Sebastian Bonhoeffer - Publications

Affiliations: 
ETH/Uni Zurich, Zürich, Zürich, Switzerland 

182 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, ... ... Bonhoeffer S, et al. Practical considerations for measuring the effective reproductive number, Rt. Plos Computational Biology. 16: e1008409. PMID 33301457 DOI: 10.1371/journal.pcbi.1008409  0.6
2020 Ashcroft P, Huisman JS, Lehtinen S, Bouman JA, Althaus CL, Regoes RR, Bonhoeffer S. COVID-19 infectivity profile correction. Swiss Medical Weekly. 150: w20336. PMID 32757177 DOI: 10.4414/smw.2020.20336  0.72
2020 von Wyl V, Bonhoeffer S, Bugnion E, Puhan MA, Salathé M, Stadler T, Troncoso C, Vayena E, Low N. A research agenda for digital proximity tracing apps. Swiss Medical Weekly. 150: w20324. PMID 32672340 DOI: 10.4414/smw.2020.20324  0.6
2020 Gostic KM, McGough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse N, Sherratt K, ... ... Bonhoeffer S, et al. Practical considerations for measuring the effective reproductive number, Rt. Medrxiv : the Preprint Server For Health Sciences. PMID 32607522 DOI: 10.1101/2020.06.18.20134858  0.6
2020 Garcia V, Bonhoeffer S, Fu F. Cancer-induced immunosuppression can enable effectiveness of immunotherapy through bistability generation: a mathematical and computational examination. Journal of Theoretical Biology. 110185. PMID 32035826 DOI: 10.1016/j.jtbi.2020.110185  0.32
2019 Tepekule B, Abel Zur Wiesch P, Kouyos RD, Bonhoeffer S. Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America. PMID 31666328 DOI: 10.1073/pnas.1912188116  0.52
2019 Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD. Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. Nature. 573: 276-280. PMID 31485077 DOI: 10.1038/s41586-019-1521-8  0.72
2018 Frenoy A, Bonhoeffer S. Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria. Plos Biology. 16: e2005056. PMID 29750784 DOI: 10.1371/journal.pbio.2005056  0.64
2017 Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, ... ... Bonhoeffer S, et al. Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity. Molecular Biology and Evolution. PMID 29029206 DOI: 10.1093/molbev/msx246  0.72
2017 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. Plos Computational Biology. 13: e1005745. PMID 28915236 DOI: 10.1371/journal.pcbi.1005745  0.64
2017 Shilaih M, Angst DC, Marzel A, Bonhoeffer S, Günthard HF, Kouyos RD. Antibacterial effects of antiretrovirals, potential implications for microbiome studies in HIV. Antiviral Therapy. PMID 28497768 DOI: 10.3851/IMP3173  0.52
2016 Mikaberidze A, Mundt CC, Bonhoeffer S. Invasiveness of plant pathogens depends on the spatial scale of host distribution. Ecological Applications : a Publication of the Ecological Society of America. 26: 1238-48. PMID 27509761 DOI: 10.5061/dryad.f2j8s  1
2015 Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T. Eight challenges in phylodynamic inference. Epidemics. 10: 88-92. PMID 25843391 DOI: 10.1016/j.epidem.2014.09.001  1
2015 Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer AU, Shilaih M, Hinkley T, Petropoulos C, Bonhoeffer S, Günthard HF. Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds. Plos Pathogens. 11: e1004722. PMID 25798934 DOI: 10.1371/journal.ppat.1004722  1
2015 Fu F, Nowak MA, Bonhoeffer S. Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy. Plos Computational Biology. 11: e1004142. PMID 25789469 DOI: 10.1371/journal.pcbi.1004142  1
