Bonhoeffer, Sebastian, Prof. Dr.

Prof. Dr.  Sebastian Bonhoeffer

Prof. Dr. Sebastian Bonhoeffer

Institut für Integrative Biologie 

CHN  K 12.1 

Universitätstrasse 16

8092 Zürich

Switzerland

  • phone +41 44 632 71 06 
  • fax +41 44 632 12 71 
  • phone (Sec.) +41 44 633 60 33 
  • mail
  • vcard www.tb.ethz.ch
  • vCard 

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

Publications

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


2016

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

2016, Trends Microbiol
DOI 

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

2016, PLoS Pathog
DOI 

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
DOI 


2015

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

2015, Nat Commun
PDF    DOI 

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

2015, Ecological Applications
PDF    DOI 

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

2015, Plant Pathology
PDF    DOI 

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
PDF    DOI 

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

2015, Curr Opin HIV AIDS
DOI 

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

2015, PLoS Comput Biol
PDF    DOI 

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

2015, Epidemics
DOI 

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
PDF    DOI 


2014

top 

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

2014, Evol Appl
PDF    DOI 

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

2014, PLoS Comput Biol
PDF    DOI 

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
PDF    DOI 

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
PDF    DOI 

Samuel Tazzyman, Sebastian Bonhoeffer
Plasmids and evolutionary rescue by drug resistance.

2014, Evolution; international journal of organic evolution
DOI 

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 genetics
PDF    DOI 

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

2014, PLoS pathogens
PDF    DOI 

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
DOI 

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

2014, Phytopathology
DOI 

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
DOI 

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
PDF    DOI 


2013

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

2013, Theoretical biology & medical modelling
PDF    DOI 

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

2013, Theoretical population biology
DOI 

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

2013, Epidemics
DOI 

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

2013, Philosophical transactions of the Royal Society of London. Series B, Biological sciences
PDF    DOI 

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

2013, Epidemics
DOI 

Tanja Stadler, Denise Kühnert, Sebastian Bonhoeffer, Drummond AJ
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).

2013, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 


2012

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

2012, PLoS Comput Biol
PDF    DOI 

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 genetics
PDF    DOI 

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 computational biology
PDF    DOI 

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 computational biology
PDF    DOI 

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

2012, Epidemics
DOI 

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

2012, J Theor Biol
DOI 

Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV.

2012, Journal of the Royal Society, Interface / the Royal Society
PDF    DOI 

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, Molecular biology and evolution
DOI 


Before 2012

top 

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
PDF    DOI 

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 pathogens
PDF    DOI 

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, The Journal of infectious diseases
DOI 

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, Nature genetics
DOI 

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 pathogens
PDF    DOI 

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

2011, PLoS computational biology
PDF    DOI 

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

2011, The Lancet infectious diseases
DOI 

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, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
PDF    DOI 

Takizawa H, Roland Regoes, Boddupalli CS, Sebastian Bonhoeffer, Manz MG
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.

2011, The Journal of experimental medicine
PDF    DOI 

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
PDF    DOI 

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

2010, Mathematical biosciences and engineering : MBE
DOI 

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

2010, Evolution; international journal of organic evolution
DOI 

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
DOI 

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, The Journal of infectious diseases
DOI 

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

2010, Antimicrobial agents and chemotherapy
PDF    DOI 

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

2009, Antonie Van Leeuwenhoek
DOI 

Misevic D, Kouyos RD, Sebastian Bonhoeffer
Predicting the evolution of sex on complex fitness landscapes.

2009, PLoS computational biology
PDF    DOI 

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

2009, The American naturalist
PDF    DOI 

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 (London, England)
DOI 

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, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
DOI 

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

2009, Epidemics
DOI 

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

2009, Epidemics

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

2009, Theoretical population biology
DOI 

The effect of opinion clustering on disease outbreaks.

2008, Journal of the Royal Society, Interface / the Royal Society
PDF    DOI 

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, Journal of acquired immune deficiency syndromes (1999)
PDF    DOI 

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

2008, Trends in ecology & evolution
DOI 

Salathé M, Kouyos RD, Roland Regoes, Sebastian Bonhoeffer
Rapid parasite adaptation drives selection for high recombination rates.

2008, Evolution; international journal of organic evolution
DOI 

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

2007, BMC evolutionary biology
PDF    DOI 

The effect of population structure on the emergence of drug resistance during influenza pandemics.

2007, Journal of the Royal Society, Interface / the Royal Society
PDF    DOI 

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

2007, Trends in ecology & evolution
DOI 

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

2006, Trends Microbiol
DOI 

Evolution of complexity in signaling pathways.

