Christophe Fraser

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 shows that slightly deleterious mutations, rather than a few large-effect mutations, explain slow viral load changes and heritability in HIV evolution.

This paper develops a multi-task learning model to predict HIV-1 resistance to multiple broadly neutralizing antibodies, showing it reduces subtype bias and identifies co-resistance patterns.

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.

The paper analyzes resistance to dolutegravir in HIV patients in Nigeria, finding low-level resistance with one case of high-level resistance.

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.

This paper introduces veSEQ-HIV, a cost-effective, high-throughput sequencing method for HIV that recovers complete genomes and quantifies viral load, enabling drug resistance monitoring and transmission analysis.

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.

The paper derives a general formula for the coalescent rate in populations with time-varying sizes and arbitrary offspring distributions, showing how differences in coalescent rates can be explained by offspring distribution variations.

The paper analyzes genetic data to show that pneumococcal capsule recombination generates novel serotypes, highlighting risks for vaccine efficacy.