Roger D. Kouyos

19 papers B 1C 1Journal 17
YearRankTypeTitle / Venue / Authors
2026 J jnl
Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.
PLoS Comput. Biol.
Sanni Översti, Mathilde Boumasmoud, Huldrych F. Günthard, Hugo Sax, Annelies S. Zinkernagel, Roger D. Kouyos, Denise Kühnert
2025 J jnl
HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.
BMC Bioinform.
Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David G. Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M. Baeten, Connie L. Celum, Ronald Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R. Mugo, Astrid Gall, François Blanquart, Margreet Bakker, Daniela Bezemer, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Günthard, Pia Kivelä, Roger D. Kouyos, Laurence Meyer, Kholoud Porter, Ard van Sighem, Mark van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Helen Ayles, David N. Burns, Sarah Fidler, Mary Kate Grabowski, Richard J. Hayes, Joshua T. Herbeck, Joseph Kagaayi, Pontiano Kaleebu, Jairam R. Lingappa, Deogratius Ssemwanga, Susan H. Eshleman, Myron S. Cohen, Oliver Ratmann, Oliver Laeyendecker, Christophe Fraser
2025 J jnl
HIVMedQA: Benchmarking large language models for HIV medical decision support.
CoRR
Gonzalo Cardenal-Antolin, Jacques Fellay, Bashkim Jaha, Roger D. Kouyos, Niko Beerenwinkel, Diane Duroux
2025 B conf
Towards Reliable Conversational Data Analytics.
EDBT
Sihem Amer-Yahia, Jasmina Bogojeska, Roberta Facchinetti, Valeria Franceschi, Aristides Gionis, Katja Hose, Georgia Koutrika, Roger D. Kouyos, Matteo Lissandrini, Silviu Maniu, Katsiaryna Mirylenka, Davide Mottin, Themis Palpanas, Mattia Rigotti, Yannis Velegrakis
2022 J jnl
Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men.
PLoS Comput. Biol.
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, Andri Rauch, Roger D. Kouyos, Luisa Salazar-Vizcaya
2021 J jnl
Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study.
PLoS Comput. Biol.
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, Huldrych F. Günthard, Andri Rauch, Roger D. Kouyos, The Swiss Hiv Cohort Study
2021 J jnl
Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19.
PLoS Comput. Biol.
Burcu Tepekule, Anthony Hauser, Viacheslav N. Kachalov, Sara Andresen, Thomas Scheier, Peter W. Schreiber, Huldrych F. Günthard, Roger D. Kouyos
2021 J jnl
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.
PLoS Comput. Biol.
Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel
2021 J jnl
Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level.
PLoS Comput. Biol.
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
2019 J jnl
Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa.
PLoS Comput. Biol.
Anthony Hauser, Katharina Kusejko, Leigh F. Johnson, Gilles Wandeler, Julien Riou, Fardo Goldstein, Matthias Egger, Roger D. Kouyos
2017 J jnl
Phylodynamics on local sexual contact networks.
PLoS Comput. Biol.
David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler
2016 J jnl
Large-scale inference of conjunctive Bayesian networks.
Bioinform.
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
2016 J jnl
The Role of Adherence and Retreatment in
PLoS Comput. Biol.
Dominique Cadosch, Pia Abel zur Wiesch, Roger D. Kouyos, Sebastian Bonhoeffer
2012 J jnl
Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase.
PLoS Comput. Biol.
Rafal Mostowy, Roger D. Kouyos, Ilka Hoof, Trevor Hinkley, Mojgan Haddad, Jeannette M. Whitcomb, Christos J. Petropoulos, Can Kesmir, Sebastian Bonhoeffer
2012 J jnl
Inferring Epidemic Contact Structure from Phylogenetic Trees.
PLoS Comput. Biol.
Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer
2011 J jnl
Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards.
PLoS Comput. Biol.
Roger D. Kouyos, Pia Abel zur Wiesch, Sebastian Bonhoeffer
2010 C conf
Evolution of Recombination on an HIV-1 Derived Fitness Landscape.
ALIFE
João Martins, Roger D. Kouyos, Trevor Hinkley, Colombe Chappey, Mojgan Haddad, Jeannette M. Whitcomb, Christos J. Petropoulos, Sebastian Bonhoeffer
2010 J jnl
Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys.
PLoS Comput. Biol.
Roger D. Kouyos, Shari N. Gordon, Silvija I. Staprans, Guido Silvestri, Roland R. Regoes
2009 J jnl
Predicting the Evolution of Sex on Complex Fitness Landscapes.
PLoS Comput. Biol.
Dusan Misevic, Roger D. Kouyos, Sebastian Bonhoeffer