Predicting the Evolution of Sex on Complex Fitness Landscapes. - Dusan Misevic; Roger D. Kouyos; Sebastian Bonhoeffer (PLoS Comput. Biol., 2009)

Evolution of Recombination on an HIV-1 Derived Fitness Landscape. - João Martins; Roger D. Kouyos; Trevor Hinkley; Colombe Chappey; Mojgan Haddad; Jeannette M. Whitcomb; Christos J. Petropoulos; Sebastian Bonhoeffer (ALIFE, 2010)

Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys. - Roger D. Kouyos; Shari N. Gordon; Silvija I. Staprans; Guido Silvestri; Roland R. Regoes (PLoS Comput. Biol., 2010)

Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards. - Roger D. Kouyos; Pia Abel zur Wiesch; Sebastian Bonhoeffer (PLoS Comput. Biol., 2011)

Inferring Epidemic Contact Structure from Phylogenetic Trees. - Gabriel E. Leventhal; Roger D. Kouyos; Tanja Stadler; Viktor von Wyl; Sabine Yerly; Jürg Böni; Cristina Cellerai; Thomas Klimkait; Huldrych F. Günthard; Sebastian Bonhoeffer (PLoS Comput. Biol., 2012)

Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase. - Rafal Mostowy; Roger D. Kouyos; Ilka Hoof; Trevor Hinkley; Mojgan Haddad; Jeannette M. Whitcomb; Christos J. Petropoulos; Can Kesmir; Sebastian Bonhoeffer (PLoS Comput. Biol., 2012)

Large-scale inference of conjunctive Bayesian networks. - Hesam Montazeri; Jack Kuipers; Roger D. Kouyos; Jürg Böni; Sabine Yerly; Thomas Klimkait; Vincent Aubert; Huldrych F. Günthard; Niko Beerenwinkel; The Swiss Hiv Cohort Study (Bioinform., 2016)

The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB. - Dominique Cadosch; Pia Abel zur Wiesch; Roger D. Kouyos; Sebastian Bonhoeffer (PLoS Comput. Biol., 2016)

Phylodynamics on local sexual contact networks. - David A. Rasmussen; Roger D. Kouyos; Huldrych F. Günthard; Tanja Stadler (PLoS Comput. Biol., 2017)

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)

Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study. - Suraj Balakrishna; Luisa Salazar-Vizcaya; Axel J. Schmidt; Viacheslav N. Kachalov; Katharina Kusejko; Maria Christine Thurnheer; Jan A. Roth; Dunja Nicca; Matthias Cavassini; Manuel Battegay; Patrick Schmid; Enos Bernasconi; et al. (PLoS Comput. Biol., 2021)

Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level. - Viacheslav N. Kachalov; Huyen Nguyen; Suraj Balakrishna; Luisa Salazar-Vizcaya; Rami Sommerstein; Stefan P. Kuster; Anthony Hauser; Pia Abel zur Wiesch; Eili Y. Klein; Roger D. Kouyos (PLoS Comput. Biol., 2021)

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. - Susana Posada-Céspedes; Gert van Zyl; Hesam Montazeri; Jack Kuipers; Soo-Yon Rhee; Roger D. Kouyos; Huldrych F. Günthard; Niko Beerenwinkel (PLoS Comput. Biol., 2021)

Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19. - Burcu Tepekule; Anthony Hauser; Viacheslav N. Kachalov; Sara Andresen; Thomas Scheier; Peter W. Schreiber; Huldrych F. Günthard; Roger D. Kouyos (PLoS Comput. Biol., 2021)

Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men. - Sara Andresen; Suraj Balakrishna; Catrina Mugglin; Axel J. Schmidt; Dominique L. Braun; Alex Marzel; Thanh Doco Lecompte; Katharine Ea Darling; Jan A. Roth; Patrick Schmid; Enos Bernasconi; Huldrych F. Günthard; et al. (PLoS Comput. Biol., 2022)

HIVMedQA: Benchmarking large language models for HIV medical decision support. - Gonzalo Cardenal-Antolin; Jacques Fellay; Bashkim Jaha; Roger D. Kouyos; Niko Beerenwinkel; Diane Duroux (CoRR, 2025)