Bonhoeffer, Sebastian, Prof. Dr.

Prof. Dr.  Sebastian Bonhoeffer

Prof. Dr. Sebastian Bonhoeffer

Institut für Integrative Biologie 

CHN  K 12.1 

Universitätstrasse 16

8092 Zürich


  • phone +41 44 632 71 06 
  • fax +41 44 632 12 71 
  • phone (Sec.) +41 44 633 60 33 
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Additional information

Curriculum Vitae

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

Prof. Bonhoeffer was born in Tübingen, Germany, on October 6, 1965. 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


2016    |   2015    |   2014    |   2013    |   2012    |   Before 2012    |  


Gabriel Leventhal, Sebastian Bonhoeffer
Potential Pitfalls in Estimating Viral Load Heritability.

2016, Trends Microbiol

Nagaraja P, Helen Alexander, Sebastian Bonhoeffer, Dixit NM
Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1.

2016, Epidemics


Alexey Mikaberidze, Bruce A. McDonald, Sebastian Bonhoeffer
Developing smarter host mixtures to control plant disease

2015, Plant Pathology

Gabriel Leventhal, Hill AL, Nowak MA, Sebastian Bonhoeffer
Evolution and emergence of infectious diseases in theoretical and real-world networks.

2015, Nat Commun

Alexey Mikaberidze, Christopher C Mundt, Sebastian Bonhoeffer
Invasiveness of plant pathogens depends on the spatial scale of host distribution

2015, Ecological Applications

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

2015, Curr Opin HIV AIDS

Feng Fu, Nowak MA, Sebastian Bonhoeffer
Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy.

2015, PLoS Comput Biol

Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer AU, Shilaih M, Hinkley T, Petropoulos C, Sebastian Bonhoeffer, Günthard HF
Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds.

2015, PLoS Pathog

Frost SD, Pybus OG, Gog JR, Viboud C, Sebastian Bonhoeffer, Bedford T
Eight challenges in phylodynamic inference.

2015, Epidemics

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

2015, PLoS Pathog



Helen Alexander, Martin G, Martin OY, Sebastian Bonhoeffer
Evolutionary rescue: linking theory for conservation and medicine.

2014, Evol Appl

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

2014, PLoS Comput Biol

Kouyos RD, Metcalf CJ, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Sebastian Bonhoeffer, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt LC, Read AF, Smith DL, Standley C, Wale N, Grenfell B
The path of least resistance: aggressive or moderate treatment?

2014, Proc Biol Sci

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

2014, Antimicrob Agents Chemother

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

2014, PLoS Genet

Avila D, Keiser O, Egger M, Kouyos R, Böni J, Yerly S, Klimkait T, Vernazza PL, Aubert V, Rauch A, Sebastian Bonhoeffer, Günthard HF, Tanja Stadler, Spycher BD
Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.

2014, Am J Epidemiol

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

2014, PLoS Pathog

Alexey Mikaberidze, McDonald BA, Sebastian Bonhoeffer
Can high-risk fungicides be used in mixtures without selecting for fungicide resistance?

2014, Phytopathology

Fraser C, Lythgoe K, Gabriel Leventhal, George Shirreff, Hollingsworth TD, Samuel Alizon, Sebastian Bonhoeffer
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.

2014, Science

Gabriel Leventhal, Günthard HF, Sebastian Bonhoeffer, Tanja Stadler
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.

2014, Mol Biol Evol


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

2013, Theor Biol Med Model

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

2013, Theor Popul Biol

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

2013, Epidemics

Tanja Stadler, Sebastian Bonhoeffer
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.

2013, Philos Trans R Soc Lond B Biol Sci

Nested model reveals potential amplification of an HIV epidemic due to drug resistance.

2013, Epidemics


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

2012, PLoS Comput Biol

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

2012, PLoS Comput Biol

Gabriel Leventhal, Kouyos R, Tanja Stadler, Wyl Vv, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard HF, Sebastian Bonhoeffer
Inferring epidemic contact structure from phylogenetic trees.

2012, PLoS Comput Biol

Kouyos RD, Gabriel Leventhal, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Sebastian Bonhoeffer
Exploring the complexity of the HIV-1 fitness landscape.

