Prof. Dr. Sebastian Bonhoeffer

Prof. Dr.  Sebastian Bonhoeffer

Prof. Dr. Sebastian Bonhoeffer

Full Professor at the Department of Environmental Systems Science
Head of Collegium Helveticum

ETH Zürich

Institut für Integrative Biologie

CHN K 12.1

Universitätstrasse 16

8092 Zürich

Switzerland

Additional information

Sebastian Bonhoeffer has been Full Professor in Theoretical Biology at the ETH Zurich since 1 July 2005.

Prof. Bonhoeffer was born in Tübingen, Germany. After studying Music in Basel, he studied Physics in Munich and Vienna and then moved to Oxford, where he did his PhD with Martin Nowak and Robert May at the Department of Zoology. After his PhD he stayed in Oxford as a Research Fellow of Wolfson College and worked as a visiting scientist with David Ho at the Rockefeller University, New York. Prior to his appointment as SNF Research Professor at the ETH in 2001, he was junior group leader at the Friedrich Miescher Institut in Basel.

His research focuses on using population biological models to understand fundamental biological processes. He has worked extensively on mathematical models describing the population dynamics of virus infections within infected individuals. Such models have provided important insights into the pathogenesis of viral infections and HIV infection in particular.

Course Catalogue

Autumn Semester 2024

Number Unit
701-0263-01L Seminar in Evolutionary Ecology of Infectious Diseases
701-1460-00L Ecology and Evolution: Term Paper

Publications

2023    |   2022    |   2021    |   2020    |   2019    |   Before 2019    |  


2023

Iffland-Stettner A, Okano H, Gralka M, Guessous G, Amarnath K, Cordero O, Hwa T, Bonhoeffer S
A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01.

2023, mSystems
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2022

Pascual Garcia A, Schwartzman J, Enke T, Iffland-Stettner A, Cordero O, Bonhoeffer S
Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles.

2022, Front Microbiol
PDF    DOI 

Ashcroft P, Lehtinen S, Bonhoeffer S
Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification.

2022, PLoS One
PDF    DOI 

Huisman JS, Vaughan T, Egli A, Tschudin-Sutter S, Stadler T, Bonhoeffer S
The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.

2022, Philos Trans R Soc Lond B Biol Sci
PDF    DOI 

Chabas H, Müller V, Bonhoeffer S, Regoes R
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.

2022, PLoS Comput Biol
PDF    DOI 

Bouman J, Kadelka S, Stringhini S, Pennacchio F, Meyer B, Yerly S, Kaiser L, Guessous I, Azman A, Bonhoeffer S, Regoes R
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva.

2022, Epidemics
PDF    DOI 

Huisman J, Benz F, Duxbury S, De Visser J, Hall A, Fischer E, Bonhoeffer S
Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods.

2022, Plasmid
DOI 

Ashcroft P, Bonhoeffer S
Constrained optimization of divisional load in hierarchically organized tissues during homeostasis.

2022, J R Soc Interface
PDF    DOI 

Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases.

2022, J Antimicrob Chemother
DOI 


2021

top 

Courcol J, Invernizzi C, Landry Z, Minisini M, Baumgartner D, Bonhoeffer S, Chabriw B, Clerc E, Daniels M, Getta P, Girod M, Kazala K, Markram H, Pasqualini A, Martínez-Pérez C, Peaudecerf F, Peaudecerf M, Pfreundt U, Roller B, Słomka J, Vasse M, Wheeler J, Metzger C, Stocker R, Schürmann F
ARC: An Open Web-Platform for Request/Supply Matching for a Prioritized and Controlled COVID-19 Response.

2021, Front Public Health
PDF    DOI 

Bakkeren E, Herter J, Huisman JS, Steiger Y, Gül E, Newson J, Brachmann A, Piel J, Regoes R, Bonhoeffer S, Diard M, Hardt W
Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut.

2021, Elife
PDF    DOI 

Manhart M, Bonhoeffer S
The search for universality in evolutionary landscapes: Comment on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics" by Susanna Manrubia, José A. Cuesta, et al.

2021, Phys Life Rev
DOI 

Gostic K, Mcgough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar P, Hellewell J, Meakin S, Munday J, Bosse N, Sherrat K, Thompson R, White L, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S
Correction: Practical considerations for measuring the effective reproductive number, Rt.

2021, PLoS Comput Biol
PDF    DOI 

Uecker H, Bonhoeffer S
Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling.

2021, J R Soc Interface
PDF    DOI 

Angst DC, Tepekule B, Sun L, Bogos B, Bonhoeffer S
Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting.

2021, Proc Natl Acad Sci U S A
PDF    DOI 

Benz F, Huisman JS, Bakkeren E, Herter J, Stadler T, Ackermann M, Diard M, Egli A, Hall A, Hardt W, Bonhoeffer S
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo.

2021, ISME J
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Bouman J, Riou J, Bonhoeffer S, Regös RR
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.

2021, PLoS Comput Biol
PDF    DOI 

On the relationship between serial interval, infectiousness profile and generation time.