2015 Bonhoeffer S, Fraser C, Leventhal GE. High heritability is compatible with the broad distribution of set point viral load in HIV carriers. Plos Pathogens. 11: e1004634. PMID 25658741 DOI: 10.1371/journal.ppat.1004634  1
2015 Leventhal GE, Hill AL, Nowak MA, Bonhoeffer S. Evolution and emergence of infectious diseases in theoretical and real-world networks. Nature Communications. 6: 6101. PMID 25592476 DOI: 10.1038/ncomms7101  1
2015 Mikaberidze A, Mcdonald BA, Bonhoeffer S. Developing smarter host mixtures to control plant disease Plant Pathology. 64: 996-1004. DOI: 10.1111/ppa.12321  1
2015 Nagaraja P, Alexander HK, Bonhoeffer S, Dixit NM. Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1 Epidemics. DOI: 10.1016/j.epidem.2015.09.001  1
2014 Alexander HK, Martin G, Martin OY, Bonhoeffer S. Evolutionary rescue: linking theory for conservation and medicine. Evolutionary Applications. 7: 1161-79. PMID 25558278 DOI: 10.1111/eva.12221  1
2014 Tazzyman SJ, Bonhoeffer S. Why there are no essential genes on plasmids. Molecular Biology and Evolution. PMID 25540453 DOI: 10.1093/molbev/msu293  1
2014 Boskova V, Bonhoeffer S, Stadler T. Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models. Plos Computational Biology. 10: e1003913. PMID 25375100 DOI: 10.1371/journal.pcbi.1003913  1
2014 Kouyos RD, Metcalf CJ, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, et al. The path of least resistance: aggressive or moderate treatment? Proceedings. Biological Sciences / the Royal Society. 281: 20140566. PMID 25253451 DOI: 10.1098/rspb.2014.0566  1
2014 Abel zur Wiesch P, Kouyos R, Abel S, Viechtbauer W, Bonhoeffer S. Cycling empirical antibiotic therapy in hospitals: meta-analysis and models. Plos Pathogens. 10: e1004225. PMID 24968123 DOI: 10.1371/journal.ppat.1004225  1
2014 Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, Engelstädter J, Bonhoeffer S. Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1. Plos Genetics. 10: e1004439. PMID 24967626 DOI: 10.1371/journal.pgen.1004439  1
2014 Ocampo PS, 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. Antimicrobial Agents and Chemotherapy. 58: 4573-82. PMID 24867991 DOI: 10.1128/AAC.02463-14  1
2014 Avila D, Keiser O, Egger M, Kouyos R, Böni J, Yerly S, Klimkait T, Vernazza PL, Aubert V, Rauch A, Bonhoeffer S, Günthard HF, Stadler T, Spycher BD. Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland. American Journal of Epidemiology. 179: 1514-25. PMID 24821749 DOI: 10.1093/aje/kwu076  1
2014 Tazzyman SJ, Bonhoeffer S. Plasmids and evolutionary rescue by drug resistance. Evolution; International Journal of Organic Evolution. 68: 2066-78. PMID 24749717 DOI: 10.1111/evo.12423  1
2014 Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science (New York, N.Y.). 343: 1243727. PMID 24653038 DOI: 10.1126/science.1243727  1
2014 Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T. Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Molecular Biology and Evolution. 31: 6-17. PMID 24085839 DOI: 10.1093/molbev/mst172  1
2014 Mikaberidze A, McDonald BA, Bonhoeffer S. Can high-risk fungicides be used in mixtures without selecting for fungicide resistance? Phytopathology. 104: 324-31. PMID 24025048 DOI: 10.1094/PHYTO-07-13-0204-R  1
2013 Hool A, Leventhal GE, Bonhoeffer S. Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution. Epidemics. 5: 174-80. PMID 24267873 DOI: 10.1016/j.epidem.2013.09.002  1
