Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. - Anthony Hauser; Katharina Kusejko; Leigh F. Johnson; Gilles Wandeler; Julien Riou; Fardo Goldstein; Matthias Egger; Roger D. Kouyos (PLoS Comput. Biol., 2019)

Accounting for uncertainty during a pandemic. - Jon Zelner; Julien Riou; Ruth Etzioni; Andrew Gelman (Patterns, 2021)

Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches. - Judith A. Bouman; Julien Riou; Sebastian Bonhoeffer; Roland R. Regoes (PLoS Comput. Biol., 2021)

Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. - Judith A. Bouman; Anthony Hauser; Simon L. Grimm; Martin Wohlfender; Samir Bhatt; Elizaveta Semenova; Andrew Gelman; Christian L. Althaus; Julien Riou (PLoS Comput. Biol., 2024)

Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. - Emma B. Hodcroft; Martin Wohlfender; Richard A. Neher; Julien Riou; Christian L. Althaus (PLoS Comput. Biol., 2025)