2021, J R Soc Interface
PDF    DOI 


2020

Gostic K, Mcgough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar P, Hellewell J, Meakin S, Munday J, Bosse N, Sherrat K, Thompson R, White L, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S
Practical considerations for measuring the effective reproductive number, Rt.

2020, PLoS Comput Biol
PDF    DOI 

Nienhold R, Ashcroft P, Zmajkovic J, Rai S, Rao T, Drexler B, Meyer S, Lundberg P, Passweg J, Leković D, Čokić V, Bonhoeffer S, Skoda R
MPN patients with low mutant JAK2 allele burden show late expansion restricted to erythroid and megakaryocytic lineages.

2020, Blood
DOI 

Von Wyl V, Bonhoeffer S, Bugnion E, Puhan M, Salathé M, Stadler T, Troncoso C, Vayena E, Low N
A research agenda for digital proximity tracing apps.

2020, Swiss Med Wkly
DOI 

Garcia V, Bonhoeffer S, Fu F
Cancer-induced immunosuppression can enable effectiveness of immunotherapy through bistability generation: A mathematical and computational examination.

2020, J Theor Biol
DOI 

Sun L, Ashcroft P, Ackermann M, Bonhoeffer S
Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations.

2020, Mol Biol Evol
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2019

Tepekule B, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota.

2019, Proc Natl Acad Sci U S A
PDF    DOI 

Bakkeren E, Huisman JS, Fattinger S, Hausmann A, Furter M, Egli A, Slack E, Sellin M, Bonhoeffer S, Regös RR, Diard M, Hardt W
Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut.

2019, Nature
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Before 2019

top 

Shilaih M, Angst DC, Marzel A, Bonhoeffer S, Günthard H, Kouyos R
Antibacterial effects of antiretrovirals, potential implications for microbiome studies in HIV.

2018, Antivir Ther
DOI 

Hozé N, Bonhoeffer S, Regös RR
Assessing the public health impact of tolerance-based therapies with mathematical models.

2018, PLoS Comput Biol
PDF    DOI 

Frenoy A, Bonhoeffer S
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.

2018, PLoS Biol
PDF    DOI 

Sun L, Alexander H, Bogos B, Kiviet D, Ackermann M, Bonhoeffer S
Effective polyploidy causes phenotypic delay and influences bacterial evolvability.

2018, PLoS Biol
PDF    DOI 

Kühnert D, Kouyos R, Shirreff G, Pečerska J, Scherrer A, Böni J, Yerly S, Klimkait T, Aubert V, Günthard H, Stadler T, Bonhoeffer S, Swiss Hiv Cohort Study C
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.

2018, PLoS Pathog
PDF    DOI 

Müller V, De Boer R, Bonhoeffer S, Szathmáry E
An evolutionary perspective on the systems of adaptive immunity.

2018, Biol Rev Camb Philos Soc
DOI 

Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard H, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer A, Müller V, Bonhoeffer S, Kouyos R, Regös RR, Swiss Hiv Cohort Study C
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.

2018, Mol Biol Evol
PDF    DOI 

Uecker H, Bonhoeffer S
Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective.

2017, Math Biosci
DOI 

Ashcroft P, Manz M, Bonhoeffer S
Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.

2017, PLoS Comput Biol
PDF    DOI 

Van Boeckel TP, Glennon E, Chen D, Gilbert M, Robinson T, Grenfell B, Levin S, Bonhoeffer S, Laxminarayan R
Reducing antimicrobial use in food animals.

2017, Science
PDF    DOI 

Tepekule B, Uecker H, Derungs I, Frenoy A, Bonhoeffer S
Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies.

2017, PLoS Comput Biol
PDF    DOI 

Allen R, Engelstädter J, Bonhoeffer S, Mcdonald B, Hall A
Reversing resistance: different routes and common themes across pathogens.

2017, Proc Biol Sci
PDF    DOI 

Liechti J, Leventhal G, Bonhoeffer S
Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.

2017, PLoS Comput Biol
PDF    DOI 

Fingerhuth S, Low N, Bonhoeffer S, Althaus C
Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study.

2017, BMC Med
PDF    DOI 

Mikaberidze A, Paveley N, Bonhoeffer S, Van Den Bosch F
Emergence of Resistance to Fungicides: The Role of Fungicide Dose.

2017, Phytopathology
DOI 

Richardson T, Liechti J, Stroeymeyt N, Bonhoeffer S, Keller L
Short-term activity cycles impede information transmission in ant colonies.

2017, PLoS Comput Biol
PDF    DOI 

Alexander H, Mayer S, Bonhoeffer S
Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load.

2017, Mol Biol Evol
PDF    DOI 

Polster R, Petropoulos C, Bonhoeffer S, Guillaume F
Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1.

2016, Mol Biol Evol
PDF    DOI 

Du Plessis L, Leventhal GE, Bonhoeffer S
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

2016, Mol Biol Evol
PDF    DOI 

Leventhal GE, Bonhoeffer S
Potential Pitfalls in Estimating Viral Load Heritability.

2016, Trends Microbiol
DOI 

Mikaberidze A, Mundt C, Bonhoeffer S
Invasiveness of plant pathogens depends on the spatial scale of host distribution.