2012, PLoS Genet

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

2012, Epidemics

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

2012, J Theor Biol

Tanja Stadler, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond AJ, Sebastian Bonhoeffer
Estimating the basic reproductive number from viral sequence data.

2012, Mol Biol Evol

Before 2012


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

2011, PLoS One

Kouyos RD, von Wyl V, Hinkley T, Petropoulos CJ, Haddad M, Whitcomb JM, Böni J, Yerly S, Cellerai C, Klimkait T, Günthard HF, Sebastian Bonhoeffer
Assessing predicted HIV-1 replicative capacity in a clinical setting.

2011, PLoS Pathog

von Wyl V, Kouyos RD, Yerly S, Böni J, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Staehelin C, Battegay M, Vernazza PL, Bernasconi E, Ledergerber B, Sebastian Bonhoeffer, Günthard HF
The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland.

2011, J Infect Dis

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

2011, Nat Genet

Kouyos RD, Abel Zur Wiesch P, Sebastian Bonhoeffer
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

zur Wiesch PA, Kouyos R, Engelstädter J, Roland Regoes, Sebastian Bonhoeffer
Population biological principles of drug-resistance evolution in infectious diseases.

2011, Lancet Infect Dis

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

2011, PLoS Comput Biol

Kouyos RD, 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 PL, Bernasconi E, Ledergerber B, Sebastian Bonhoeffer, Günthard HF
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

Samuel Alizon, von Wyl V, Tanja Stadler, Kouyos RD, Yerly S, Hirschel B, Böni J, Shah C, Klimkait T, Furrer H, Rauch A, Vernazza PL, Bernasconi E, Battegay M, Bürgisser P, Telenti A, Günthard HF, Sebastian Bonhoeffer
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.

2010, PLoS Pathog

Sebastian Bonhoeffer, Wiesch PA, Kouyos RD
Rotating antibiotics does not minimize selection for resistance.

2010, Math Biosci Eng

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

2010, Evolution

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

2010, Epidemics

Kouyos RD, 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 PL, Bernasconi E, Rickenbach M, Ledergerber B, Sebastian Bonhoeffer, Günthard HF
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland.

2010, J Infect Dis

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

2010, Antimicrob Agents Chemother

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

2009, Antonie Van Leeuwenhoek

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

2009, Am Nat

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

2009, AIDS

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

2009, Clin Infect Dis

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

2009, Epidemics

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

2009, Epidemics

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

2009, Theor Popul Biol

Salathé M, Kouyos RD, Sebastian Bonhoeffer
The state of affairs in the kingdom of the Red Queen.

2008, Trends Ecol Evol

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

2008, J Acquir Immune Defic Syndr

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

2007, BMC Evol Biol

Kouyos RD, Silander OK, Sebastian Bonhoeffer
Epistasis between deleterious mutations and the evolution of recombination.

2007, Trends Ecol Evol

Kouyos RD, Christian Althaus, Sebastian Bonhoeffer
Stochastic or deterministic: what is the effective population size of HIV-1?

2006, Trends Microbiol

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

2006, J Virol

Funk GA, Oxenius A, Fischer M, Opravil M, Joos B, Flepp M, Weber R, Günthard HF, Sebastian Bonhoeffer
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

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

2006, Ecol Lett

Almut Scherer, Salathé M, Sebastian Bonhoeffer
High epitope expression levels increase competition between T cells.

2006, PLoS Comput Biol

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

2006, Am Nat

Roland Regoes, Bowen EF, Cope AV, Gor D, Hassan-Walker AF, Prentice HG, Johnson MA, Sweny P, Burroughs AK, Griffiths PD, Sebastian Bonhoeffer, Emery VC
Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis.

2006, Proc Biol Sci

Soyer OS, Pfeiffer T, Sebastian Bonhoeffer
Simulating the evolution of signal transduction pathways.

2006, J Theor Biol

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

2006, Mol Biol Evol

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

2006, AIDS

Soyer OS, Salathé M, Sebastian Bonhoeffer
Signal transduction networks: topology, response and biochemical processes.