2006, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

2006, Journal of virology
PDF    DOI 

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, Journal of medical virology
DOI 

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

2006, Ecology letters
DOI 

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, Proceedings. Biological sciences / The Royal Society
PDF    DOI 

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

2006, PLoS computational biology
PDF    DOI 

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, The American naturalist
DOI 

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

2006, Journal of theoretical biology
DOI 

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 (London, England)
DOI 

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

2006, Mol Biol Evol
DOI 

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

2006, Journal of theoretical biology
DOI 

Salathé M, May RM, Sebastian Bonhoeffer
The evolution of network topology by selective removal.

2005, Journal of the Royal Society, Interface / the Royal Society
PDF    DOI 

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

2005, Journal of virology
PDF    DOI 

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

2005, AIDS research and human retroviruses
DOI 

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

2005, Proceedings. Biological sciences / The Royal Society
PDF    DOI 

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

2005, Trends in genetics : TIG
DOI 

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

2005, Journal of theoretical biology
DOI 

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

2005, Microbiology (Reading, England)
DOI 

Funk GA, Jansen VA, Sebastian Bonhoeffer, Killingback T
Spatial models of virus-immune dynamics.

2005, Journal of theoretical biology
DOI 

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

2004, Science (New York, N.Y.)
DOI 

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, Journal of virology
PDF    DOI 

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, Clinical and experimental immunology
DOI 

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
DOI 

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
DOI 

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

2004, The Plant cell
DOI 

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

2004, BioEssays : news and reviews in molecular, cellular and developmental biology
DOI 

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, Journal of virology
PDF    DOI 

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

2003, Current drug targets. Infectious disorders
DOI 

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

2003, Trends in microbiology
DOI 

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, The Journal of infectious diseases
DOI 

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

2003, Trends in immunology
DOI 

Quantitative constraints on the scope of negative selection.

2003, Trends in immunology
DOI 

An evolutionary scenario for the transition to undifferentiated multicellularity.

2003, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

2002, Journal of virology
PDF    DOI 

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

2002, Proceedings. Biological sciences / The Royal Society
PDF    DOI 

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, Journal of virology
PDF    DOI 

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, Journal of virology
PDF    DOI 

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, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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 (London, England)
DOI 

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

2001, Science (New York, N.Y.)
DOI 

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, Journal of acquired immune deficiency syndromes (1999)
DOI 

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

2000, AIDS (London, England)
DOI 

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, Molecular medicine (Cambridge, Mass.)
PDF   

Production of resistant HIV mutants during antiretroviral therapy.

2000, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

2000, Journal of immunology (Baltimore, Md. : 1950)
DOI 

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
DOI 

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, The Journal of infectious diseases
DOI 

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
DOI 

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, The Journal of clinical investigation
PDF    DOI 

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, The Journal of infectious diseases
DOI 

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

1999, Science (New York, N.Y.)
DOI 

A stochastic model for primary HIV infection: optimal timing of therapy.

1999, AIDS (London, England)
DOI 

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, Journal of virology
PDF   

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, Journal of virology
PDF   

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

1998, AIDS patient care and STDs
DOI 

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, Journal of virology
PDF   

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, The Journal of experimental medicine
PDF    DOI 

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 (New York, N.Y.)
DOI 

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

1998, AIDS (London, England)
DOI 

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

1998, Science (New York, N.Y.)
DOI 

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, The American journal of the medical sciences
DOI 

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

1997, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

Sebastian Bonhoeffer, May RM, Shaw GM, Nowak MA
Virus dynamics and drug therapy.

1997, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

Pre-existence and emergence of drug resistance in HIV-1 infection.

1997, Proceedings. Biological sciences / The Royal Society
PDF    DOI 

Sebastian Bonhoeffer, Coffin JM, Nowak MA
Human immunodeficiency virus drug therapy and virus load.

1997, Journal of virology
PDF   

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

1997, Journal of theoretical biology
DOI 

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

1996, Science (New York, N.Y.)
DOI 

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

1996, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

1996, Proceedings. Biological sciences / The Royal Society
DOI 

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

1996, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

1996, Physical review letters
DOI 

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

1996, Science (New York, N.Y.)
DOI 

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
DOI 

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
DOI 

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

1994, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

Nowak MA, Sebastian Bonhoeffer, May RM
Spatial games and the maintenance of cooperation.

1994, Proceedings of the National Academy of Sciences of the United States of America
PDF    DOI 

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

1993, Eur Biophys J
DOI 

 
 
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