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- HexSE: Simulating evolution in overlapping reading frames. Virus evolution 9, vead009 (2023).
- Clustering Highly Divergent Homologous Proteins: An Alignment-Free Method. Current protocols 3, e666 (2023).
- bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression. Virus evolution 9, veac120 (2023).
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications. PLoS computational biology 18, e1010745 (2022).
- Molecular source attribution. PLoS computational biology 18, e1010649 (2022).
- Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. eLife 11, (2022).
- Revisiting the recombinant history of HIV-1 group M with dynamic network community detection. Proceedings of the National Academy of Sciences of the United States of America 119, e2108815119 (2022).
- Using networks to analyze and visualize the distribution of overlapping genes in virus genomes. PLoS pathogens 18, e1010331 (2022).
- Network science inspires novel tree shape statistics. PloS one 16, e0259877 (2021).
- Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses 13, (2021).
- Tuning intrinsic disorder predictors for virus proteins. Virus evolution 7, veaa106 (2021).
- Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir. Virus evolution 7, veaa104 (2021).
- Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. The Journal of antimicrobial chemotherapy 75, 3525-3533 (2020).
- A targeted reactivation of latent HIV-1 using an activator vector in patient samples from acute infection. EBioMedicine 59, 102853 (2020).
- Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection. Virus evolution 6, veaa011 (2020).
- Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4+ T Cell Subsets during Long-Term Combination Antiretroviral Therapy. Journal of virology 94, (2020).
- HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular biology and evolution 37, 295-299 (2020).
- Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution 5, vez022 (2019).
- Tree shape-based approaches for the comparative study of cophylogeny. Ecology and evolution 9, 6756-6771 (2019).