J. Cury

Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons

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

The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae

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.

Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold

This study investigates the evolution of viperin genes across prokaryotes and eukaryotes, revealing their conservation, diversification mechanisms, and immune functions.

Systematic and quantitative view of the antiviral arsenal of prokaryotes

The paper develops DefenseFinder to systematically analyze anti-phage systems in prokaryotes, revealing average of five systems per genome across 20,000 genomes.

Simulation of bacterial populations with SLiM

This paper demonstrates how to simulate bacterial populations using SLiM, a forward-in-time simulator, and validates its results against existing tools and theoretical expectations.

Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation

This paper proposes deep learning methods for inferring population size history from SNP data and compares them to ABC, showing competitive performance and potential for combination.

Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements

The paper compares integrative and extrachromosomal mobile genetic elements to explain their co-existence through differences in genetic plasticity and host range.