Global Distribution and Conservation of Evolutionary Distinctness in Birds von Jetz, Walter, Thomas, Gavin H., Joy, Jeffrey B., Redding, David W., Hartmann, Klaas, Mooers, Arne O.

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The emergence of SARS-CoV-2 in Europe and North America von Worobey, Michael, Pekar, Jonathan, Larsen, Brendan B., Nelson, Martha I., Hill, Verity, Joy, Jeffrey B., Rambaut, Andrew, Suchard, Marc A., Wertheim, Joel O., Lemey, Philippe

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Symbiosis catalyses niche expansion and diversification von Joy, Jeffrey B.

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Ancestral Reconstruction von Joy, Jeffrey B, Liang, Richard H, McCloskey, Rosemary M, Nguyen, T, Poon, Art F Y

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Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference von Jones, Bradley R, Joy, Jeffrey B

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Fundamental Identifiability Limits in Molecular Epidemiology von Louca, Stilianos, McLaughlin, Angela, MacPherson, Ailene, Joy, Jeffrey B, Pennell, Matthew W

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Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation von Watson, Corey T., Steinberg, Karyn M., Huddleston, John, Warren, Rene L., Malig, Maika, Schein, Jacqueline, Willsey, A. Jeremy, Joy, Jeffrey B., Scott, Jamie K., Graves, Tina A., Wilson, Richard K., Holt, Robert A., Eichler, Evan E., Breden, Felix

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HIV-1 variants are archived throughout infection and persist in the reservoir von Brooks, Kelsie, Jones, Bradley R., Dilernia, Dario A., Wilkins, Daniel J., Claiborne, Daniel T., McInally, Samantha, Gilmour, Jill, Kilembe, William, Joy, Jeffrey B., Allen, Susan A., Brumme, Zabrina L., Hunter, Eric

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Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus von Tisthammer, Kaho H, Solis, Caroline, Orcales, Faye, Nzerem, Madu, Winstead, Ryan, Dong, Weiyan, Joy, Jeffrey B, Pennings, Pleuni S

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Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution von MacPherson, Ailene, Louca, Stilianos, McLaughlin, Angela, Joy, Jeffrey B, Pennell, Matthew W

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HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy von Shahid, Aniqa, Jones, Bradley R, Yang, Julia S. W, Dong, Winnie, Shaipanich, Tawimas, Donohoe, Kathryn, Brumme, Chanson J, Joy, Jeffrey B, Leung, Janice M, Brumme, Zabrina L

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Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada von McLaughlin, Angela, Montoya, Vincent, Miller, Rachel L, Mordecai, Gideon J, Worobey, Michael, Poon, Art FY, Joy, Jeffrey B

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Global priorities for conserving the evolutionary history of sharks, rays and chimaeras von Stein, R. William, Mull, Christopher G., Kuhn, Tyler S., Aschliman, Neil C., Davidson, Lindsay N. K., Joy, Jeffrey B., Smith, Gordon J., Dulvy, Nicholas K., Mooers, Arne O.

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The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada von Poon, Art F. Y., Joy, Jeffrey B., Woods, Conan K., Shurgold, Susan, Colley, Guillaume, Brumme, Chanson J., Hogg, Robert S., Montaner, Julio S. G., Harrigan, P. Richard

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The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study von Joy, Jeffrey B, Dr, McCloskey, Rosemary M, BSc, Nguyen, Thuy, BSc, Liang, Richard H, PhD, Khudyakov, Yury, PhD, Olmstead, Andrea, PhD, Krajden, Mel, MD, Ward, John W, MD, Harrigan, P Richard, PhD, Montaner, Julio S G, MD, Poon, Art F Y, PhD

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Phylogenetic approach to recover integration dates of latent HIV sequences within-host von Jones, Bradley R., Kinloch, Natalie N., Horacsek, Joshua, Ganase, Bruce, Harris, Marianne, Harrigan, P. Richard, Jones, R. Brad, Brockman, Mark A., Joy, Jeffrey B., Poon, Art F. Y., Brumme, Zabrina L.

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Variable routes to genomic and host adaptation among coronaviruses von Montoya, Vincent, McLaughlin, Angela, Mordecai, Gideon J., Miller, Rachel L., Joy, Jeffrey B.

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Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison von Ratmann, Oliver, Hodcroft, Emma B, Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon, Hossain, A S Md Mukarram, Joy, Jeffrey B, Kendall, Michelle, Kühnert, Denise, Leventhal, Gabriel E, Liang, Richard, Plazzotta, Giacomo, Poon, Art F Y, Rasmussen, David A, Stadler, Tanja, Volz, Erik, Weis, Caroline, Leigh Brown, Andrew J, Fraser, Christophe

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Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods von Kamelian, Kimia, Montoya, Vincent, Olmstead, Andrea, Dong, Winnie, Harrigan, Richard, Morshed, Muhammad, Joy, Jeffrey B.

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HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy von Miller, Rachel L, Ponte, Rosalie, Jones, Bradley R, Kinloch, Natalie N, Omondi, Fredrick H, Jenabian, Mohammad-Ali, Dupuy, Franck P, Fromentin, Remi, Brassard, Pierre, Mehraj, Vikram, Chomont, Nicolas, Poon, Art F Y, Joy, Jeffrey B, Brumme, Zabrina L, Routy, Jean-Pierre

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