Structure Content
Department: Genomes and Genetics
All Publications
2025
Ravneet Kaur Sidhu, Guillem Mas Fiol, Pierre Lê-Bury, Christian E Demeure, Emelyne Bougit, Rémi Beau, Charlotte Balière, Aurelia Kwasiborski, Valérie Caro, Jennifer Klunk, Daniel J Salkeld, Ann Carmichael, Nükhet Varlık, Debi Poinar, David J D Earn, Benjamin M Bolker, Jonathan Dushoff, G Brian Golding, Nicolas Rascovan, Olivier Dussurget, Edward C Holmes, Javier Pizarro-Cerdá, Hendrik N Poinar,
Attenuation of virulence in Yersinia pestis across three plague pandemics,
Science, 2025, 388 (6750), pp.eadt3880. ⟨10.1126/science.adt3880⟩.
2025
Charles Bernard, Yannick Labreuche, Carine Diarra, Pauline Daszkowski, Karine Cahier, David Goudenège, Martin G Lamarche, Gregory B Whitfield, Manon Lang, Jeffrey Valencia, Justine Groseille, Damien Piel, Yan-Jiun Lee, Peter Weigele, Yves V Brun, Eduardo P. C. Rocha, Frédérique Le Roux,
Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages,
The International Society of Microbiologial Ecology Journal, In press, pp.wraf063. ⟨10.1093/ismejo/wraf063⟩.
2025
Léa Deltourbe, Jamie Sugrue, Elizabeth Maloney, Florian Dubois, Anthony Jaquaniello, Jacob Bergstedt, Etienne Patin, Lluis Quintana-Murci, Molly Ingersoll, Darragh Duffy,
Steroid hormone levels vary with sex, aging, lifestyle, and genetics,
Science Advances , 2025, 11 (13), pp.eadu6094. ⟨10.1126/sciadv.adu6094⟩.
2025
Léa Meneu, Christophe Chapard, Jacques Serizay, Alex Westbrook, Etienne Routhier, Myriam Ruault, Manon Perrot, Alexandros Minakakis, Fabien Girard, Amaury Bignaud, Antoine Even, Géraldine Gourgues, Domenico Libri, Carole Lartigue, Aurèle Piazza, Agnès Thierry, Angela Taddei, Frédéric Beckouët, Julien Mozziconacci, Romain Koszul,
Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus,
Science, 2025, 387 (6734), pp.eadm9466. ⟨10.1126/science.adm9466⟩.
2025
Michella Khoury Damaa, Jacques Serizay, Rémi Balagué, Amélie-Rose Boudjema, Marion Faucourt, Nathalie Delgehyr, Kim Jee Goh, Hao Lu, Ee Kim Tan, Cameron T James, Catherine Faucon, Rana Mitri, Diana Carolin Bracht, Colin D Bingle, Norris Ray Dunn, Sebastian J Arnold, Laure-Emmanuelle Zaragosi, Pascal Barbry, Romain Koszul, Heymut Omran, Gabriel Gil-Gómez, Estelle Escudier, Marie Legendre, Sudipto Roy, Nathalie Spassky, Alice Meunier,
Cyclin O controls entry into the cell-cycle variant required for multiciliated cell differentiation,
Cell Reports, 2025, 44 (1), pp.115117. ⟨10.1016/j.celrep.2024.115117⟩.
2024
Manuel Ares-Arroyo, Amandine Nucci, Eduardo Rocha,
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids,
Nature Microbiology, In press, ⟨10.1038/s41564-024-01844-1⟩.
2024
Rémi Planel, Victoire Baillet, Rachel Torchet, Vincent Guillemot, Pascal Campagne, Jean Jaubert, Marion Rincel, Christian A. J. Vosshenrich, Xavier Montagutelli, Caroline Manet,
ccqtl-db,
2024, ⟨swh:1:dir:b3362746041f9acd17180af8a77dc963f9ec5443;origin=https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db;visit=swh:1:snp:ee61a4e0ae9068c1d9dd665bd485ffc6a5287dfd;anchor=swh:1:rev:d796db76a93e9c192563777fa07656da3db747a8⟩.
