Matthew R. McKay

Linkage-aware inference of fitness from short-read time-series genomic data

This paper introduces a method to infer fitness effects from short-read time-series genomic data while accounting for genetic linkage, validated on HIV and SARS-CoV-2 datasets.

Back-projection improves inference from sparsely sampled genomic surveillance data

This study introduces a back-projection model to improve inference from sparse genomic surveillance data by estimating infection times and accounting for sampling biases in SARS-CoV-2 variants.

HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies

The paper investigates how E1-E2 interactions in HCV affect viral fitness and antibody escape, identifying mutations and antibodies with implications for vaccine development.

COVIDep platform for real-time reporting of vaccine target recommendations for SARS-CoV-2: Description and connections with COVID-19 immune responses and preclinical vaccine trials

The paper introduces a web-based platform called COVIDep that provides immune target recommendations for SARS-CoV-2 vaccine development by integrating genetic and epitope data.

Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies

This study identifies conserved B and T cell epitopes between SARS-CoV and SARS-CoV-2 to guide vaccine development against the novel coronavirus.

Co-evolution networks of HIV/HCV are modular with direct association to structure and function

The paper identifies modular co-evolution networks in HIV and HCV proteins linked to structural and functional domains using sparse principal component analysis.