2013 Tazzyman SJ, Bonhoeffer S. Fixation probability of mobile genetic elements such as plasmids. Theoretical Population Biology. 90: 49-55. PMID 24080312 DOI: 10.1016/j.tpb.2013.09.012  1
2013 Oña L, Kouyos RD, Lachmann M, Bonhoeffer S. On the role of resonance in drug failure under HIV treatment interruption. Theoretical Biology & Medical Modelling. 10: 44. PMID 23844869 DOI: 10.1186/1742-4682-10-44  1
2013 Saenz RA, Bonhoeffer S. Nested model reveals potential amplification of an HIV epidemic due to drug resistance. Epidemics. 5: 34-43. PMID 23438429 DOI: 10.1016/j.epidem.2012.11.002  1
2013 Stadler T, Bonhoeffer S. Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120198. PMID 23382421 DOI: 10.1098/rstb.2012.0198  1
2013 Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences of the United States of America. 110: 228-33. PMID 23248286 DOI: 10.1073/pnas.1207965110  1
2013 Moslonka-Lefebvre M, Bonhoeffer S, Alizon S. Corrigendum to "Weighting for sex acts to understand the spread of STI on networks" [J. Theor. Biol. 311 (2012) 46-53] Journal of Theoretical Biology. 317: 429. DOI: 10.1016/j.jtbi.2012.11.009  1
2012 Alexander HK, Bonhoeffer S. Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics. 4: 187-202. PMID 23351371 DOI: 10.1016/j.epidem.2012.10.001  1
2012 Arnoldini M, Mostowy R, Bonhoeffer S, Ackermann M. Evolution of stress response in the face of unreliable environmental signals. Plos Computational Biology. 8: e1002627. PMID 22916000 DOI: 10.1371/journal.pcbi.1002627  1
2012 Moslonka-Lefebvre M, Bonhoeffer S, Alizon S. Weighting for sex acts to understand the spread of STI on networks. Journal of Theoretical Biology. 311: 46-53. PMID 22766360 DOI: 10.1016/j.jtbi.2012.06.031  1
2012 Mostowy R, Kouyos RD, Hoof I, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Ke?mir C, Bonhoeffer S. Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. Plos Computational Biology. 8: e1002525. PMID 22654656 DOI: 10.1371/journal.pcbi.1002525  1
2012 Cadosch D, Bonhoeffer S, Kouyos R. Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV. Journal of the Royal Society, Interface / the Royal Society. 9: 2309-20. PMID 22417909 DOI: 10.1098/rsif.2012.0127  1
2012 Kouyos RD, Leventhal GE, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Bonhoeffer S. Exploring the complexity of the HIV-1 fitness landscape. Plos Genetics. 8: e1002551. PMID 22412384 DOI: 10.1371/journal.pgen.1002551  1
2012 Leventhal GE, Kouyos R, Stadler T, Wyl Vv, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard HF, Bonhoeffer S. Inferring epidemic contact structure from phylogenetic trees. Plos Computational Biology. 8: e1002413. PMID 22412361 DOI: 10.1371/journal.pcbi.1002413  1
2012 Stadler T, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond AJ, Bonhoeffer S. Estimating the basic reproductive number from viral sequence data. Molecular Biology and Evolution. 29: 347-57. PMID 21890480 DOI: 10.1093/molbev/msr217  1
2011 Kouyos RD, von Wyl V, Hinkley T, Petropoulos CJ, Haddad M, Whitcomb JM, Böni J, Yerly S, Cellerai C, Klimkait T, Günthard HF, Bonhoeffer S. Assessing predicted HIV-1 replicative capacity in a clinical setting. Plos Pathogens. 7: e1002321. PMID 22072960 DOI: 10.1371/journal.ppat.1002321  1