2024
Matthieu Haudiquet, Julie Le Bris, Amandine Nucci, Rémy A Bonnin, Pilar Domingo-Calap, Eduardo P C Rocha, Olaya Rendueles,
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency,
Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩.
2024
Valentin Bonnet, Erik Maikranz, Marianne Madec, Nadia Vertti-Quintero, Céline Cuche, Marta Mastrogiovanni, Andrés Alcover, Vincenzo Di Bartolo, Charles N Baroud,
Cancer-on-a-chip model shows that the adenomatous polyposis coli mutation impairs T cell engagement and killing of cancer spheroids,
Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (11), pp.e2316500121. ⟨10.1073/pnas.2316500121⟩.
2024
Egill Richard, Baptiste Darracq, Eloi Littner, Claire Vit, Clémence Whiteway, Julia Bos, Florian Fournes, Geneviève Garriss, Valentin Conte, Delphine Lapaillerie, Vincent Parissi, François Rousset, Ole Skovgaard, David Bikard, Eduardo P. C. Rocha, Didier Mazel, Céline Loot,
Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems.,
Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.
2023
Ludivine Amable, Luis Antonio Ferreira Martins, Remi Pierre, Marcio Do Cruseiro, Ghita Chabab, Arnauld Sergé, Camille Kergaravat, Marc Delord, Christophe Viret, Jean Jaubert, Chaohong Liu, Saoussen Karray, Julien C Marie, Magali Irla, Hristo Georgiev, Emmanuel Clave, Antoine Toubert, Bruno Lucas, Jihene Klibi, Kamel Benlagha,
Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation,
Nature Communications, 2023, 14 (1), pp.7922. ⟨10.1038/s41467-023-43424-7⟩.
2023
Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi,
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods,
Microbiome, 2023, 11 (1), pp.1-12. ⟨10.1186/s40168-023-01670-3⟩.
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
Ségolène Gracias, Maxime Chazal, Alice Decombe, Yves Unterfinger, Adrià Sogues, Lauryne Pruvost, Valentine Robert, Sandrine Lacour, Manon Lemasson, Marion Sourisseau, Zhi Li, Jennifer Richardson, Sandra Pellegrini, Etienne Decroly, Vincent Caval, Nolwenn Jouvenet,
Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2.,
EMBO Reports, In press, pp.e57424. ⟨10.15252/embr.202357424⟩.
2023
Selam Mihreteab, Lucien Platon, Araia Berhane, Barbara Stokes, Marian Warsame, Pascal Campagne, Alexis Criscuolo, Laurence Ma, Nathalie Petiot, Cécile Doderer-Lang, Eric Legrand, Kurt Ward, Assefash Zehaie Kassahun, Pascal Ringwald, David Fidock, Didier Ménard,
Increasing Prevalence of Artemisinin-Resistant HRP2-Negative Malaria in Eritrea,
New England Journal of Medicine, 2023, 389 (13), pp.1191-1202. ⟨10.1056/NEJMoa2210956⟩.
2023
Laure Mancini, Boris Guirao, Sara Ortica, Miriam Labusch, Felix Cheysson, Valentin Bonnet, Minh Son Phan, Sébastien Herbert, Pierre Mahou, Emilie Menant, Sébastien Bedu, Jean-Yves Tinevez, Charles Baroud, Emmanuel Beaurepaire, Yohanns Bellaiche, Laure Bally-Cuif, Nicolas Dray,
Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression,
Science Advances , 2023, 9 (35), pp.eadg7519. ⟨10.1126/sciadv.adg7519⟩.
2023
Yann Aquino, Aurélie Bisiaux, Zhi Li, Mary O'Neill, Javier Mendoza-Revilla, Sarah Hélène Merkling, Gaspard Kerner, Milena Hasan, Valentina Libri, Vincent Bondet, Nikaïa Smith, Camille de Cevins, Mickaël Ménager, Francesca Luca, Roger Pique-Regi, Giovanna Barba-Spaeth, Stefano Pietropaoli, Olivier Schwartz, Geert Leroux-Roels, Cheuk-Kwong Lee, Kathy Leung, Joseph Wu, Malik Peiris, Roberto Bruzzone, Laurent Abel, Jean-Laurent Casanova, Sophie Valkenburg, Darragh Duffy, Etienne Patin, Maxime Rotival, Lluis Quintana-Murci,
Dissecting human population variation in single-cell responses to SARS-CoV-2,
Nature, 2023, 53 (8), pp.e2250307. ⟨10.1038/s41586-023-06422-9⟩.
