Alice Ledda

Natural selection driven by escape from shifting antibody classes shapes SARS-CoV-2 evolution

This study traces how natural selection on SARS-CoV-2 has shifted during the pandemic, favoring antibody escape and ACE2 binding, with dynamic pressures across antibody classes.

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

This study evaluates Nanopore long-read only genome assembly for clinical Enterobacterales isolates, finding Autocycler with Medaka polishing achieves accuracy comparable to hybrid assemblies.

Large-scale genomic characterisation of phage-plasmids in clinical Enterobacteriaceae isolates

This study characterizes phage-plasmids in clinical Enterobacteriaceae isolates, finding they are common and associated with antimicrobial resistance and disease severity.

Plasmid conjugation drives within-patient plasmid diversity

This study shows that plasmid conjugation is the main driver of within-patient plasmid diversity, as most patients share identical OXA-48 plasmids across different bacterial hosts.

Genetic distance between complex repeats

The paper introduces a method to compute genetic distances between complex repeats, accounting for mutations, insertions, deletions, and duplications, and applies it to study PRDM9 zinc-finger repeats in house mice.

Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

The paper decomposes the site frequency spectrum into components of tree topology and waiting times, showing their impact on neutrality tests like Tajima's D and Fay and Wu's H.