Microbes, S1931-3128(22)00104-4

Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons
Klompe S, Jaber N, Bel L, Mohabir J,  Bernheim A, Sternberg S.
Molecular Cell 82 (3), 616-628e5