2006, J Theor Biol

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

2005, J Virol

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

2005, AIDS Res Hum Retroviruses

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

2005, Proc Biol Sci

Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation.

2005, Trends Genet

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

2005, J Theor Biol

The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off.

2005, Microbiology

Sebastian Bonhoeffer, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ
Evidence for positive epistasis in HIV-1.

2004, Science

Ciuffi A, Bleiber G, Muñoz M, Martinez R, Loeuillet C, Rehr M, Fischer M, Günthard HF, Oxenius A, Meylan P, Sebastian Bonhoeffer, 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

Hersberger M, Sebastian Bonhoeffer, Rampini SK, Opravil M, Marti-Jaun J, Telenti A, Hänseler E, Ledergerber B, Speck RF
CCTTT-repeat polymorphism of the inducible nitric oxide synthase is not associated with HIV pathogenesis.

2004, Clin Exp Immunol

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

2004, Blood

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

2004, Virology

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

2004, Plant Cell

Bretscher MT, Christian Althaus, Müller V, Sebastian Bonhoeffer
Recombination in HIV and the evolution of drug resistance: for better or for worse?

2004, Bioessays

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

2003, J Virol

Mathematical approaches in the study of viral kinetics and drug resistance in HIV-1 infection.

2003, Curr Drug Targets Infect Disord

Sebastian Bonhoeffer, Funk GA, Günthard HF, Fischer M, Müller V
Glancing behind virus load variation in HIV-1 infection.

2003, Trends Microbiol

Metzner KJ, Sebastian Bonhoeffer, Fischer M, Karanicolas R, Allers K, Joos B, Weber R, Hirschel B, Kostrikis LG, Günthard HF
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

Response to Bandeira and Faro: Closing the circle of constraints.

2003, Trends Immunol

An evolutionary scenario for the transition to undifferentiated multicellularity.

2003, Proc Natl Acad Sci U S A

Sebastian Bonhoeffer, Barbour AD, De Boer RJ
Procedures for reliable estimation of viral fitness from time-series data.

2002, Proc Biol Sci

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

2002, J Virol

Ortiz GM, Hu J, Goldwitz JA, Chandwani R, Larsson M, Bhardwaj N, Sebastian Bonhoeffer, Ramratnam B, Zhang L, Markowitz MM, Nixon DF
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

Betts MR, Ambrozak DR, Douek DC, Sebastian Bonhoeffer, Brenchley JM, Casazza JP, Koup RA, Picker LJ
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

Ortiz GM, Wellons M, Brancato J, Vo HT, Zinn RL, Clarkson DE, Van Loon K, Sebastian Bonhoeffer, Miralles GD, Montefiori D, Bartlett JA, Nixon DF
Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects.

2001, Proc Natl Acad Sci U S A

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

2001, AIDS

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

2001, J Acquir Immune Defic Syndr

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

2001, Science

Sebastian Bonhoeffer, Rembiszewski M, Ortiz GM, Nixon DF
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection.

2000, AIDS

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

2000, Mol Med

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

2000, J Immunol

Binley JM, Clas B, Gettie A, Vesanen M, Montefiori DC, Sawyer L, Booth J, Lewis M, Marx PA, Sebastian Bonhoeffer, Moore JP
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

Jin X, Demoitie MA, Donahoe SM, Ogg GS, Sebastian Bonhoeffer, Kakimoto WM, Gillespie G, Moss PA, Dyer W, Kurilla MG, Riddell SR, Downie J, Sullivan JS, McMichael AJ, Workman C, Nixon DF
High frequency of cytomegalovirus-specific cytotoxic T-effector cells in HLA-A*0201-positive subjects during multiple viral coinfections.

2000, J Infect Dis

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

1999, Lancet

Ortiz GM, Nixon DF, Trkola A, Binley J, Jin X, Sebastian Bonhoeffer, Kuebler PJ, Donahoe SM, Demoitie MA, Kakimoto WM, Ketas T, Clas B, Heymann JJ, Zhang L, Cao Y, Hurley A, Moore JP, Ho DD, 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

Parkin NT, Lie YS, Hellmann N, Markowitz M, Sebastian Bonhoeffer, Ho DD, Petropoulos CJ
Phenotypic changes in drug susceptibility associated with failure of human immunodeficiency virus type 1 (HIV-1) triple combination therapy.

