Nucleic Acids Research Kevin Debatisse, Manon Brunie, Baptiste Darracq, Elia Bandini, Eloi Littner, Eduardo P C Rocha, Didier Mazel, Céline Loot Summary Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibiotics. They enable bacterial on-demand adaptation through capture and shuffling of the cassettes under stress conditions. Our results underscore the significant role of horizontal gene

Communications medicine Bloch, E., Baudemont, G., Donnadieu, F. et al.  Investigation of the sero-epidemiology of vaccine preventable diseases and common viral infections in French populations. Background Vaccine-preventable diseases and common viral infections pose substantial public health challenges worldwide. Applying multiplex serological assays to samples collected from cross-sectional studies allows assessment of population-level immunity to a broad range of pathogens.

Communications Biol ogy Boetto, C., Romero, V.B., Henches, L. et al.  The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals. Summary The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of

Nature Methods Huizing, GJ., Samaran, J., Capocefalo, D. et al. Summary In dynamic biological processes such as development, spatial transcriptomics is revolutionizing the study of the mechanisms underlying spatial organization within tissues. Inferring cell fate trajectories from spatial transcriptomics profiled at several time points has thus emerged as a critical goal, requiring novel computational methods. Wasserstein gradient flow learning is a promising framework for an

PLOS Genetics Corneloup T, Bellengier J, Rosinski-Chupin I, Magnan M, Chavan A, et al. (2025) High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli . Summary Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli, horizontal gene transfer via conjugation and transdu

The Journal of Infectious Diseases Michael T White, Gaëlle Baudemont, Françoise Donnadieu, Arona Sabene Diatta, Ibrahima Sarr, Aissatou Diagne, Aissatou Toure-Balde, Fatoumata Diene Sarr, Joseph Faye, Cheikh Sokhna, Hubert Bassene, Inès Vigan-Womas, Stéphane Pelleau, Makhtar Niang Summary Background Serological assays are key tools in infectious disease surveillance, enabling detection of past infections by measuring antibody responses. Determining appropriate seropositivity

Molecular Biology and Evolution Fanny Mazzamurro, Marie Touchon, Xavier Charpentier, Eduardo P C Rocha Summary Natural transformation is the only process of gene exchange under the exclusive control of the recipient bacteria. It has often been considered as a source of novel genes, but quantitative assessments of this claim are lacking. To investigate the potential role of natural transformation in gene acquisition, we analyzed a large collection of genomes of Acinetobacter b

Biology Psychiatry: Cognitive Neurosciences and Neuroimaging. Auvergne A, Traut N, Henches L, Troubat L, Frouin A, Boetto C, Kazem S, Julienne H, Toro R, Aschard H. Background There is increasing evidence of shared genetic factors between psychiatric disorders and brain magnetic resonance imaging (MRI) phenotypes. However, deciphering the joint genetic architecture of these outcomes has proven to be challenging, and new approaches are needed to infer the genetic structures t

Nucleic Acid Research Maria Pilar Garcillán-Barcia, Fernando de la Cruz, Eduardo P C Rocha Summary Plasmids play key roles in the...

HGG Advances Léo Henches, Jihye Kim, Zhiyu Yang, Simone Rubinacci, Gabriel Pires, Clara Albiñana, Christophe Boetto, Hanna Julienne,...