Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Zehava Grossman; Michael B. Gravenor; Douglas D. Richman; Andrew J. Leigh Brown (PLoS Comput. Biol., 2006)

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)

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection. - Erik M. Volz; James S. Koopman; Melissa J. Ward; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2012)

Automated analysis of phylogenetic clusters. - Manon Ragonnet-Cronin; Emma B. Hodcroft; Stéphane Hué; Esther Fearnhill; Valerie Delpech; Andrew J. Leigh Brown; Samantha Lycett (BMC Bioinform., 2013)

Employing phylogenetic tree shape statistics to resolve the underlying host population structure. - Jonathan K. Kayondo; Alfred Ssekagiri; Grace Nabakooza; Nicholas Bbosa; Deogratius Ssemwanga; Pontiano Kaleebu; Samuel Mwalili; John Mango Magero; Andrew J. Leigh Brown; Roberto A. Saenz; Ronald Galiwango; John M. Kitayimbwa (BMC Bioinform., 2021)

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. - Steven Weaver; Vanessa M. Dávila Conn; Daniel Ji; Hannah Verdonk; Santiago Ávila-Rios; Andrew J. Leigh Brown; Joel O. Wertheim; Sergei L. Kosakovsky Pond (Frontiers Bioinform., 2024)