Spatial Games and Evolution of Cooperation. - Robert M. May; Sebastian Bonhoeffer; Martin A. Nowak (ECAL, 1995)

High Epitope Expression Levels Increase Competition between T Cells. - Almut Scherer; Marcel Salathé; Sebastian Bonhoeffer (PLoS Comput. Biol., 2006)

Red Queen Dynamics with Non-Standard Fitness Interactions. - Jan Engelstädter; Sebastian Bonhoeffer (PLoS Comput. Biol., 2009)

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)

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)

Evolution of Stress Response in the Face of Unreliable Environmental Signals. - Markus Arnoldini; Rafal Mostowy; Sebastian Bonhoeffer; Martin Ackermann (PLoS Comput. Biol., 2012)

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)

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models. - Veronika Boskova; Sebastian Bonhoeffer; Tanja Stadler (PLoS Comput. Biol., 2014)

Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy. - Feng Fu; Martin A. Nowak; Sebastian Bonhoeffer (PLoS Comput. Biol., 2015)

From "What Is?" to "What Isn't?" Computational Biology. - Ruth Nussinov; Sebastian Bonhoeffer; Jason A. Papin; Olaf Sporns (PLoS Comput. Biol., 2015)

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)

Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments. - Peter Ashcroft; Markus G. Manz; Sebastian Bonhoeffer (PLoS Comput. Biol., 2017)

Host population structure impedes reversion to drug sensitivity after discontinuation of treatment. - Jonas Liechti; Gabriel E. Leventhal; Sebastian Bonhoeffer (PLoS Comput. Biol., 2017)

Short-term activity cycles impede information transmission in ant colonies. - Thomas O. Richardson; Jonas Liechti; Nathalie Stroeymeyt; Sebastian Bonhoeffer; Laurent Keller (PLoS Comput. Biol., 2017)

Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies. - Burcu Tepekule; Hildegard Uecker; Isabel Derungs; Antoine Frénoy; Sebastian Bonhoeffer (PLoS Comput. Biol., 2017)

Assessing the public health impact of tolerance-based therapies with mathematical models. - Nathanaël Hozé; Sebastian Bonhoeffer; Roland R. Regoes (PLoS Comput. Biol., 2018)

A time resolved clustering method revealing longterm structures and their short-term internal dynamics. - Jonas I. Liechti; Sebastian Bonhoeffer (CoRR, 2019)

Practical considerations for measuring the effective reproductive number, Rt. - Katelyn M. Gostic; Lauren McGough; Edward B. Baskerville; Sam Abbott; Keya Joshi; Christine Tedijanto; Rebecca Kahn; Rene Niehus; James A. Hay; Pablo M. De Salazar; Joel Hellewell; Sophie Meakin; et al. (PLoS Comput. Biol., 2020)

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)

Correction: Practical considerations for measuring the effective reproductive number, Rt. - Katelyn M. Gostic; Lauren McGough; Edward B. Baskerville; Sam Abbott; Keya Joshi; Christine Tedijanto; Rebecca Kahn; Rene Niehus; James A. Hay; Pablo M. De Salazar; Joel Hellewell; Sophie Meakin; et al. (PLoS Comput. Biol., 2021)

Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems. - Hélène Chabas; Viktor Müller; Sebastian Bonhoeffer; Roland R. Regoes (PLoS Comput. Biol., 2022)

estimateR: an R package to estimate and monitor the effective reproductive number. - Jérémie Scire; Jana S. Huisman; Ana Grosu; Daniel C. Angst; Adrian Lison; Jinzhou Li; Marloes H. Maathuis; Sebastian Bonhoeffer; Tanja Stadler (BMC Bioinform., 2023)