Jean Cury

Publications

Article dans une revue (27)

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements Florian Tesson,Erin Huiting,Linlin Wei,Jie Ren,Matthew Johnsonet al. Nucleic Acids Research, 2025, 53 (1), ⟨10.1093/nar/gkae1171⟩ Article dans une revue hal-05230529v1
Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons Hugo Vaysset,Chance Meers,Jean Cury,Aude Bernheim,Samuel Sternberg Nature Microbiology, 2025, 10 (1), pp.20-27. ⟨10.1038/s41564-024-01889-2⟩ Article dans une revue hal-05230530v1
A human homolog of SIR2 antiphage proteins mediates immunity via the Toll-like receptor pathway Delphine Bonhomme,Hugo Vaysset,Eirene Marie Q. Ednacot,Vasco Rodrigues,Yazan Salloumet al. Science, 2025, 389 (6758), pp.eadr8536. ⟨10.1126/science.adr8536⟩ Article dans une revue hal-05230522v1
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae Florian Fournes,Manuel Campos,Jean Cury,Caroline Schiavon,Carine Pagèset al. Nucleic Acids Research, 2025, 53 (2), pp.gkae1300. ⟨10.1093/nar/gkae1300⟩ Article dans une revue hal-04888819v1
A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases Florian Tesson,Rémi Planel,A. Egorov,Héloïse Georjon,Hugo Vayssetet al. Peer Community Journal, 2024, ⟨10.24072/pcjournal.470⟩ Article dans une revue hal-04600530v2
Conservation of antiviral systems across domains of life reveals immune genes in humans Jean Cury,Matthieu Haudiquet,Veronica Hernandez Trejo,Ernest Mordret,Anael Hanounaet al. Cell Host & Microbe, 2024, 32 (9), pp.1594-1607.e5. ⟨10.1016/j.chom.2024.08.002⟩ Article dans une revue hal-04735152v1
The immune modules conserved across the tree of life: Towards a definition of ancestral immunity Aude Bernheim,Jean Cury,Enzo Poirier PLoS Biology, 2024, 22 (7), pp.e3002717. ⟨10.1371/journal.pbio.3002717⟩ Article dans une revue hal-05230525v1
Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold Helena Shomar,Héloïse Georjon,Yanlei Feng,Bismarck Olympio,Marie Guillaumeet al. Nature Ecology & Evolution, 2024, 8 (9), pp.667-1679. ⟨10.1038/s41559-024-02463-z⟩ Article dans une revue hal-04690206v1
Integron cassettes commonly integrate into bacterial genomes via widespread non-classical attG sites Céline Loot,Gael A Millot,Egill Richard,Eloi Littner,Claire Vitet al. Nature Microbiology, 2024, 9 (1), pp.228-240. ⟨10.1038/s41564-023-01548-y⟩ Article dans une revue pasteur-04384854v1
dnadna: a deep learning framework for population genetics inference Théophile Sanchez,Erik Madison Bray,Pierre Jobic,Jérémy Guez,Anne-Catherine Letournelet al. Bioinformatics, 2023, 39 (1), pp.btac765. ⟨10.1093/bioinformatics/btac765⟩ Article dans une revue hal-03352910v4
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences Jérémy Guez,Guillaume Achaz,François Bienvenu,Jean Cury,Bruno Toupanceet al. Genetics, 2023, 223 (4), pp.iyad007. ⟨10.1093/genetics/iyad007⟩ Article dans une revue hal-03875721v1
Systematic and quantitative view of the antiviral arsenal of prokaryotes Florian Tesson,Alexandre Hervé,Ernest Mordret,Marie Touchon,Camille D’humièreset al. Nature Communications, 2022, 13 (1), pp.2561. ⟨10.1038/s41467-022-30269-9⟩ Article dans une revue hal-03823827v2
A descriptive study of IgG4-related disease in children and young adults. Benjamin de Sainte Marie,Mickael Ebbo,Aurélie Grados,Vinciane Rebours,Heloise Reumauxet al. Autoimmunity Reviews, 2022, Autoimmunity Reviews, 21 (4), pp.103035. ⟨10.1016/j.autrev.2022.103035⟩ Article dans une revue hal-04502819v1
Simulation of bacterial populations with SLiM Jean Cury,Benjamin C Haller,Guillaume Achaz,Flora Jay Peer Community Journal, 2022, 2, pp.e7. ⟨10.24072/pcjournal.72⟩ Article dans une revue hal-03152153v3
IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella Bertrand Néron,Eloi Littner,Matthieu Haudiquet,Amandine Perrin,Jean Curyet al. Microorganisms, 2022, 10 (4), pp.700. ⟨10.3390/microorganisms10040700⟩ Article dans une revue hal-03655020v1
Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation Théophile Sanchez,Jean Cury,Guillaume Charpiat,Flora Jay Molecular Ecology Resources, 2020, 21 (8), pp.2645-2660. ⟨10.1111/1755-0998.13224⟩ Article dans une revue hal-02942328v1
Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells Julie Dauverd -Girault,Charlène Planchenault,Marine C Pons,Caroline Schiavon,Patricia Siguieret al. Journal of Molecular Biology, 2020, 432 (3), pp.745-761. ⟨10.1016/j.jmb.2019.11.027⟩ Article dans une revue hal-02392007v1
Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement Aleksandra Nivina,Maj Svea Grieb,Céline Loot,David Bikard,Jean Curyet al. Science Advances , 2020, 6 (30), pp.eaay2922. ⟨10.1126/sciadv.aay2922⟩ Article dans une revue hal-03084479v1
A simple, reproducible and cost- effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach Camille d'Humières,Marie Touchon,Sara Dion,Jean Cury,Amine Ghozlaneet al. Scientific Reports, 2019, ⟨10.1038/s41598-019-47656-w⟩ Article dans une revue hal-02329655v1
Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements Jean Cury,Pedro De Oliveira,Fernando de La Cruz,Eduardo P C Rocha Molecular Biology and Evolution, 2018, 35 (9), pp.2230-2239. ⟨10.1093/molbev/msy123⟩ Article dans une revue pasteur-02098387v1
The chromosomal organization of horizontal gene transfer in bacteria Pedro H. Oliveira,Marie Touchon,Jean Cury,Eduardo P C Rocha Nature Communications, 2017, 8 (1), pp.841. ⟨10.1038/s41467-017-00808-w⟩ Article dans une revue hal-04325283v1
Integrative and conjugative elements and their hosts: composition, distribution and organization Jean Cury,Marie Touchon,Eduardo P. C. Rocha Nucleic Acids Research, 2017, 45 (15), pp.8943 - 8956. ⟨10.1093/nar/gkx607⟩ Article dans une revue pasteur-04076019v1
Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance Céline Loot,Aleksandra Nivina,Jean Cury,José Antonio Escudero,Magaly Ducos-Galandet al. mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩ Article dans une revue pasteur-01689524v1
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain Amandine Perrin,Elise Larsonneur,Ainsley Nicholson,David Edwards,Kristin Gundlachet al. Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩ Article dans une revue hal-02613118v1
Identification of protein secretion systems in bacterial genomes Sophie S. Abby,Jean Cury,Julien Guglielmini,Bertrand Néron,Marie Touchonet al. Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩ Article dans une revue pasteur-01374967v1
Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury,Thomas Jové,Marie Touchon,Bertrand Néron,Eduardo Pc Rocha Nucleic Acids Research, 2016, 44 (10), pp.4539 - 4550. ⟨10.1093/nar/gkw319⟩ Article dans une revue pasteur-01374968v1
The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Marie Touchon,Jean Cury,Eun-Jeong Yoon,Lenka Krizova,Gustavo C Cerqueiraet al. Genome Biology and Evolution, 2014, 6 (10), pp.2866-82. ⟨10.1093/gbe/evu225⟩ Article dans une revue pasteur-01132634v1

