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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Optimized phylogenetic clustering of HIV-1 sequence data for public health applications von Chato, Connor, Feng, Yi, Ruan, Yuhua, Xing, Hui, Herbeck, Joshua, Kalish, Marcia, Poon, Art F Y

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Molecular source attribution von Chao, Elisa, Chato, Connor, Vender, Reid, Olabode, Abayomi S, Ferreira, Roux-Cil, Poon, Art F. Y

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Network science inspires novel tree shape statistics von Chindelevitch, Leonid, Hayati, Maryam, Poon, Art F Y, Colijn, Caroline

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Using networks to analyze and visualize the distribution of overlapping genes in virus genomes von Muñoz-Baena, Laura, Poon, Art F Y

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Assessment of a screening tool to aid home-based identification of adolescents (aged 10-14) living with HIV in Zambia and South Africa: HPTN 071 (PopART) study von Chaila, Mwate Joseph, Mcleod, David, Vermund, Sten H, Mbolongwe-Thornicroft, Moomba, Mbewe, Madalitso, Mubekapi-Musadaidzwa, Constance, Harper, Abigail, Schaap, Albertus, Floyd, Sian, Hoddinott, Graeme, Hayes, Richard, Fidler, Sarah, Ayles, Helen, Shanaube, Kwame

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A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation von McCloskey, Rosemary M, Poon, Art F Y

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

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Prospects for a sequence-based taxonomy of influenza A virus subtypes von Poon, Art F. Y

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Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses von Poon, Art F Y, Walker, Lorne W, Murray, Heather, McCloskey, Rosemary M, Harrigan, P Richard, Liang, Richard H

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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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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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Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study von Poon, Art F Y, Dr, Gustafson, Réka, MD, Daly, Patricia, MD, Zerr, Laura, MN, Demlow, S Ellen, MPH, Wong, Jason, MD, Woods, Conan K, BSc, Hogg, Robert S, Prof, Krajden, Mel, Prof, Moore, David, MDCM, Kendall, Perry, FRCPC, Montaner, Julio S G, Prof, Harrigan, P Richard, Prof

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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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Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses von Muhire, Brejnev Muhizi, Golden, Michael, Murrell, Ben, Lefeuvre, Pierre, Lett, Jean-Michel, Gray, Alistair, Poon, Art Y F, Ngandu, Nobubelo Kwanele, Semegni, Yves, Tanov, Emil Pavlov, Monjane, Adérito Luis, Harkins, Gordon William, Varsani, Arvind, Shepherd, Dionne Natalie, Martin, Darren Patrick

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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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Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay von Lapointe, Hope R, Dong, Weiyan, Dong, Winnie W Y, Kirkby, Don, Woods, Conan, Poon, Art F Y, Howe, Anita Y M, Harrigan, P Richard, Brumme, Chanson J

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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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