2016, Ecol Appl
DOI 

Fingerhuth S , Bonhoeffer S, Low N, Althaus C
Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners.

2016, PLoS Pathog
PDF    DOI 

Legros M, Bonhoeffer S
A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs.

2016, J R Soc Interface
PDF    DOI 

Cadosch DR, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.

2016, PLoS Comput Biol
PDF    DOI 

Nagaraja P, Alexander HK, Bonhoeffer S, Dixit N
Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1.

2016, Epidemics
DOI 

Tazzyman S, Bonhoeffer S
Why There Are No Essential Genes on Plasmids.

2015, Mol Biol Evol
DOI 

Mikaberidze A, Mcdonald B, Bonhoeffer S
Developing smarter host mixtures to control plant disease

2015, Plant Pathol
DOI 

Nussinov R, Bonhoeffer S, Papin J, Sporns O
From "What Is?" to "What Isn't?" Computational Biology.

2015, PLoS Comput Biol
PDF    DOI 

Vuilleumier S, Bonhoeffer S
Contribution of recombination to the evolutionary history of HIV.

2015, Curr Opin HIV AIDS
DOI 

Frost S, Pybus O, Gog J, Viboud C, Bonhoeffer S, Bedford T
Eight challenges in phylodynamic inference.

2015, Epidemics
DOI 

Fu F, Nowak M, Bonhoeffer S
Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy.

2015, PLoS Comput Biol
PDF    DOI 

Yang W, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer A, Shilaih M, Hinkley T, Petropoulos C, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study (Shcs) C
Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds.

2015, PLoS Pathog
PDF    DOI 

Bonhoeffer S, Fraser C, Leventhal GE
High heritability is compatible with the broad distribution of set point viral load in HIV carriers.

2015, PLoS Pathog
PDF    DOI 

Leventhal GE, Hill A, Nowak M, Bonhoeffer S
Evolution and emergence of infectious diseases in theoretical and real-world networks.

2015, Nat Commun
PDF    DOI 

Alexander HK, Martin G, Martin O, Bonhoeffer S
Evolutionary rescue: linking theory for conservation and medicine.

2014, Evol Appl
PDF    DOI 

Kouyos R, Metcalf C, Birger R, Klein E, Abel Zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich T, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt L, Read A, Smith D, Standley C, Wale N, Grenfell B
The path of least resistance: aggressive or moderate treatment?

2014, Proc Biol Sci
PDF    DOI 

Boskova V, Bonhoeffer S, Stadler T
Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models.

2014, PLoS Comput Biol
PDF    DOI 

Ocampo P, Lázár V, Papp B, Arnoldini M, Abel Zur Wiesch P, Busa-Fekete R, Fekete G, Pál C, Ackermann M, Bonhoeffer S
Antagonism between bacteriostatic and bactericidal antibiotics is prevalent.

2014, Antimicrob Agents Chemother
PDF    DOI 

Tazzyman S, Bonhoeffer S
Plasmids and evolutionary rescue by drug resistance.

2014, Evolution
DOI 

Avila D, Keiser O, Egger M, Kouyos R, Böni J, Yerly S, Klimkait T, Vernazza P, Aubert V, Rauch A, Bonhoeffer S, Günthard H, Stadler T, Spycher B, Swiss Hiv Cohort Study C
Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.

2014, Am J Epidemiol
DOI 

Abel Zur Wiesch P, Kouyos R, Abel S, Viechtbauer W, Bonhoeffer S
Cycling empirical antibiotic therapy in hospitals: meta-analysis and models.

2014, PLoS Pathog
PDF    DOI 

Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos C, Engelstädter J, Bonhoeffer S
Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1.

2014, PLoS Genet
PDF    DOI 

Mikaberidze A, Mcdonald B, Bonhoeffer S
Can high-risk fungicides be used in mixtures without selecting for fungicide resistance?

2014, Phytopathology
DOI 

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth T, Alizon S, Bonhoeffer S
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.

2014, Science
PDF    DOI 

Leventhal GE, Günthard H, Bonhoeffer S, Stadler T
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.

2014, Mol Biol Evol
PDF    DOI 

Tazzyman S, Bonhoeffer S
Fixation probability of mobile genetic elements such as plasmids.

2013, Theor Popul Biol
DOI 

Hool A, Leventhal GE, Bonhoeffer S
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution.

2013, Epidemics
DOI 

Oña L, Kouyos R, Lachmann M, Bonhoeffer S
On the role of resonance in drug failure under HIV treatment interruption.

2013, Theor Biol Med Model
PDF    DOI 

Stadler T, Bonhoeffer S
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.

2013, Philos Trans R Soc Lond B Biol Sci
PDF    DOI 

Saenz R, Bonhoeffer S
Nested model reveals potential amplification of an HIV epidemic due to drug resistance.

2013, Epidemics
DOI 

Stadler T, Kühnert D, Bonhoeffer S, Drummond A
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).

2013, Proc Natl Acad Sci U S A
PDF    DOI 

Leventhal GE, Kouyos R, Stadler T, Wyl V, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard H, Bonhoeffer S
Inferring epidemic contact structure from phylogenetic trees.

