Publications

Nov 26, 2024

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes

Nature Microbiology Lukas Hafner, Enzo Gadin, Lei Huang, Arthur Frouin, Fabien Laporte, Charlotte Gaultier, Afonso Vieira, Claire Maudet,...

Nov 20, 2024

Assessing the effect of model specificationand prior sensitivity on Bayesian tests oftemporal signal

PLOS COMPUTATIONAL BIOLOGY John H. Tay, Arthur Kocher, Sebastian Duchene* Abstract Our understanding of the evolution of many microbes...

Nov 14, 2024

Expanding the diversity of origin of transfer-containing sequences inmobilizable plasmids

Nature Microbiology Manuel Ares-Arroyo, Amandine Nucci & Eduardo P. C. Rocha Abstract Conjugative plasmids are important drivers of...

Nov 5, 2024

Integrating information from historical datainto mechanistic models for influenzaforecasting

PLOS COMPUTATIONAL BIOLOGY Alessio Andronico, Juliette Paireau*, Simon Cauchemez Abstract Seasonal influenza causes significant annual...

Nov 5, 2024

Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin

Nature Adrianna M. Turner, Lucy Li, Ian R. Monk, Jean Y. H. Lee, Danielle J. Ingle, Stephanie Portelli, Norelle L. Sherry, Nicole Isles,...

Oct 15, 2024

Emergence of the B.1.214.2 SARS‑CoV‑2 lineage with an Omicron‑like spike insertion and a unique upper airway immune signature

BMC Infectious Diseases Andrew Holtz*†, Johan Van Weyenbergh*†, Samuel L. Hong, Lize Cuypers, Áine O’Toole, Gytis Dudas, Marco Gerdol,...

Sep 24, 2024

Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

Nature Communications Mona L. Taouk, George Taiaroa, Sebastian Duchene, Soo Jen Low, Charlie K. Higgs, Darren Y. J. Lee, Shivani...

Sep 17, 2024

Antigenic sin and multiple breakthrough infectionsdrive converging evolution of COVID-19 neutralizingresponses

Cell Reports Ida Paciello, Giulio Pierleoni, Elisa Pantano, Giada Antonelli, Piero Pileri, Giuseppe Maccari, Dario Cardamone, Giulia...

Sep 11, 2024

A Genetic Bridge Between Medicine and Neurodiversity for Autism

Annual Review of Genetics Claire S. Leblond, Thomas Rolland, Eli Barthome, Zakaria Mougin, Mathis Fleury, Christine Ecker, Stéf...

Sep 10, 2024

Risk of SARS-CoV-2 infection in professional settings, shops, shared transport, and leisure activities in France, 2020–2022

BMC Public Health Simon Galmiche*, Tiffany Charmet, Arthur Rakover, Olivia Chény, Faïza Omar, Christophe David, Alexandra Mailles,...

Sep 9, 2024

scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features

Nature Communications Jules Samaran, Gabriel Peyré & Laura Cantini Summary The abundance of unpaired multimodal single-cell data has...

Sep 5, 2024

Hijackers, hitchhikers, or co-drivers? Themysteries of mobilizable genetic elements

PLOS Biology Manuel Ares-Arroyo, Charles Coluzzi, Jorge A. Moura de Sousa, Eduardo P. C. Rocha* Abstract Mobile genetic elements shape...

Sep 4, 2024

CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data

PLOS Biology Estibaliz Gomez-de-Mariscal, Hanna Grobe, Joanna W. Pylvanainen, Laura Xenard, Ricardo Henriques, Jean-Yves Tinevez,...

Aug 7, 2024

Three-dimensional cell cultureconditions promoted theMesenchymal-AmoeboidTransition in the Triple-NegativeBreast Cancer cell line MDAMB-231

Frontiers in Cell and Developmental Biology Daniela Rodríguez-Cruz, Aleix Boquet-Pujadas, Eunice López-Muñoz, Ruth Rincón-Heredia,...

Aug 6, 2024

Fibronectin induces a transition fromamoeboid to a fan morphology and modifiesmigration in Entamoeba histolytica

PLOS PATHOGENS Maria Manich, Pascal Bochet, Aleix Boquet-Pujadas, Thierry Rose, Gertjan Laenen, Nancy Guillen, Jean-Christophe...

Aug 5, 2024

Trait selection strategy in multi-traitGWAS: Boosting SNP discoverability

HGG Advances Yuka Suzuki*, Hervé Ménager, Bryan Brancotte, Raphael Vernet, Cyril Nerin, Christophe Boetto, Antoine Auvergne, Christophe...

Aug 1, 2024

Transformation of spatial representations alonghippocampal circuits

iScience Bérénice Gandit, Lorenzo Posani, Chun-Lei Zhang, Soham Saha, Cantin Ortiz, Manuela Allegra* and Christoph Schmidt-Hieber*...

Jul 29, 2024

Zanamivir and baloxavir combination to cure persistent influenza and coronavirus infections after hematopoietic stem cell transplant

International Journal of Antimicrobial Agents Victor Euzen ∗, Aliénor Xhaard ∗, Samar Berreira-Ibraim ∗, Laure Deville, Aude Quentin,...

Jul 28, 2024

In Vitro and In Vivo Neutralizing Efficacy of Monoclonal Antibodies Against Sars-Cov-2 Variants in KidneyTransplant Recipients

Transplant International Ilies Benotmane*†, Martin Jungbauer-Groznica†, Isabelle Staropoli, Delphine Planas, Océane Dehan, Angela...

Jul 23, 2024

Anthropic cut marks in extinct megafaunabones from the Pampean region (Argentina)at the last glacial maximum

PLOS ONE Mariano Del Papa, Martin De Los Reyes, Daniel G. Poire, Nicolas Rascovan, Guillermo Jofre, Miguel Delgado* Abstract The initial...