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SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic.
- Published in:
- Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03414-w
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- Article
Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation.
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- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-54319-y
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- Article
Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses.
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- Molecular Biology & Evolution, 2023, v. 40, n. 8, p. 1, doi. 10.1093/molbev/msad164
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- Article
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda.
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- Virus Evolution, 2023, v. 9, n. 2, p. 1, doi. 10.1093/ve/vead046
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- Article
SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications.
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- NAR Genomics & Bioinformatics, 2023, v. 5, n. 2, p. 1, doi. 10.1093/nargab/lqad038
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- Article
Clustering Highly Divergent Homologous Proteins: An Alignment‐Free Method.
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- Current Protocols, 2023, v. 3, n. 2, p. 1, doi. 10.1002/cpz1.666
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- Article
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.
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- Virus Evolution, 2023, v. 9, n. 1, p. 1, doi. 10.1093/ve/veac120
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- Article
From components to communities: bringing network science to clustering for molecular epidemiology.
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- Virus Evolution, 2023, v. 9, n. 1, p. 1, doi. 10.1093/ve/vead026
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- Article
HexSE: Simulating evolution in overlapping reading frames.
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- Virus Evolution, 2023, v. 9, n. 1, p. 1, doi. 10.1093/ve/vead009
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- Article
Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.
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- PLoS Computational Biology, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.pcbi.1010745
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- Article
Molecular source attribution.
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- PLoS Computational Biology, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.pcbi.1010649
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- Article
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada.
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- eLife, 2022, p. 1, doi. 10.7554/eLife.73896
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- Article
Using networks to analyze and visualize the distribution of overlapping genes in virus genomes.
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- PLoS Pathogens, 2022, p. 1, doi. 10.1371/journal.ppat.1010331
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- Article
Network science inspires novel tree shape statistics.
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- PLoS ONE, 2021, v. 16, n. 12, p. 1, doi. 10.1371/journal.pone.0259877
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- Article
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes.
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- Virus Evolution, 2021, v. 7, n. 2, p. 1, doi. 10.1093/ve/veab092
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- Article
Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay.
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- Viruses (1999-4915), 2021, v. 13, n. 9, p. 1721, doi. 10.3390/v13091721
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- Article
Tuning intrinsic disorder predictors for virus proteins.
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- Virus Evolution, 2021, v. 7, n. 1, p. 1, doi. 10.1093/ve/veaa106
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- Article
Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir.
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- Virus Evolution, 2021, v. 7, n. 1, p. 1, doi. 10.1093/ve/veaa104
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- Article
Addressing Ethical Challenges in US-Based HIV Phylogenetic Research.
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- 2020
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- journal article
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.
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- 2020
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- Publication type:
- journal article
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.
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- Molecular Biology & Evolution, 2020, v. 37, n. 1, p. 295, doi. 10.1093/molbev/msz197
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- Article
Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection.
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- Virus Evolution, 2020, v. 6, n. 1, p. 1, doi. 10.1093/ve/veaa011
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- Article
Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.
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- Virus Evolution, 2019, v. 5, n. 2, p. N.PAG, doi. 10.1093/ve/vez022
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- Article
Tree shape‐based approaches for the comparative study of cophylogeny.
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- Ecology & Evolution (20457758), 2019, v. 9, n. 12, p. 6756, doi. 10.1002/ece3.5185
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- Article
First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda.
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- AIDS Research & Therapy, 2019, v. 16, n. 1, p. N.PAG, doi. 10.1186/s12981-019-0218-2
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- Article
Evidence for a recombinant origin of HIV-1 Group M from genomic variation.
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- Virus Evolution, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1093/ve/vey039
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- Article
An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes.
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- PLoS ONE, 2018, v. 13, n. 11, p. 1, doi. 10.1371/journal.pone.0206409
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- Article
Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.
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- Retrovirology, 2018, v. 15, n. 1, p. N.PAG, doi. 10.1186/s12977-018-0426-1
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- Article
The use of CT in forensic post-mortem examination to facilitate targeted dissection methods.
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- Canadian Journal of Pathology, 2018, v. 10, p. 48
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- Article
Quantifying the Aftermath: Recent Outbreaks Among People Who Inject Drugs and the Utility of Phylodynamics.
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- 2018
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- Publication type:
- editorial
Genetic Cluster Analysis for HIV Prevention.
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- Current HIV/AIDS Reports, 2018, v. 15, n. 2, p. 182, doi. 10.1007/s11904-018-0384-1
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- Article
Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.
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- PLoS Pathogens, 2018, v. 14, n. 1, p. 1, doi. 10.1371/journal.ppat.1006754
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- Article
Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries.
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- Infectious Diseases of Poverty, 2017, v. 6, p. 1, doi. 10.1186/s40249-017-0377-0
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- Article
A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.
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- PLoS Computational Biology, 2017, v. 13, n. 11, p. 1, doi. 10.1371/journal.pcbi.1005868
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- Article
node.dating: dating ancestors in phylogenetic trees in R.
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- Bioinformatics, 2017, v. 33, n. 6, p. 932, doi. 10.1093/bioinformatics/btw744
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- Article
Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load.
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- 2017
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- journal article
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
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- Molecular Biology & Evolution, 2017, v. 34, n. 1, p. 185, doi. 10.1093/molbev/msw217
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- Article
Ancestral Reconstruction.
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- PLoS Computational Biology, 2016, v. 12, n. 7, p. 1, doi. 10.1371/journal.pcbi.1004763
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- Article
Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction.
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- Scientific Reports, 2015, v. 5, n. 1, p. 17607, doi. 10.1038/srep17607
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- Article
The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis.
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- PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0131437
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- Article
Global Origin and Transmission of Hepatitis C Virus Nonstructural Protein 3 Q80K Polymorphism.
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- Journal of Infectious Diseases, 2015, v. 211, n. 8, p. 1288, doi. 10.1093/infdis/jiu613
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- Article
The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada.
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- Journal of Infectious Diseases, 2015, v. 211, n. 6, p. 926, doi. 10.1093/infdis/jiu560
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- Article
Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.
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- Nucleic Acids Research, 2014, v. 42, n. 12, p. e98, doi. 10.1093/nar/gku355
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- Article
“Deep” Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1.
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- PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0099508
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- Article
Mapping the Shapes of Phylogenetic Trees from Human and Zoonotic RNA Viruses.
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- PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0078122
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- Article
Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.
- Published in:
- 2013
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- Publication type:
- Journal Article
Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.
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- Journal of Antimicrobial Chemotherapy (JAC), 2013, v. 68, n. 9, p. 2007, doi. 10.1093/jac/dkt153
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- Article
Use of Cellular HIV DNA to Predict Virologic Response to Maraviroc: Performance of Population-Based and Deep Sequencing.
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- Clinical Infectious Diseases, 2013, v. 56, n. 11, p. 1659, doi. 10.1093/cid/cit105
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- Article
Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data.
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- PLoS Computational Biology, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.pcbi.1002753
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- Article
Characterizing HIV Transmission Networks Across the United States.
- Published in:
- Clinical Infectious Diseases, 2012, v. 55, n. 8, p. 1135, doi. 10.1093/cid/cis612
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- Article