Modeling HIV-1 Drug Resistance as Episodic Directional Selection. - Ben Murrell; Tulio de Oliveira; Chris Seebregts; Sergei L. Kosakovsky Pond; Konrad Scheffler (PLoS Comput. Biol., 2012)

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. - N. Lance Hepler; Konrad Scheffler; Steven Weaver; Ben Murrell; Douglas D. Richman; Dennis R. Burton; Pascal Poignard; Davey M. Smith; Sergei L. Kosakovsky Pond (PLoS Comput. Biol., 2014)

RIFRAF: a frame-resolving consensus algorithm. - Kemal Eren; Ben Murrell (Bioinform., 2018)

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. - Kemal Eren; Steven Weaver; Robert Ketteringham; Morné Valentyn; Melissa Laird Smith; Venkatesh Kumar; Sanjay Mohan; Sergei L. Kosakovsky Pond; Ben Murrell (PLoS Comput. Biol., 2018)