Pré-publication, Document de travail (4)

Ancient genomic insights into Salmonella enterica Paratyphi C from Central Mexico Miriam Bravo-Lopez,Eduardo Arrieta-Donato,Viridiana Villa-Islas,Åshild Joanne Vågene,Ana Villaseñor-Altamiranoet al. 2025 Pré-publication, Document de travail hal-05407381v1
Protein and genomic language models chart a vast landscape of antiphage defenses Ernest Mordret,Alexandre Hervé,Hugo Vaysset,Tyler Clabby,Florian Tessonet al. 2025 Pré-publication, Document de travail hal-05407383v1
A new route for integron cassette dissemination among bacterial genomes Céline Loot,Gael A Millot,Egill Richard,Claire Vit,Baptiste Darracqet al. 2022 Pré-publication, Document de travail pasteur-03826688v1
Intracellular positioning systems limit the entropic eviction of secondary replicons toward the nucleoid edges in bacterial cells Charlene Planchenault,Marine C Pons,Caroline Schiavon,Patricia Siguier,Jérôme Rechet al. 2019 Pré-publication, Document de travail hal-02366139v1

Logiciel (1)

Integron_Finder Bertrand Néron,Jean Cury,Eduardo Rocha,Amandine Perrin 2024, ⟨swh:1:dir:6cc5d36f34974f2264a2ea9e195edb1981b2f9ba;origin=https://github.com/gem-pasteur/Integron_Finder;visit=swh:1:snp:f5d82d096a64d390358869946048ca7f801b2ded;anchor=swh:1:rev:0388197211bd9b232082a2dd9275623b62c5599a⟩ Logiciel hal-04603009v1

Communication dans un congrès (1)

Inferring effective population sizes of bacterial populations while accounting for unknown recombination and selection: a deep learning approach Jean Cury,Théophile Sanchez,Erik Madison Bray,Jazeps Medina-Tretmanis,María Ávila-Arcoset al. ECML PKDD 2022 - Machine Learning for Microbial Genomics workshop, Sep 2022, Grenoble, France Communication dans un congrès hal-05554282v1

Poster de conférence (1)

Understanding and inferring cultural transmission of reproductive success Jérémy Guez,Guillaume Achaz,François Bienvenu,Jean Cury,Bruno Toupanceet al. Probabilistic Modeling in Genomics, Mar 2022, Oxford, United Kingdom Poster de conférence hal-04016758v1

Chapitre d'ouvrage (1)

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan Jean Cury,Sophie S. Abby,Olivia Doppelt-Azeroual,Bertrand Néron,Eduardo P C Rocha Fernando de la Cruz. Horizontal Gene Transfer : Methods and Protocols, Springer Science; Business Media, pp.265-283, 2019, 978-1-4939-9876-0. ⟨10.1007/978-1-4939-9877-7_19⟩ Chapitre d'ouvrage pasteur-02867882v1

Thèse (1)

Evolutionary genomics of conjugative elements and integrons Jean Cury Human health and pathology. Université Sorbonne Paris Cité, 2017. English. ⟨NNT : 2017USPCB062⟩ Thèse tel-02130756v1