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

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

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Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. by Vera Tai, Art F Y Poon, Ian T Paulsen, Brian Palenik

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HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. by Susanna L Lamers, Art F Y Poon, Michael S McGrath

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

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

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

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

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

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Tree shape‐based approaches for the comparative study of cophylogeny by Mariano Avino, Garway T. Ng, Yiying He, Mathias S. Renaud, Bradley R. Jones, Art F. Y. Poon

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

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Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance by Nazanin Mohammadzadeh, Robin P. Love, Richard Gibson, Eric J. Arts, Art F.Y. Poon, Linda Chelico

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

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Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. by Art F Y Poon, Sergei L Kosakovsky Pond, Phil Bennett, Douglas D Richman, Andrew J Leigh Brown, Simon D W Frost

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Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. by Guinevere Q Lee, Luke C Swenson, Art F Y Poon, Jeffrey N Martin, Hiroyu Hatano, Steven G Deeks, P Richard Harrigan

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

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"Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1. by David J H F Knapp, Rachel A McGovern, Art F Y Poon, Xiaoyin Zhong, Dennison Chan, Luke C Swenson, Winnie Dong, P Richard Harrigan

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Parsing social network survey data from hidden populations using stochastic context-free grammars. by Art F Y Poon, Kimberly C Brouwer, Steffanie A Strathdee, Michelle Firestone-Cruz, Remedios M Lozada, Sergei L Kosakovsky Pond, Douglas D Heckathorn, Simon D W Frost

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

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First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda by Art F. Y. Poon, Emmanuel Ndashimye, Mariano Avino, Richard Gibson, Cissy Kityo, Fred Kyeyune, Immaculate Nankya, Miguel E. Quiñones-Mateu, Eric J. ARTS, The Ugandan Drug Resistance Study Team

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