2023
Amandine Nucci, Eduardo P C Rocha, Olaya Rendueles,
Latent evolution of biofilm formation depends on life-history and genetic background,
npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.
2023
Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E White, Arthur Kocher, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G Serrano, Julien Fumey, Kadir T Özdoğan, Kelly E Blevins, Kevin G Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J Bravo-Lopez, Mohamed S Sarhan, Nihan D Dagtas, Nikolay Oskolkov, Olivia S Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L Ramachandran, Valentina Vanghi, Christina Warinner, James A Fellows Yates,
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT,
F1000Research, 2023, 12, pp.926. ⟨10.12688/f1000research.134798.1⟩.
2022
Matthieu Haudiquet,
How capsules protect the cell, shape genetic exchanges and drive bacterial evolution
Comment la capsule protège la cellule, façonne les échanges génétiques et influence l’évolution bactérienne,
Life Sciences [q-bio]. Universite Paris Cité, 2022. English. ⟨NNT : ⟩.
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
Gaspard Kerner, Etienne Patin, Lluis Quintana-Murci,
New insights into human immunity from ancient genomics,
Current Opinion in Immunology, 2021, 72, pp.116-125. ⟨10.1016/j.coi.2021.04.006⟩.
2021
Jan Madacki, Mickael Orgeur, Guillem Mas Fiol, Wafa Frigui, Laurence Ma, Roland Brosch,
ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains,
mBio, 2021, 12 (3), ⟨10.1128/mBio.00965-21⟩.
2021
Azimdine Habib, Lova Andrianonimiadana, Maheninasy Rakotondrainipiana, Prisca Andriantsalama, Ravaka Randriamparany, Rindra Vatosoa Randremanana, Rado Rakotoarison, Inès Vigan‑womas, Armand Rafalimanantsoa, Pascale Vonaesch, Philippe J. Sansonetti, Jean-Marc Collard, The Afribiota Investigators,
High prevalence of intestinal parasite infestations among stunted and control children aged 2 to 5 years old in two neighborhoods of Antananarivo, Madagascar,
PLoS Neglected Tropical Diseases, 2021, 15 (4), pp.e0009333. ⟨10.1371/journal.pntd.0009333⟩.
2020
Petter Brodin, Lluis Quintana-Murci,
Editorial overview: Evolutionary and systems immunology – methods to understand human immune system variation,
Current Opinion in Immunology, 2020, 65, ⟨10.1016/j.coi.2020.11.001⟩.
2020
Aleksandra Nivina, Maj Svea Grieb, Céline Loot, David Bikard, Jean Cury, Laila Shehata, Juliana Bernardes, Didier Mazel,
Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement,
Science Advances , 2020, 6 (30), pp.eaay2922. ⟨10.1126/sciadv.aay2922⟩.
2020
Jihène Klibi, Shamin Li, Ludivine Amable, Claudine Joseph, Stéphane Brunet, Marc Delord, Véronique Parietti, Jean Jaubert, Julien C. Marie, Saoussen Karray, Gérard Eberl, Bruno Lucas, Antoine Toubert, Kamel Benlagha,
Characterization of the developmental landscape of murine RORγt+ iNKT cells,
International Immunology, 2019, 32 (2), pp.105-116. ⟨10.1093/intimm/dxz064⟩.
2019
Jing Zhang, Megan Teh, Jamie Kim, Megan Eva, Romain Cayrol, Rachel Meade, Anastasia Nijnik, Xavier Montagutelli, Danielle Malo, Jean Jaubert,
A Loss-of-Function Mutation in the Integrin Alpha L ( Itgal ) Gene Contributes to Susceptibility to Salmonella enterica Serovar Typhimurium Infection in Collaborative Cross Strain CC042,
Infection and Immunity, 2019, 88 (1), pp.e00656-19. ⟨10.1128/IAI.00656-19⟩.
