Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. - Art F. Y. Poon; Fraser I. Lewis; Simon D. W. Frost; Sergei L. Kosakovsky Pond (Bioinform., 2008)

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. - Sergei L. Kosakovsky Pond; David Posada; Eric W. Stawiski; Colombe Chappey; Art F. Y. Poon; Gareth Hughes; Esther Fearnhill; Mike B. Gravenor; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2009)

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

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform. - Konrad Scheffler; N. Lance Hepler; Martin D. Smith; Wayne Delport; Art F. Y. Poon; Douglas D. Richman; Sergei L. Kosakovsky Pond (ICCABS, 2012)

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data. - Art F. Y. Poon; Luke C. Swenson; Evelien M. Bunnik; Diana Edo-Matas; Hanneke Schuitemaker; Angélique B. van 't Wout; P. Richard Harrigan (PLoS Comput. Biol., 2012)

Ancestral Reconstruction. - Jeffrey B. Joy; Richard H. Liang; Rosemary M. McCloskey; T. Nguyen; Art F. Y. Poon (PLoS Comput. Biol., 2016)

node.dating: dating ancestors in phylogenetic trees in R. - Bradley R. Jones; Art F. Y. Poon (Bioinform., 2017)

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation. - Rosemary M. McCloskey; Art F. Y. Poon (PLoS Comput. Biol., 2017)

sierra-local: A lightweight standalone application for drug resistance prediction. - Jasper Ho; Garway Ng; Mathias Renaud; Art F. Y. Poon (J. Open Source Softw., 2019)

Molecular source attribution. - Elisa Chao; Connor Chato; Reid Vender; Abayomi S. Olabode; Roux-Cil Ferreira; Art F. Y. Poon (PLoS Comput. Biol., 2022)

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications. - Connor Chato; Yi Feng; Yuhua Ruan; Hui Xing; Joshua T. Herbeck; Marcia Kalish; Art F. Y. Poon (PLoS Comput. Biol., 2022)