2012, PLoS Comput Biol
PDF    DOI 

Kouyos R, Leventhal GE, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Bonhoeffer S
Exploring the complexity of the HIV-1 fitness landscape.

2012, PLoS Genet
PDF    DOI 

Arnoldini M, Mostowy R, Bonhoeffer S, Ackermann M
Evolution of stress response in the face of unreliable environmental signals.

2012, PLoS Comput Biol
PDF    DOI 

Mostowy R, Kouyos R, Hoof I, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Keşmir C, Bonhoeffer S
Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.

2012, PLoS Comput Biol
PDF    DOI 

Alexander HK, Bonhoeffer S
Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics.

2012, Epidemics
DOI 

Moslonka-Lefebvre M, Bonhoeffer S, Alizon S
Weighting for sex acts to understand the spread of STI on networks.

2012, J Theor Biol
DOI 

Cadosch DR, Bonhoeffer S, Kouyos R
Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV.

2012, J R Soc Interface
PDF    DOI 

Stadler T, Kouyos R, Von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard H, Drummond A, Bonhoeffer S, Swiss Hiv Cohort Study C
Estimating the basic reproductive number from viral sequence data.

2012, Mol Biol Evol
DOI 

Kouyos R, Von Wyl V, Hinkley T, Petropoulos C, Haddad M, Whitcomb J, Böni J, Yerly S, Cellerai C, Klimkait T, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Assessing predicted HIV-1 replicative capacity in a clinical setting.

2011, PLoS Pathog
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Von Wyl V, Kouyos R, Yerly S, Böni J, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Staehelin C, Battegay M, Vernazza P, Bernasconi E, Ledergerber B, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study C
The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland.

2011, J Infect Dis
DOI 

Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb J, Petropoulos C, Bonhoeffer S
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase.

2011, Nat Genet
DOI 

Kouyos R, Abel Zur Wiesch P, Bonhoeffer S
On being the right size: the impact of population size and stochastic effects on the evolution of drug resistance in hospitals and the community.

2011, PLoS Pathog
PDF    DOI 

Zur Wiesch P, Kouyos R, Engelstädter J, Regös RR, Bonhoeffer S
Population biological principles of drug-resistance evolution in infectious diseases.

2011, Lancet Infect Dis
DOI 

Kouyos R, Abel Zur Wiesch P, Bonhoeffer S
Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards.

2011, PLoS Comput Biol
PDF    DOI 

Takizawa H, Regös RR, Boddupalli C, Bonhoeffer S, Manz M
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.

2011, J Exp Med
PDF    DOI 

Kouyos R, Von Wyl V, Yerly S, Böni J, Rieder P, Joos B, Taffé P, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Rauch A, Battegay M, Vernazza P, Bernasconi E, Ledergerber B, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study C
Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection.

2011, Clin Infect Dis
PDF    DOI 

Mostowy R, Kouyos R, Fouchet D, Bonhoeffer S
The role of recombination for the coevolutionary dynamics of HIV and the immune response.

2011, PLoS One
PDF    DOI 

Bonhoeffer S, Wiesch P, Kouyos R
Rotating antibiotics does not minimize selection for resistance.

2010, Math Biosci Eng
DOI 

Alizon S, Von Wyl V, Stadler T, Kouyos R, Yerly S, Hirschel B, Böni J, Shah C, Klimkait T, Furrer H, Rauch A, Vernazza P, Bernasconi E, Battegay M, Bürgisser P, Telenti A, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.

2010, PLoS Pathog
PDF    DOI 

Martins J, Chappey C, Haddad M, Whitcomb J, Stawiski E, Petropoulos C, Bonhoeffer S
Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments.

2010, Epidemics
DOI 

Mostowy R, Salathé M, Kouyos R, Bonhoeffer S
On the evolution of sexual reproduction in hosts coevolving with multiple parasites.

2010, Evolution
DOI 

Schulz Zur Wiesch P, Engelstädter J, Bonhoeffer S
Compensation of fitness costs and reversibility of antibiotic resistance mutations.

2010, Antimicrob Agents Chemother
PDF    DOI 

Kouyos R, Von Wyl V, Yerly S, Böni J, Taffé P, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Furrer H, Battegay M, Vernazza P, Bernasconi E, Rickenbach M, Ledergerber B, Bonhoeffer S, Günthard H
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland.

2010, J Infect Dis
DOI 

Novak M, Pfeiffer T, Ackermann M, Bonhoeffer S
Bacterial growth properties at low optical densities.

2009, Antonie Van Leeuwenhoek
DOI 

Misevic D, Kouyos R, Bonhoeffer S
Predicting the evolution of sex on complex fitness landscapes.

2009, PLoS Comput Biol
PDF    DOI 

Engelstädter J, Bonhoeffer S
Red Queen dynamics with non-standard fitness interactions.

2009, PLoS Comput Biol
PDF    DOI 

Salathé M, Kouyos R, Bonhoeffer S
On the causes of selection for recombination underlying the red queen hypothesis.

