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

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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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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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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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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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Symbiosis catalyses niche expansion and diversification von 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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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 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 reservoirs are dominated by genetically younger and clonally enriched proviruses von Kinloch, Natalie N, Shahid, Aniqa, Dong, Winnie, Kirkby, Don, Jones, Bradley R, Beelen, Charlotte J, MacMillan, Daniel, Lee, Guinevere Q, Mota, Talia M, Sudderuddin, Hanwei, Barad, Evan, Harris, Marianne, Brumme, Chanson J, Jones, R Brad, Brockman, Mark A, Joy, Jeffrey B, Brumme, Zabrina L

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Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART von Brooks, Kelsie, Omondi, F. Harrison, Liang, Richard H., Sudderuddin, Hanwei, Jones, Bradley R., Joy, Jeffrey B., Brumme, Chanson J., Hunter, Eric, Brumme, Zabrina L.

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HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy von Omondi, Harrison, Sudderuddin, Hanwei, Shahid, Aniqa, Kinloch, Natalie N., Jones, Bradley R., Miller, Rachel L., Tsai, Olivia, MacMillan, Daniel, Trocha, Alicja, Brockman, Mark A., Brumme, Chanson J., Joy, Jeffrey B., Liang, Richard, Walker, Bruce D., Brumme, Zabrina L.

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ADAPTIVE RADIATION OF GALL-INDUCING INSECTS WITHIN A SINGLE HOST-PLANT SPECIES von Joy, Jeffrey B, Crespi, Bernard J

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Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a von Tisthammer, Kaho H., Dong, Weiyan, Joy, Jeffrey B., Pennings, Pleuni S.

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Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs von Montoya, Vincent, Howe, Anita Y. M., Dong, Weiyan Y., Dong, Winnie, Brumme, Chanson J., Olmstead, Andrea D., Hayashi, Kanna, Richard Harrigan, P., Joy, Jeffrey B.

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Island phytophagy: explaining the remarkable diversity of plant-feeding insects von Joy, Jeffrey B., Crespi, Bernard J.

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Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study von Sudderuddin, Hanwei, Kinloch, Natalie N., Jin, Steven W., Miller, Rachel L., Jones, Bradley R., Brumme, Chanson J., Joy, Jeffrey B., Brockman, Mark A., Brumme, Zabrina L.

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