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)

Probing of viral diversity by global haplotype prediction. - Armin Töpfer; Francesca Di Giallonardo; Karin J. Metzner; Huldrych F. Günthard; Niko Beerenwinkel (ICCABS, 2013)

The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients. - Niko Beerenwinkel; Hesam Montazeri; Heike Schuhmacher; Patrick Knupfer; Viktor von Wyl; Hansjakob Furrer; Manuel Battegay; Bernard Hirschel; Matthias Cavassini; Pietro Vernazza; Enos Bernasconi; Sabine Yerly; et al. (PLoS Comput. Biol., 2013)

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells. - Christian L. Althaus; Beda Joos; Alan S. Perelson; Huldrych F. Günthard (PLoS Comput. Biol., 2014)

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)

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

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)

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)