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- Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins. PLoS pathogens 22, e1014457 (2026).
- Pervasive HIV recombination limits the utility of circulating recombinant form nomenclature. PLoS pathogens 22, e1014286 (2026).
- Estimating HIV-1 Viremic Time From Reservoir Sequence Diversity With Uncertainty Quantification. The Journal of infectious diseases 233, e1165-e1172 (2026).
- Ancestral reconstruction supports that loss of Nef-mediated T cell modulation coincided with the emergence of pathogenic lentiviruses. Journal of virology 99, e0154825 (2025).
- Spatiotemporal structure of SARS-CoV-2 mutational frequencies in wastewater samples from Ontario. PloS one 20, e0333945 (2025).
- Variability of Clinical Metrics in Small Population Communities Drive Perceived Wastewater and Environmental Surveillance Data Quality: Ontario, Canada-Wide Study. ACS ES&T water 5, 1605-1619 (2025).
- Association between HIV-1 Nef-mediated MHC-I downregulation and the maintenance of the replication-competent latent viral reservoir in individuals with virally suppressed HIV-1 in Uganda: an exploratory cohort study. The Lancet. Microbe 6, 101018 (2025).
- The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. Microbial genomics 10, (2024).
- Prospects for a sequence-based taxonomy of influenza A virus subtypes. Virus evolution 10, veae064 (2024).
- SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic. Scientific data 11, 656 (2024).
- Impact of Variable Sampling on Estimates of HIV-1 Reservoir Formation Dates. The Journal of infectious diseases 230, 928-932 (2024).
- Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microbial genomics 10, (2024).
- The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. ArXiv (2024).
- Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. EBioMedicine 102, 105040 (2024).
- Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation. Scientific reports 14, 3728 (2024).
- Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda. Virus evolution 9, vead046 (2023).
- Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Molecular biology and evolution 40, (2023).
- Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. medRxiv : the preprint server for health sciences (2023).
- From components to communities: bringing network science to clustering for molecular epidemiology. Virus evolution 9, vead026 (2023).
- SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications. NAR genomics and bioinformatics 5, lqad038 (2023).
- 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).