2011 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, ... Bonhoeffer S, et al. The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. The Journal of Infectious Diseases. 204: 1095-103. PMID 21881125 DOI: 10.1093/infdis/jir491  1
2011 Kouyos RD, 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. Plos Pathogens. 7: e1001334. PMID 21533212 DOI: 10.1371/journal.ppat.1001334  1
2011 Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb JM, Petropoulos CJ, Bonhoeffer S. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nature Genetics. 43: 487-9. PMID 21441930 DOI: 10.1038/ng.795  1
2011 Kouyos RD, Abel Zur Wiesch P, Bonhoeffer S. Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards. Plos Computational Biology. 7: e1001094. PMID 21390265 DOI: 10.1371/journal.pcbi.1001094  1
2011 zur Wiesch PA, Kouyos R, Engelstädter J, Regoes RR, Bonhoeffer S. Population biological principles of drug-resistance evolution in infectious diseases. The Lancet. Infectious Diseases. 11: 236-47. PMID 21371657 DOI: 10.1016/S1473-3099(10)70264-4  1
2011 Mostowy R, Kouyos RD, Fouchet D, Bonhoeffer S. The role of recombination for the coevolutionary dynamics of HIV and the immune response. Plos One. 6: e16052. PMID 21364750 DOI: 10.1371/journal.pone.0016052  1
2011 Takizawa H, Regoes RR, Boddupalli CS, Bonhoeffer S, Manz MG. Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation. The Journal of Experimental Medicine. 208: 273-84. PMID 21300914 DOI: 10.1084/jem.20101643  1
2011 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, ... ... Bonhoeffer S, et al. Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 52: 532-9. PMID 21220770 DOI: 10.1093/cid/ciq164  1
2010 Martins JZ, Chappey C, Haddad M, Whitcomb JM, Stawiski E, Petropoulos CJ, Bonhoeffer S. Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments. Epidemics. 2: 85-91. PMID 21352778 DOI: 10.1016/j.epidem.2010.03.003  1
2010 Bonhoeffer S, Wiesch PA, Kouyos RD. Rotating antibiotics does not minimize selection for resistance. Mathematical Biosciences and Engineering : Mbe. 7: 919-22. PMID 21077715 DOI: 10.3934/mbe.2010.7.919  1
2010 Alizon S, von Wyl V, Stadler T, Kouyos RD, Yerly S, Hirschel B, Böni J, Shah C, Klimkait T, Furrer H, Rauch A, Vernazza PL, Bernasconi E, Battegay M, Bürgisser P, ... ... Bonhoeffer S, et al. Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. Plos Pathogens. 6: e1001123. PMID 20941398 DOI: 10.1371/journal.ppat.1001123  1
2010 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, ... ... Bonhoeffer S, et al. Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. The Journal of Infectious Diseases. 201: 1488-97. PMID 20384495 DOI: 10.1086/651951  1
2010 Schulz zur Wiesch P, Engelstädter J, Bonhoeffer S. Compensation of fitness costs and reversibility of antibiotic resistance mutations. Antimicrobial Agents and Chemotherapy. 54: 2085-95. PMID 20176903 DOI: 10.1128/AAC.01460-09  1
2010 Mostowy R, Salathé M, Kouyos RD, Bonhoeffer S. On the evolution of sexual reproduction in hosts coevolving with multiple parasites. Evolution; International Journal of Organic Evolution. 64: 1644-56. PMID 20100222 DOI: 10.1111/j.1558-5646.2010.00951.x  1
2009 Bonhoeffer S, Ferguson N, Heesterbeek H, Korber B. Research on infectious disease dynamics. Introduction. Epidemics. 1: 1. PMID 21462555  1
2009 Kouyos RD, Fouchet D, Bonhoeffer S. Recombination and drug resistance in HIV: population dynamics and stochasticity. Epidemics. 1: 58-69. PMID 21352751 DOI: 10.1016/j.epidem.2008.11.001  1