2009, Am Nat
PDF    DOI 

Müller V, Von Wyl V, Yerly S, Böni J, Klimkait T, Bürgisser P, Ledergerber B, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study.

2009, AIDS
DOI 

Von Wyl V, Yerly S, Bürgisser P, Klimkait T, Battegay M, Bernasconi E, Cavassini M, Furrer H, Hirschel B, Vernazza P, Francioli P, Bonhoeffer S, Ledergerber B, Günthard H, Swiss Hiv Cohort Study C
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland.

2009, Clin Infect Dis
DOI 

Bonhoeffer S, Ferguson N, Heesterbeek H, Korber B
Research on infectious disease dynamics. Introduction.

2009, Epidemics

Kouyos R, Fouchet D, Bonhoeffer S
Recombination and drug resistance in HIV: population dynamics and stochasticity.

2009, Epidemics
DOI 

Magnus C, Rusert P, Bonhoeffer S, Trkola A, Regös RR
Estimating the stoichiometry of human immunodeficiency virus entry.

2009, J Virol
PDF    DOI 

Kouyos R, Salathé M, Otto S, Bonhoeffer S
The role of epistasis on the evolution of recombination in host-parasite coevolution.

2009, Theor Popul Biol
DOI 

Salathé M, Bonhoeffer S
The effect of opinion clustering on disease outbreaks.

2008, J R Soc Interface
PDF    DOI 

Salathé M, Kouyos R, Bonhoeffer S
The state of affairs in the kingdom of the Red Queen.

2008, Trends Ecol Evol
DOI 

Marconi V, Bonhoeffer S, Paredes R, Lu J, Hoh R, Martin J, Deeks S, Kuritzkes D
Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide.

2008, J Acquir Immune Defic Syndr
PDF    DOI 

Salathé M, Kouyos R, Regös RR, Bonhoeffer S
Rapid parasite adaptation drives selection for high recombination rates.

2008, Evolution
DOI 

Kouyos R, Salathé M, Bonhoeffer S
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations.

2007, BMC Evol Biol
PDF    DOI 

Débarre F, Bonhoeffer S, Regös RR
The effect of population structure on the emergence of drug resistance during influenza pandemics.

2007, J R Soc Interface
PDF    DOI 

Kouyos R, Silander O, Bonhoeffer S
Epistasis between deleterious mutations and the evolution of recombination.

2007, Trends Ecol Evol
DOI 

Kouyos R, Althaus C, Bonhoeffer S
Stochastic or deterministic: what is the effective population size of HIV-1?

2006, Trends Microbiol
DOI 

Soyer O, Bonhoeffer S
Evolution of complexity in signaling pathways.

2006, Proc Natl Acad Sci U S A
PDF    DOI 

Brandin E, Thorstensson R, Bonhoeffer S, Albert J
Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy.

2006, J Virol
PDF    DOI 

Funk G, Oxenius A, Fischer M, Opravil M, Joos B, Flepp M, Weber R, Günthard H, Bonhoeffer S
HIV replication elicits little cytopathic effects in vivo: analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death.

2006, J Med Virol
DOI 

Salathé M, Salathé R, Schmid-Hempel P, Bonhoeffer S
Mutation accumulation in space and the maintenance of sexual reproduction.

2006, Ecol Lett
DOI 

Novak M, Pfeiffer T, Lenski R, Sauer U, Bonhoeffer S
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli.

2006, Am Nat
DOI 

Scherer A, Salathé M, Bonhoeffer S
High epitope expression levels increase competition between T cells.

2006, PLoS Comput Biol
PDF    DOI 

Regös RR, Bowen E, Cope A, Gor D, Hassan-Walker A, Prentice H, Johnson M, Sweny P, Burroughs A, Griffiths P, Bonhoeffer S, Emery V
Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis.

2006, Proc Biol Sci
PDF    DOI 

Soyer O, Pfeiffer T, Bonhoeffer S
Simulating the evolution of signal transduction pathways.

2006, J Theor Biol
DOI 

Kouyos R, Otto S, Bonhoeffer S
Effect of varying epistasis on the evolution of recombination.

2006, Genetics
PDF    DOI 

Regös RR, Bonhoeffer S
Emergence of drug-resistant influenza virus: population dynamical considerations.

2006, Science
DOI 

Müller V, Ledergerber B, Perrin L, Klimkait T, Furrer H, Telenti A, Bernasconi E, Vernazza P, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Stable virulence levels in the HIV epidemic of Switzerland over two decades.

2006, AIDS
DOI 

Salathé M, Ackermann M, Bonhoeffer S
The effect of multifunctionality on the rate of evolution in yeast.

2006, Mol Biol Evol
DOI 

Soyer O, Salathé M, Bonhoeffer S
Signal transduction networks: topology, response and biochemical processes.

2006, J Theor Biol
DOI 

Salathé M, May R, Bonhoeffer S
The evolution of network topology by selective removal.

2005, J R Soc Interface
PDF    DOI 

Althaus C, Bonhoeffer S
Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1.

