Luca Ferretti A

The paper identifies a bias in phylogenetic branch lengths when using the discrete Gamma model and recommends replacing it with the FreeRate model.

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.

The paper develops a theoretical framework to detect genetic signatures of rapid adaptation to extreme environmental changes using population genetics models.

The paper quantifies bias in genetic diversity and neutrality tests caused by neutral polymorphic structural variants and proposes corrected estimators.

This study compares mutation rates and genetic diversity in parthenogenetic and sexual nematode species, finding lower mutation rates and higher nucleotide diversity in asexual populations.

The paper evaluates two tools for HIV transmission direction prediction using short and long-read sequencing data from serodiscordant couples, showing long reads improve phylogenetic resolution and transmission prediction accuracy.

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

The paper develops new measures to compare geographic histories in pathogens' genomes, revealing diverse diffusion paths in viral evolution.

The paper studies 45 common human polymorphic inversions, showing their functional and evolutionary impact, including gene disruption and association with phenotypic traits.

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.

The paper derives the conditional Site Frequency Spectrum for a genomic region linked to a focal mutation and presents formulas for neutrality tests in non-recombining regions.

This paper computes the third moments of the site frequency spectrum and derives analytical results for the bias of 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.