Jean Cury

The paper identifies and characterizes defence hotspots in P2-like phages and P4-like satellites, revealing rapid modular evolution of antiviral systems through gene swapping and recombination.

This study identifies ancient S. enterica Paratyphi C DNA in 19th-century Mexico, linking it to European strains and showing its persistence in urban settings.

The paper identifies SIRanc, a human homolog of bacterial antiphage SIR2 proteins, and shows it mediates innate immunity via the TLR pathway by degrading NAD+.

The paper uses language models to predict novel antiphage defense proteins in Actinomycetota, discovering six new defense systems and over 45,000 uncharacterized protein families.

This study identifies evolutionary links between bacterial IS110 transposons and archaeal/eukaryotic RNA modification systems, suggesting RNA-guided mechanisms evolved from transposon components.

The paper identifies that XerCD recombination is used by large plasmids and chromids for dimer resolution, similar to chromosomes, and shows this is required for their faithful inheritance.

The paper develops AntiDefenseFinder to detect anti-defense systems in prokaryotes, phages, and MGEs, identifying 47,981 systems and revealing their distribution and evolutionary dynamics.

The paper introduces DefenseFinder, a resource for antiphage defense systems, including a web service, wiki, and databases with structure predictions.

The paper demonstrates that integron integrase can insert cassettes outside classical att sites, leading to new recombination sites called attG and expanding integron roles in bacterial evolution.

The paper expands the stdpopsim species catalog and improves genome simulations by adding non-crossover recombination and species-specific annotations, making simulations more realistic for non-model organisms.

This paper shows that cultural transmission of reproductive success affects genomic diversity, coalescent tree topologies, and demographic inferences by altering effective population size and distorting tree structures.

The paper identifies novel human antiviral genes by comparing conserved antiphage systems across prokaryotes and eukaryotes.

IntegronFinder 2.0 identifies and analyzes integrons in bacterial genomes, revealing a large diversity of integrons and antibiotic resistance genes in Klebsiella pneumoniae.

The paper characterizes integrative and conjugative elements (ICEs) across bacterial genomes, revealing their functional organization and distribution.

The paper identifies integrons and cassette arrays in bacterial genomes, revealing their distribution patterns and evolutionary implications.

The paper develops models to identify protein secretion systems in bacterial genomes, finding T1SS and T5SS are most common, while T6SSiii and T9SS are restricted to Bacteroidetes.