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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Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology von Delport, Wayne, Poon, Art F. Y., Frost, Simon D. W., Kosakovsky Pond, Sergei L.

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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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Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology von Poon, Art F Y

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Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure von MANOSUTHI, Weerawat, BUTLER, David M, PEREZ-SANTIAGO, Josué, POON, Art F. Y, PILLAI, Satish K, MEHTA, Sanjay R, PACOLD, Mary E, RICHMAN, Douglas D, KOSAKOVSKY POND, Sergei, SMITH, Davey M

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An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1 von Kosakovsky Pond, Sergei L, Posada, David, Stawiski, Eric, Chappey, Colombe, Poon, Art F Y, Hughes, Gareth, Fearnhill, Esther, Gravenor, Mike B, Leigh Brown, Andrew J, Frost, Simon D W

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Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda von Ndashimye, Emmanuel, Avino, Mariano, Kyeyune, Fred, Nankya, Immaculate, Gibson, Richard M, Nabulime, Eva, Poon, Art F Y, Kityo, Cissy, Mugyenyi, Peter, Quiñones-Mateu, Miguel E, Arts, Eric J

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Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada von Jacka, Brendan, Applegate, Tanya, Krajden, Mel, Olmstead, Andrea, Harrigan, P. Richard, Marshall, Brandon D.L., DeBeck, Kora, Milloy, M.‐J., Lamoury, Francois, Pybus, Oliver G., Lima, Viviane D., Magiorkinis, Gkikas, Montoya, Vincent, Montaner, Julio, Joy, Jeffrey, Woods, Conan, Dobrer, Sabina, Dore, Gregory J., Poon, Art F.Y., Grebely, Jason

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HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men von Dennis, Ann M, Volz, Erik, Frost, A S Md Simon D W, Hossain, Mukarram, Poon, Art F Y, Rebeiro, Peter F, Vermund, Sten H, Sterling, Timothy R, Kalish, Marcia L

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Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data von Poon, Art F Y, Swenson, Luke C, Bunnik, Evelien M, Edo-Matas, Diana, Schuitemaker, Hanneke, van 't Wout, Angélique B, Harrigan, P Richard

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Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations von Karakas, Aram, Brumme, Zabrina L, Poon, Art F Y

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An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope von Poon, Art F Y, Lewis, Fraser I, Pond, Sergei L Kosakovsky, Frost, Simon D W

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Use of Cellular HIV DNA to Predict Virologic Response to Maraviroc: Performance of Population-Based and Deep Sequencing von Swenson, Luke C., Dong, Winnie W. Y., Mo, Theresa, Demarest, James, Chapman, Doug, Ellery, Suzanne, Heera, Jayvant, Valdez, Hernan, Poon, Art F. Y., Harrigan, P. Richard

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Evolutionary Fingerprinting of Genes von Kosakovsky Pond, Sergei L., Scheffler, Konrad, Gravenor, Michael B., Poon, Art F.Y., Frost, Simon D.W.

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Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing von Liang, Richard H, Mo, Theresa, Dong, Winnie, Lee, Guinevere Q, Swenson, Luke C, McCloskey, Rosemary M, Woods, Conan K, Brumme, Chanson J, Ho, Cynthia K Y, Schinkel, Janke, Joy, Jeffrey B, Harrigan, P Richard, Poon, Art F Y

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Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1 von Poon, Art F Y, Swenson, Luke C, Dong, Winnie W Y, Deng, Wenjie, Kosakovsky Pond, Sergei L, Brumme, Zabrina L, Mullins, James I, Richman, Douglas D, Harrigan, P Richard, Frost, Simon D W

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An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data von McCloskey, Rosemary M, Liang, Richard H, Harrigan, P Richard, Brumme, Zabrina L, Poon, Art F Y

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Replication Fitness of Multiple Nonnucleoside Reverse Transcriptase-Resistant HIV-1 Variants in the Presence of Etravirine Measured by 454 Deep Sequencing von Brumme, Chanson J, Huber, Kelly D, Dong, Winnie, Poon, Art F Y, Harrigan, P Richard, Sluis-Cremer, Nicolas

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A comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection von Dalby, Andrew R

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Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope von Poon, Art F Y, Lewis, Fraser I, Pond, Sergei L Kosakovsky, Frost, Simon D W

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