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.
Prof. Dr. Sebastian Bonhoeffer
Prof. Dr. Sebastian Bonhoeffer
Full Professor at the Department of Environmental Systems Science
Head of Collegium Helveticum
ETH Zürich
- +41 44 632 71 06
- +41 44 633 60 33 (Sec.)
- www.tb.ethz.ch
- Tel: +41 44 632 23 07
- 0000-0001-8052-3925
- V-Card (vcf, 1kb)
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
Spring Semester 2025
| Number | Unit |
|---|---|
| 701-1418-00L | Modelling Course in Population and Evolutionary Biology (Block course) |
| 701-1424-00L | Guarda-Workshop in Evolutionary Biology (Block course) |
| 701-1461-00L | Ecology and Evolution: Seminar |
| 701-1708-00L | Infectious Disease Dynamics |
Publications
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.
Ashcroft P, Lehtinen S, Bonhoeffer S
Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification.
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.
Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2.
Chabas H, Müller V, Bonhoeffer S, Regoes R
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.
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.
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.
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
Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics.
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.
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.
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.
Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases.
Uecker H, Bonhoeffer S
Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling.
Evolutionary mechanisms that determine which bacterial genes are carried on plasmids.
Angst DC, Tepekule B, Sun L, Bogos B, Bonhoeffer S
Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting.
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.
Bouman J, Riou J, Bonhoeffer S, Regös RR
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.
Quantifying the impact of quarantine duration on COVID-19 transmission.
Lehtinen S, Ashcroft P, Bonhoeffer S
On the relationship between serial interval, infectiousness profile and generation time.
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.
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
Witzany C, Bonhoeffer S, Rolff J
Is antimicrobial resistance evolution accelerating?
COVID-19 infectivity profile correction.
2020, Swiss Med Wkly
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
Pascual Garcia A, Bonhoeffer S, Bell T
Metabolically cohesive microbial consortia and ecosystem functioning.
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.
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.
Van Boeckel TP, Do Couto Pires J, Silvester R, Zhao C, Song J, Criscuolo N, Gilbert M, Bonhoeffer S, Laxminarayan R
Global trends in antimicrobial resistance in animals in low- and middle-income countries.
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.
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.
Frenoy A, Bonhoeffer S
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.
Sun L, Alexander H, Bogos B, Kiviet D, Ackermann M, Bonhoeffer S
Effective polyploidy causes phenotypic delay and influences bacterial evolvability.
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.
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.
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.
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.
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.
Allen R, Engelstädter J, Bonhoeffer S, Mcdonald B, Hall A
Reversing resistance: different routes and common themes across pathogens.
Liechti J, Leventhal G, Bonhoeffer S
Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.
Fingerhuth S, Low N, Bonhoeffer S, Althaus C
Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study.
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.
Alexander H, Mayer S, Bonhoeffer S
Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load.
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.
Du Plessis L, Leventhal GE, Bonhoeffer S
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
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.
Legros M, Bonhoeffer S
A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs.
Cadosch DR, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.
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
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.
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.
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.
Bonhoeffer S, Fraser C, Leventhal GE
High heritability is compatible with the broad distribution of set point viral load in HIV carriers.
Leventhal GE, Hill A, Nowak M, Bonhoeffer S
Evolution and emergence of infectious diseases in theoretical and real-world networks.
Alexander HK, Martin G, Martin O, Bonhoeffer S
Evolutionary rescue: linking theory for conservation and medicine.
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?
Boskova V, Bonhoeffer S, Stadler T
Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models.
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.
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.
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.
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.
Leventhal GE, Günthard H, Bonhoeffer S, Stadler T
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.
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.
Stadler T, Bonhoeffer S
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.
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).
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.
Kouyos R, Leventhal GE, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Bonhoeffer S
Exploring the complexity of the HIV-1 fitness landscape.
Arnoldini M, Mostowy R, Bonhoeffer S, Ackermann M
Evolution of stress response in the face of unreliable environmental signals.
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.
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.
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.
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.
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.
Takizawa H, Regös RR, Boddupalli C, Bonhoeffer S, Manz M
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.
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.
Mostowy R, Kouyos R, Fouchet D, Bonhoeffer S
The role of recombination for the coevolutionary dynamics of HIV and the immune response.
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.
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.
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.
Engelstädter J, Bonhoeffer S
Red Queen dynamics with non-standard fitness interactions.
Salathé M, Kouyos R, Bonhoeffer S
On the causes of selection for recombination underlying the red queen hypothesis.
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.
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.
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.
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.
Débarre F, Bonhoeffer S, Regös RR
The effect of population structure on the emergence of drug resistance during influenza pandemics.
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.
Brandin E, Thorstensson R, Bonhoeffer S, Albert J
Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy.
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.
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.
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.
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.
Althaus C, Bonhoeffer S
Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1.
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.
Pfeiffer T, Rutte C, Killingback T, Taborsky M, Bonhoeffer S
Evolution of cooperation by generalized reciprocity.
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.
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
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.
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.
Bonhoeffer S, Barbour A, De Boer R
Procedures for reliable estimation of viral fitness from time-series data.
Müller V, Vigueras-Gómez J, Bonhoeffer S
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection.
Regös RR, Staprans S, Feinberg M, Bonhoeffer S
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis.
Regös RR, Ebert D, Bonhoeffer S
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology.
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.
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.
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.
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.
Ribeiro R, Bonhoeffer S
Production of resistant HIV mutants during antiretroviral therapy.
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.
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.
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.
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.
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.
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.
Bonhoeffer S, May R, Shaw G, Nowak M
Virus dynamics and drug therapy.
Bonhoeffer S, Nowak M
Pre-existence and emergence of drug resistance in HIV-1 infection.
Bonhoeffer S, Coffin J, Nowak M
Human immunodeficiency virus drug therapy and virus load.
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.
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.
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.
Nowak M, Bonhoeffer S, May R
Spatial games and the maintenance of cooperation.
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