1999, J Infect Dis

Nixon DF, Douek D, Kuebler PJ, Jin X, Vesanen M, Sebastian Bonhoeffer, Cao Y, Koup RA, Ho DD, 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

Levin BR, Lipsitch M, Sebastian Bonhoeffer
Population biology, evolution, and infectious disease: convergence and synthesis.

1999, Science

Zhang L, Dailey PJ, He T, Gettie A, Sebastian Bonhoeffer, Perelson AS, Ho DD
Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques.

1999, J Virol

Ogg GS, Jin X, Sebastian Bonhoeffer, Moss P, Nowak MA, Monard S, Segal JP, Cao Y, Rowland-Jones SL, Hurley A, Markowitz M, Ho DD, McMichael AJ, Nixon DF
Decay kinetics of human immunodeficiency virus-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy.

1999, J Virol

Connor RI, Montefiori DC, Binley JM, Moore JP, Sebastian Bonhoeffer, Gettie A, Fenamore EA, Sheridan KE, Ho DD, Dailey PJ, Marx PA
Temporal analyses of virus replication, immune responses, and efficacy in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine.

1998, J Virol

Morris L, Binley JM, Clas BA, Sebastian Bonhoeffer, Astill TP, Kost R, Hurley A, Cao Y, Markowitz M, Ho DD, Moore JP
HIV-1 antigen-specific and -nonspecific B cell responses are sensitive to combination antiretroviral therapy.

1998, J Exp Med

Ogg GS, Jin X, Sebastian Bonhoeffer, Dunbar PR, Nowak MA, Monard S, Segal JP, Cao Y, Rowland-Jones SL, Cerundolo V, Hurley A, Markowitz M, Ho DD, Nixon DF, McMichael AJ
Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA.

1998, Science

Ribeiro RM, Sebastian Bonhoeffer, Nowak MA
The frequency of resistant mutant virus before antiviral therapy.

1998, AIDS

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

1998, Science

Levin BR, Antia R, Berliner E, Bloland P, Sebastian Bonhoeffer, Cohen M, DeRouin T, Fields PI, Jafari H, Jernigan D, Lipsitch M, McGowan JE Jr, 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

Sebastian Bonhoeffer, Lipsitch M, Levin BR
Evaluating treatment protocols to prevent antibiotic resistance.

1997, Proc Natl Acad Sci U S A

Nowak MA, Sebastian Bonhoeffer, Shaw GM, May RM
Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations.

1997, J Theor Biol

Nowak MA, Anderson RM, Boerlijst MC, Sebastian Bonhoeffer, May RM, McMichael AJ
HIV-1 evolution and disease progression.

1996, Science

Herz AV, Sebastian Bonhoeffer, Anderson RM, May RM, Nowak MA
Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay.

1996, Proc Natl Acad Sci U S A

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

1996, Proc Biol Sci

Nowak MA, Sebastian Bonhoeffer, Hill AM, Boehme R, Thomas HC, McDade H
Viral dynamics in hepatitis B virus infection.

1996, Proc Natl Acad Sci U S A

Sebastian Bonhoeffer, Herz AV, Boerlijst MC, Nee S, Nowak MA, May RM
No signs of hidden language in noncoding DNA.

1996, Phys Rev Lett

Sebastian Bonhoeffer, Herz AV, Boerlijst MC, Nee S, Nowak MA, May RM
Explaining "linguistic features" of noncoding DNA.

1996, Science

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

1995, Nature

Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Sebastian Bonhoeffer, Nowak MA, Hahn BH
Viral dynamics in human immunodeficiency virus type 1 infection.

1995, Nature

Intra-host versus inter-host selection: viral strategies of immune function impairment.

1994, Proc Natl Acad Sci U S A

Sebastian Bonhoeffer, McCaskill JS, Tanja Stadler, Schuster P
RNA multi-structure landscapes. A study based on temperature dependent partition functions.

1993, Eur Biophys J

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