2005, J Virol
PDF    DOI 

Salathé M, Scherer A, Bonhoeffer S
Neutral drift and polymorphism in gene-for-gene systems.

2005, Ecol Lett
DOI 

Brandin E, Broström C, Gille E, Bonhoeffer S, Albert J
Short communication: HIV type 2 dynamics.

2005, AIDS Res Hum Retroviruses
DOI 

Pfeiffer T, Soyer O, Bonhoeffer S
The evolution of connectivity in metabolic networks.

2005, PLoS Biol
PDF    DOI 

Pfeiffer T, Rutte C, Killingback T, Taborsky M, Bonhoeffer S
Evolution of cooperation by generalized reciprocity.

2005, Proc Biol Sci
PDF    DOI 

Regös RR, Bonhoeffer S
The HIV coreceptor switch: a population dynamical perspective.

2005, Trends Microbiol
DOI 

Müller V, Bonhoeffer S
Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation.

2005, Trends Genet
DOI 

Scherer A, Bonhoeffer S
Epitope down-modulation as a mechanism for the coexistence of competing T-cells.

2005, J Theor Biol
DOI 

Funk G, Jansen V, Bonhoeffer S, Killingback T
Spatial models of virus-immune dynamics.

2005, J Theor Biol
DOI 

Kreft J, Bonhoeffer S
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off.

2005, Microbiology
DOI 

Bonhoeffer S, Chappey C, Parkin N, Whitcomb J, Petropoulos C
Evidence for positive epistasis in HIV-1.

2004, Science
DOI 

Ciuffi A, Bleiber G, Muñoz M, Martinez R, Loeuillet C, Rehr M, Fischer M, Günthard H, Oxenius A, Meylan P, Bonhoeffer S, Trono D, Telenti A
Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection.

2004, J Virol
PDF    DOI 

Hersberger M, Bonhoeffer S, Rampini S, Opravil M, Marti-Jaun J, Telenti A, Hänseler E, Ledergerber B, Speck R, Swiss Hiv Cohort Study C
CCTTT-repeat polymorphism of the inducible nitric oxide synthase is not associated with HIV pathogenesis.

2004, Clin Exp Immunol
DOI 

Trkola A, Kuster H, Leemann C, Oxenius A, Fagard C, Furrer H, Battegay M, Vernazza P, Bernasconi E, Weber R, Hirschel B, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study C
Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point.

2004, Blood
DOI 

Rusert P, Fischer M, Joos B, Leemann C, Kuster H, Flepp M, Bonhoeffer S, Günthard H, Trkola A
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol.

2004, Virology
DOI 

Pfeiffer T, Bonhoeffer S
Evolution of cross-feeding in microbial populations.

2004, Am Nat
DOI 

Molinier J, Ries G, Bonhoeffer S, Hohn B
Interchromatid and interhomolog recombination in Arabidopsis thaliana.

2004, Plant Cell
DOI 

Bretscher M, Althaus C, Müller V, Bonhoeffer S
Recombination in HIV and the evolution of drug resistance: for better or for worse?

2004, Bioessays
DOI 

Müller V, Bonhoeffer S
Mathematical approaches in the study of viral kinetics and drug resistance in HIV-1 infection.

2003, Curr Drug Targets Infect Disord
DOI 

Trkola A, Kuster H, Leemann C, Ruprecht C, Joos B, Telenti A, Hirschel B, Weber R, Bonhoeffer S, Günthard H, Swiss Hiv Cohot Study C
Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection.

2003, J Virol
PDF    DOI 

Bonhoeffer S, Funk G, Günthard H, Fischer M, Müller V
Glancing behind virus load variation in HIV-1 infection.

2003, Trends Microbiol
DOI 

Metzner K, Bonhoeffer S, Fischer M, Karanicolas R, Allers K, Joos B, Weber R, Hirschel B, Kostrikis L, Günthard H, Swiss Hiv Cohort Study C
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions.

2003, J Infect Dis
DOI 

Müller V, Bonhoeffer S
Response to Bandeira and Faro: Closing the circle of constraints.

2003, Trends Immunol
DOI 

Müller V, Bonhoeffer S
Quantitative constraints on the scope of negative selection.

2003, Trends Immunol
DOI 

Pfeiffer T, Bonhoeffer S
An evolutionary scenario for the transition to undifferentiated multicellularity.

2003, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Sniegowski P
Virus evolution: the importance of being erroneous.

2002, Nature
DOI 

Bonhoeffer S, Barbour A, De Boer R
Procedures for reliable estimation of viral fitness from time-series data.

2002, Proc Biol Sci
PDF    DOI 

Müller V, Vigueras-Gómez J, Bonhoeffer S
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection.

2002, J Virol
PDF    DOI 

Regös RR, Bonhoeffer S
HIV coreceptor usage and drug treatment.

2002, J Theor Biol
DOI 

Regös RR, Staprans S, Feinberg M, Bonhoeffer S
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis.

2002, J Virol
PDF    DOI 

Regös RR, Ebert D, Bonhoeffer S
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology.

