The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. - Robert J. Gifford; Tommy F. Liu; Soo-Yon Rhee; Mark Kiuchi; Stéphane Hué; Deenan Pillay; Robert W. Shafer (Bioinform., 2009)

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)

Using machine learning and big data to explore the drug resistance landscape in HIV. - Luc Blassel; Anna Tostevin; Christian Julian Villabona-Arenas; Martine Peeters; Stéphane Hué; Olivier Gascuel (PLoS Comput. Biol., 2021)