A. F. Poon

Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

This paper develops a new clustering method to detect recombinant HIV-1 genomes and finds that most HIV-1 genomes are recombinant.

Tuning Intrinsic Disorder Predictors for Virus Proteins

The paper evaluates 21 intrinsic disorder predictors on virus proteins and finds a random forest ensemble improves prediction accuracy by 36% in Matthews correlation coefficient.

Detection of novel HIV-1 drug resistance mutations by support vector analysis of deep sequence data and experimental validation

This study identifies novel HIV-1 drug resistance mutations in non-subtype B infections using deep sequencing, SVM analysis, and experimental validation.

Tree Shape-based approaches for the Comparative study of Cophylogeny

This paper evaluates tree shape distance metrics to quantify cophylogeny in host-pathogen interactions and identifies metrics that best capture coevolutionary parameters.

Evidence for a Recombinant Origin of HIV-1 group M from Genomic Variation

This study uses a sliding window approach on HIV-1/M genome sequences to detect recombination breakpoints and estimate the origin of the pandemic, finding evidence of early recombination events.