2002, Proc Biol Sci
PDF    DOI 

Ortiz G, Hu J, Goldwitz J, Chandwani R, Larsson M, Bhardwaj N, Bonhoeffer S, Ramratnam B, Zhang L, Markowitz M, Nixon D
Residual viral replication during antiretroviral therapy boosts human immunodeficiency virus type 1-specific CD8+ T-cell responses in subjects treated early after infection.

2002, J Virol
PDF    DOI 

Betts M, Ambrozak D, Douek D, Bonhoeffer S, Brenchley J, Casazza J, Koup R, Picker L
Analysis of total human immunodeficiency virus (HIV)-specific CD4(+) and CD8(+) T-cell responses: relationship to viral load in untreated HIV infection.

2001, J Virol
PDF    DOI 

Ortiz G, Wellons M, Brancato J, Vo H, Zinn R, Clarkson D, Van Loon K, Bonhoeffer S, Miralles G, Montefiori D, Bartlett J, Nixon D
Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects.

2001, Proc Natl Acad Sci U S A
PDF    DOI 

García F, Plana M, Ortiz G, Bonhoeffer S, Soriano A, Vidal C, Cruceta A, Arnedo M, Gil C, Pantaleo G, Pumarola T, Gallart T, Nixon D, Miró J, Gatell J
The virological and immunological consequences of structured treatment interruptions in chronic HIV-1 infection.

2001, AIDS
DOI 

Funk G, Fischer M, Joos B, Opravil M, Günthard H, Ledergerber B, Bonhoeffer S
Quantification of in vivo replicative capacity of HIV-1 in different compartments of infected cells.

2001, J Acquir Immune Defic Syndr
DOI 

Pfeiffer T, Schuster S, Bonhoeffer S
Cooperation and competition in the evolution of ATP-producing pathways.

2001, Science
DOI 

Bonhoeffer S, Rembiszewski M, Ortiz G, Nixon D
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection.

2000, AIDS
DOI 

Jin X, Ogg G, Bonhoeffer S, Safrit J, Vesanen M, Bauer D, Chen D, Cao Y, Demoitie M, Zhang L, Markowitz M, Nixon D, Mcmichael A, Ho D
An antigenic threshold for maintaining human immunodeficiency virus type 1-specific cytotoxic T lymphocytes.

2000, Mol Med
PDF    DOI 

Ribeiro R, Bonhoeffer S
Production of resistant HIV mutants during antiretroviral therapy.

2000, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Mohri H, Ho D, Perelson A
Quantification of cell turnover kinetics using 5-bromo-2'-deoxyuridine.

2000, J Immunol
DOI 

Binley J, Clas B, Gettie A, Vesanen M, Montefiori D, Sawyer L, Booth J, Lewis M, Marx P, Bonhoeffer S, Moore J
Passive infusion of immune serum into simian immunodeficiency virus-infected rhesus macaques undergoing a rapid disease course has minimal effect on plasma viremia.

2000, Virology
DOI 

Regös RR, Nowak M, Bonhoeffer S
Evolution of virulence in a heterogeneous host population.

2000, Evolution
DOI 

Jin , Demoitie , Donahoe , Ogg G, Bonhoeffer S, Kakimoto , Gillespie , Moss , Dyer , Kurilla , Riddell , Downie , Sullivan , Mcmichael , Workman , Nixon
High frequency of cytomegalovirus-specific cytotoxic T-effector cells in HLA-A*0201-positive subjects during multiple viral coinfections.

2000, J Infect Dis
DOI 

Ramratnam B, Bonhoeffer S, Binley J, Hurley A, Zhang L, Mittler J, Markowitz M, Moore J, Perelson A, Ho D
Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis.

1999, Lancet
DOI 

Parkin N, Lie Y, Hellmann N, Markowitz M, Bonhoeffer S, Ho D, Petropoulos C
Phenotypic changes in drug susceptibility associated with failure of human immunodeficiency virus type 1 (HIV-1) triple combination therapy.

1999, J Infect Dis
DOI 

Ortiz G, Nixon D, Trkola A, Binley J, Jin X, Bonhoeffer S, Kuebler P, Donahoe S, Demoitie M, Kakimoto W, Ketas T, Clas B, Heymann J, Zhang L, Cao Y, Hurley A, Moore J, Ho D, Markowitz M
HIV-1-specific immune responses in subjects who temporarily contain virus replication after discontinuation of highly active antiretroviral therapy.

1999, J Clin Invest
PDF    DOI 

Nixon D, Douek D, Kuebler P, Jin X, Vesanen M, Bonhoeffer S, Cao Y, Koup R, Ho D, Markowitz M
Molecular tracking of an Human Immunodeficiency Virus nef specific cytotoxic T-cell clone shows persistence of clone-specific T-cell receptor DNA but not mRNA following early combination antiretroviral therapy.

1999, Immunol Lett
DOI 

Levin B, Lipsitch M, Bonhoeffer S
Population biology, evolution, and infectious disease: convergence and synthesis.

1999, Science
DOI 

Ribeiro R, Bonhoeffer S
A stochastic model for primary HIV infection: optimal timing of therapy.