2018
Etienne Patin, Lluis Quintana-Murci,
The demographic and adaptive history of central African hunter-gatherers and farmers,
Current Opinion in Genetics and Development, 2018, 53, pp.90-97. ⟨10.1016/j.gde.2018.07.008⟩.
2018
Brenna Henn, Lluis Quintana-Murci,
Editorial overview: The history, geography and adaptation of human genes: A tribute to L. Luca Cavalli-Sforza,
Current Opinion in Genetics and Development, 2018, 53, pp.iii-v. ⟨10.1016/j.gde.2018.11.004⟩.
2018
Jianqiang Bao, Carlos Perez, Jeesun Kim, Huan Zhang, Caitlin Murphy, Tewfik Hamidi, Jean Jaubert, Craig Platt, Janet Chou, Meichun Deng, Meng-Hua Zhou, Yuying Huang, Héctor Gaitán-Peñas, Jean-Louis Guénet, Kevin Lin, Yue Lu, Taiping Chen, Mark Bedford, Sharon Y.R. Dent, John Richburg, Raúl Estévez, Hui-Lin Pan, Raif Geha, Qinghua Shi, Fernando Benavides,
Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice,
JCI Insight, 2018, 3 (16), pp.e99767. ⟨10.1172/jci.insight.99767⟩.
2018
Jing Zhang, Danielle Malo, Richard P Mott, Jean-Jacques Panthier, Xavier Montagutelli, Jean Jaubert,
Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice,
BMC Genomics, 2018, 19 (1), pp.303. ⟨10.1186/s12864-018-4667-0⟩.
2017
Emilia Pachulec, Rym Ben Abdelwahed Bagga, Lucie Chevallier, Hope O'Donnell, Chloé Guillas, Jean Jaubert, Xavier Montagutelli, Elisabeth Carniel, Christian E. Demeure,
Enhanced Macrophage M1 Polarization and Resistance to Apoptosis Enable Resistance to Plague,
Journal of Infectious Diseases, 2017, 216 (6), pp.761-770. ⟨10.1093/infdis/jix348⟩.
2017
P. Parize, E. Muth, C. Richaud, M. Gratigny, B. Pilmis, A. Lamamy, J.-L. Mainardi, J. Cheval, L. de Visser, F. Jagorel, L. Ben Yahia, G. Bamba, M. Dubois, O. Join-Lambert, M. Leruez-Ville, X. Nassif, A. Lefort, F. Lanternier, F. Suarez, O. Lortholary, M. Lecuit, Marc Eloit,
Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study,
Clinical Microbiology and Infection, 2017, 23 (8), pp.574.e1-574.e6. ⟨10.1016/j.cmi.2017.02.006⟩.
2017
Céline Loot, Aleksandra Nivina, Jean Cury, José Antonio Escudero, Magaly Ducos-Galand, David Bikard, Eduardo P C Rocha, Didier Mazel,
Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.,
mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩.
2015
Yue Cui, Katarzyna Franciszkiewicz, Yvonne K Mburu, Stanislas Mondot, Lionel Le Bourhis, Virginie Premel, Emmanuel Martin, Alexandra Kachaner, Livine Duban, Molly A Ingersoll, Sylvie Rabot, Jean Jaubert, Jean-Pierre de Villartay, Claire Soudais, Olivier Lantz,
Mucosal-associated invariant T cell–rich congenic mouse strain allows functional evaluation,
Journal of Clinical Investigation, 2015, 125 (11), pp.4171 - 4185. ⟨10.1172/JCI82424⟩.
2015
Carlos Perez, Lars Mecklenburg, Jean Jaubert, Lucia Martinez-Santamaria, Brian Iritani, Alexsandra Espejo, Eleonora Napoli, Gyu Song, Marcela del Rio, John Digiovanni, Cecilia Giulivi, Mark Bedford, Sharon Y.R. Dent, Richard Wood, Donna F. Kusewitt, Jean-Louis Guénet, Claudio Conti, Fernando Benavides,
Increased Susceptibility to Skin Carcinogenesis Associated with a Spontaneous Mouse Mutation in the Palmitoyl Transferase Zdhhc13 Gene,
Journal of Investigative Dermatology, 2015, 135 (12), pp.3133-3143. ⟨10.1038/jid.2015.314⟩.