2009 Misevic D, Kouyos RD, Bonhoeffer S. Predicting the evolution of sex on complex fitness landscapes. Plos Computational Biology. 5: e1000510. PMID 19763171 DOI: 10.1371/journal.pcbi.1000510  1
2009 Engelstädter J, Bonhoeffer S. Red Queen dynamics with non-standard fitness interactions. Plos Computational Biology. 5: e1000469. PMID 19680432 DOI: 10.1371/journal.pcbi.1000469  1
2009 Müller V, von Wyl V, Yerly S, Böni J, Klimkait T, Bürgisser P, Ledergerber B, Günthard HF, Bonhoeffer S. African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. Aids (London, England). 23: 1269-76. PMID 19461503 DOI: 10.1097/QAD.0b013e32832d4096  1
2009 Salathé M, Kouyos RD, Bonhoeffer S. On the causes of selection for recombination underlying the red queen hypothesis. The American Naturalist. 174: S31-42. PMID 19441976 DOI: 10.1086/599085  1
2009 Novak M, Pfeiffer T, Ackermann M, Bonhoeffer S. Bacterial growth properties at low optical densities. Antonie Van Leeuwenhoek. 96: 267-74. PMID 19390987 DOI: 10.1007/s10482-009-9342-7  1
2009 von Wyl V, Yerly S, Bürgisser P, Klimkait T, Battegay M, Bernasconi E, Cavassini M, Furrer H, Hirschel B, Vernazza PL, Francioli P, Bonhoeffer S, Ledergerber B, Günthard HF. Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 48: 979-87. PMID 19228107 DOI: 10.1086/597352  1
2009 Magnus C, Rusert P, Bonhoeffer S, Trkola A, Regoes RR. Estimating the stoichiometry of human immunodeficiency virus entry. Journal of Virology. 83: 1523-31. PMID 19019953 DOI: 10.1128/JVI.01764-08  1
2009 Kouyos RD, Salathé M, Otto SP, Bonhoeffer S. The role of epistasis on the evolution of recombination in host-parasite coevolution. Theoretical Population Biology. 75: 1-13. PMID 18957303 DOI: 10.1016/j.tpb.2008.09.007  1
2008 Salathé M, Bonhoeffer S. The effect of opinion clustering on disease outbreaks. Journal of the Royal Society, Interface / the Royal Society. 5: 1505-8. PMID 18713723 DOI: 10.1098/rsif.2008.0271  1
2008 Marconi V, Bonhoeffer S, 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. Journal of Acquired Immune Deficiency Syndromes (1999). 48: 572-6. PMID 18645515 DOI: 10.1097/QAI.0b013e31817bbc4e  1
2008 Salathé M, Kouyos RD, Bonhoeffer S. The state of affairs in the kingdom of the Red Queen. Trends in Ecology & Evolution. 23: 439-45. PMID 18597889 DOI: 10.1016/j.tree.2008.04.010  1
2008 Salathé M, Kouyos RD, Regoes RR, Bonhoeffer S. Rapid parasite adaptation drives selection for high recombination rates. Evolution; International Journal of Organic Evolution. 62: 295-300. PMID 18039325 DOI: 10.1111/j.1558-5646.2007.00265.x  1
2008 Müller V, Bonhoeffer S. Intra-Host Dynamics and Evolution of HIV Infection Origin and Evolution of Viruses. 279-301. DOI: 10.1016/B978-0-12-374153-0.00014-X  1
2008 Bonhoeffer S. Evidence for positive epistasis in HIV-1 (Science (1547)) Science. 320: 746.  1
2007 Kouyos RD, Salathé M, Bonhoeffer S. The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations. Bmc Evolutionary Biology. 7: 211. PMID 17986336 DOI: 10.1186/1471-2148-7-211  1
2007 Débarre F, Bonhoeffer S, Regoes RR. The effect of population structure on the emergence of drug resistance during influenza pandemics. Journal of the Royal Society, Interface / the Royal Society. 4: 893-906. PMID 17609176 DOI: 10.1098/rsif.2007.1126  1