1999, AIDS
DOI 

Zhang L, Dailey P, He T, Gettie A, Bonhoeffer S, Perelson A, Ho D
Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques.

1999, J Virol
PDF    DOI 

Ogg G, Jin X, Bonhoeffer S, Moss P, Nowak M, Monard S, Segal J, Cao Y, Rowland-Jones S, Hurley A, Markowitz M, Ho D, Mcmichael A, Nixon D
Decay kinetics of human immunodeficiency virus-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy.

1999, J Virol
PDF    DOI 

Models of viral kinetics and drug resistance in HIV-1 infection.

1998, AIDS Patient Care STDS
DOI 

Connor R, Montefiori D, Binley J, Moore J, Bonhoeffer S, Gettie A, Fenamore E, Sheridan K, Ho D, Dailey P, Marx P
Temporal analyses of virus replication, immune responses, and efficacy in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine.

1998, J Virol
PDF    DOI 

Morris L, Binley J, Clas B, Bonhoeffer S, Astill T, Kost R, Hurley A, Cao Y, Markowitz M, Ho D, Moore J
HIV-1 antigen-specific and -nonspecific B cell responses are sensitive to combination antiretroviral therapy.

1998, J Exp Med
PDF    DOI 

Ribeiro R, Bonhoeffer S, Nowak M
The frequency of resistant mutant virus before antiviral therapy.

1998, AIDS
DOI 

Ogg G, Jin X, Bonhoeffer S, Dunbar P, Nowak M, Monard S, Segal J, Cao Y, Rowland-Jones S, Cerundolo V, Hurley A, Markowitz M, Ho D, Nixon D, Mcmichael A
Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA.

1998, Science
DOI 

Levin B, Antia R, Berliner E, Bloland P, Bonhoeffer S, Cohen M, Derouin T, Fields P, Jafari H, Jernigan D, Lipsitch M, Mcgowan J, Mead P, Nowak M, Porco T, Sykora P, Simonsen L, Spitznagel J, Tauxe R, Tenover F
Resistance to antimicrobial chemotherapy: a prescription for research and action.

1998, Am J Med Sci
DOI 

Mohri H, Bonhoeffer S, Monard S, Perelson A, Ho D
Rapid turnover of T lymphocytes in SIV-infected rhesus macaques.

1998, Science
DOI 

Bonhoeffer S, Lipsitch M, Levin B
Evaluating treatment protocols to prevent antibiotic resistance.

1997, Proc Natl Acad Sci U S A
PDF    DOI 

Bittner B, Bonhoeffer S, Nowak M
Virus load and antigenic diversity.

1997, Bull Math Biol
DOI 

Bonhoeffer S, May R, Shaw G, Nowak M
Virus dynamics and drug therapy.

1997, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Nowak M
Pre-existence and emergence of drug resistance in HIV-1 infection.

1997, Proc Biol Sci
PDF    DOI 

Bonhoeffer S, Coffin J, Nowak M
Human immunodeficiency virus drug therapy and virus load.

1997, J Virol
PDF    DOI 

Nowak M, Bonhoeffer S, Shaw G, May R
Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations.

1997, J Theor Biol
DOI 

Nowak M, Anderson R, Boerlijst M, Bonhoeffer S, May R, Mcmichael A
HIV-1 evolution and disease progression.

1996, Science
DOI 

Herz A, Bonhoeffer S, Anderson R, May R, Nowak M
Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay.

1996, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Lenski R, Ebert D
The curse of the pharaoh: the evolution of virulence in pathogens with long living propagules.

1996, Proc Biol Sci
DOI 

Nowak M, Bonhoeffer S, Hill A, Boehme R, Thomas H, Mcdade H
Viral dynamics in hepatitis B virus infection.

1996, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Herz , Boerlijst , Nee , Nowak , May
No signs of hidden language in noncoding DNA.

1996, Phys Rev Lett
DOI 

Bonhoeffer S, Herz , Boerlijst , Nee , Nowak , May
Explaining "linguistic features" of noncoding DNA.

1996, Science
DOI 

Nowak M, Bonhoeffer S, Loveday C, Balfe P, Semple M, Kaye S, Tenant-Flowers M, Tedder R
HIV results in the frame. Results confirmed.

1995, Nature
DOI 

Bonhoeffer S, Nowak M
Can live attenuated virus work as post-exposure treatment?

1995, Immunol Today
DOI 

Wei , Ghosh , Taylor , Johnson , Emini , Deutsch , Lifson , Bonhoeffer S, Nowak , Hahn
Viral dynamics in human immunodeficiency virus type 1 infection.

1995, Nature
DOI 

Bonhoeffer S, Nowak M
Intra-host versus inter-host selection: viral strategies of immune function impairment.

1994, Proc Natl Acad Sci U S A
PDF    DOI 

Nowak M, Bonhoeffer S, May R
Spatial games and the maintenance of cooperation.

1994, Proc Natl Acad Sci U S A
PDF    DOI 

Bonhoeffer S, Mccaskill J, Stadler P, Schuster P
RNA multi-structure landscapes. A study based on temperature dependent partition functions.

1993, Eur Biophys J
DOI