S. K. Hilton

Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis

This study examines how Bayesian phylogenetic inference is affected by model misspecification due to pairwise epistasis and shows that tree accuracy improves with alignment size even when sites are epistatically coupled.

High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization

This study maps the neutralizing and binding specificities of polyclonal rabbit serum against HIV Env trimers using mutational antigenic profiling and EMPEM.

Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

This study maps mutations in the SARS-CoV-2 spike RBD that escape antibody recognition, revealing escape mutation patterns and enabling the design of antibody cocktails.

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

The paper experimentally measures the effects of all amino-acid mutations in the SARS-CoV-2 RBD on protein folding and ACE2 binding, identifying constrained regions and tolerated mutations.

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence

The paper models site-specific amino-acid preferences to improve phylogenetic estimates of viral divergence times, finding longer branches for influenza virus hemagglutinin.

Mapping mutational effects along the evolutionary landscape of HIV envelope

The paper quantifies how amino-acid mutations affect HIV Env protein fitness across two diverged viral strains, finding most sites have conserved preferences but some show shifted mutational tolerance.

phydms: Software for phylogenetic analyses informed by deep mutational scanning

phydms enables efficient phylogenetic analyses using substitution models informed by deep mutational scanning, allowing comparison of lab and natural selection pressures.