2014
Marine Livrozet, Sophie Vandermeersch, Laurent Mesnard, Elizabeth Thioulouse, Jean Jaubert, Jean-Jacques Boffa, Jean-Philippe Haymann, Laurent Baud, Dominique Bazin, Michel Daudon, Letavernier Emmanuel,
An Animal Model of Type A Cystinuria Due to Spontaneous Mutation in 129S2/SvPasCrl Mice,
PLoS ONE, 2014, 9 (7), pp.e102700. ⟨10.1371/journal.pone.0102700⟩.
2014
Darragh Duffy, Vincent Rouilly, Valentina Libri, Milena Hasan, Benoit Beitz, Mikael David, Alejandra Urrutia, Aurélie Bisiaux, Samuel T Labrie, Annick Dubois, Ivo G Boneca, Cécile Delval, Stéphanie Thomas, Lars Rogge, Manfred Schmolz, Lluis Quintana-Murci, Matthew L Albert, Laurent Abel, Andres Alcover, Philippe Bousso, Ana Cumano, Marc Daëron, Caroline Demangel, Ludovic Deriano, James Di santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Antonio Freitas, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Marie-Noëlle Ungeheuer,
Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli.,
Immunity, 2014, 40 (3), pp.436-50. ⟨10.1016/j.immuni.2014.03.002⟩.
2012
Lucie Chevallier, Charlène Blanchet, Jean Jaubert, Emilia Pachulec, Christian E. Demeure, Elisabeth Carniel, Jean-Jacques Panthier, Xavier Montagutelli,
Resistance to plague of Mus spretus SEG/Pas mice requires the combined action of at least four genetic factors,
Genes and Immunity, 2013, 14 (1), pp.35-41. ⟨10.1038/gene.2012.50⟩.
2011
Christian E. Demeure, Charlène Blanchet, Catherine Fitting, Corinne Fayolle, Huot Khun, Marek Szatanik, Geneviève Milon, Jean-Jacques Panthier, Jean Jaubert, Xavier Montagutelli, Michel Huerre, Jean-Marc Cavaillon, Elisabeth Carniel,
Early Systemic Bacterial Dissemination and a Rapid Innate Immune Response Characterize Genetic Resistance to Plague of SEG Mice,
Journal of Infectious Diseases, 2012, 205 (1), pp.134-143. ⟨10.1093/infdis/jir696⟩.
2010
Charlène Blanchet, Jean Jaubert, Elisabeth Carniel, Corinne Fayolle, Geneviève Milon, Marek Szatanik, Jean-Jacques Panthier, Xavier Montagutelli,
Mus spretus SEG/Pas mice resist virulent Yersinia pestis, under multigenic control,
Genes and Immunity, 2011, 12 (1), pp.23-30. ⟨10.1038/gene.2010.45⟩.
2010
Carlos Perez, Jean Jaubert, Jean-Louis Guénet, Kirstin Barnhart, Catherine Ross-Inta, Vicente Quintanilla, Isabelle Aubin, Jimi Brandon, Nancy Otto, John Digiovanni, Irma Gimenez-Conti, Cecilia Giulivi, Donna F. Kusewitt, Claudio Conti, Fernando Benavides,
Two Hypomorphic Alleles of Mouse Ass1 as a New Animal Model of Citrullinemia Type I and Other Hyperammonemic Syndromes,
American Journal of Pathology, 2010, 177 (4), pp.1958-1968. ⟨10.2353/ajpath.2010.100118⟩.
2010
Ronan Jambou, Axel Martinelli, João Pinto, Simonetta Gribaldo, Eric Legrand, Makhtar Niang, Nimol Kim, Lim Pharath, Béatrice Volnay, Marie Therese Ekala, Christiane Bouchier, Thierry Fandeur, Pedro Berzosa, Agustin Benito, Isabel Dinis Ferreira, Cynthia Ferreira, Pedro Paulo Vieira, Maria das Graças Alecrim, Odile Mercereau-Puijalon, Pedro Cravo,
Geographic structuring of the Plasmodium falciparum sarco(endo)plasmic reticulum Ca2+ ATPase (PfSERCA) gene diversity.,
PLoS ONE, 2010, 5 (2), pp.e9424. ⟨10.1371/journal.pone.0009424⟩.