2007 Kouyos RD, Silander OK, Bonhoeffer S. Epistasis between deleterious mutations and the evolution of recombination. Trends in Ecology & Evolution. 22: 308-15. PMID 17337087 DOI: 10.1016/j.tree.2007.02.014  1
2006 Soyer OS, Bonhoeffer S. Evolution of complexity in signaling pathways. Proceedings of the National Academy of Sciences of the United States of America. 103: 16337-42. PMID 17060629 DOI: 10.1073/pnas.0604449103  1
2006 Kouyos RD, Althaus CL, Bonhoeffer S. Stochastic or deterministic: what is the effective population size of HIV-1? Trends in Microbiology. 14: 507-11. PMID 17049239 DOI: 10.1016/j.tim.2006.10.001  1
2006 Brandin E, Thorstensson R, Bonhoeffer S, Albert J. Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy. Journal of Virology. 80: 9861-4. PMID 16973590 DOI: 10.1128/JVI.00394-06  1
2006 Scherer A, Salathé M, Bonhoeffer S. High epitope expression levels increase competition between T cells. Plos Computational Biology. 2: e109. PMID 16933984 DOI: 10.1371/journal.pcbi.0020109  1
2006 Salathé M, Salathé R, Schmid-Hempel P, Bonhoeffer S. Mutation accumulation in space and the maintenance of sexual reproduction. Ecology Letters. 9: 941-6. PMID 16913937 DOI: 10.1111/j.1461-0248.2006.00942.x  1
2006 Novak M, Pfeiffer T, Lenski RE, Sauer U, Bonhoeffer S. Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. The American Naturalist. 168: 242-51. PMID 16874633 DOI: 10.1086/506527  1
2006 Funk GA, Oxenius A, Fischer M, Opravil M, Joos B, Flepp M, Weber R, Günthard HF, 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. Journal of Medical Virology. 78: 1141-6. PMID 16847964 DOI: 10.1002/jmv.20674  1
2006 Regoes RR, Bowen EF, Cope AV, Gor D, Hassan-Walker AF, Prentice HG, Johnson MA, Sweny P, Burroughs AK, Griffiths PD, Bonhoeffer S, Emery VC. Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis. Proceedings. Biological Sciences / the Royal Society. 273: 1961-7. PMID 16822758 DOI: 10.1098/rspb.2006.3506  1
2006 Regoes RR, Bonhoeffer S. Emergence of drug-resistant influenza virus: population dynamical considerations. Science (New York, N.Y.). 312: 389-91. PMID 16627735 DOI: 10.1126/science.1122947  1
2006 Müller V, Ledergerber B, Perrin L, Klimkait T, Furrer H, Telenti A, Bernasconi E, Vernazza P, Günthard HF, Bonhoeffer S. Stable virulence levels in the HIV epidemic of Switzerland over two decades. Aids (London, England). 20: 889-94. PMID 16549973 DOI: 10.1097/01.aids.0000218553.51908.6b  1
2006 Kouyos RD, Otto SP, Bonhoeffer S. Effect of varying epistasis on the evolution of recombination. Genetics. 173: 589-97. PMID 16547114 DOI: 10.1534/genetics.105.053108  1
2006 Soyer OS, Pfeiffer T, Bonhoeffer S. Simulating the evolution of signal transduction pathways. Journal of Theoretical Biology. 241: 223-32. PMID 16403533 DOI: 10.1016/j.jtbi.2005.11.024  1
2006 Salathé M, Ackermann M, Bonhoeffer S. The effect of multifunctionality on the rate of evolution in yeast. Molecular Biology and Evolution. 23: 721-2. PMID 16380406 DOI: 10.1093/molbev/msj086  1
2006 Soyer OS, Salathé M, Bonhoeffer S. Signal transduction networks: topology, response and biochemical processes. Journal of Theoretical Biology. 238: 416-25. PMID 16045939 DOI: 10.1016/j.jtbi.2005.05.030  1
2005 Salathé M, May RM, Bonhoeffer S. The evolution of network topology by selective removal. Journal of the Royal Society, Interface / the Royal Society. 2: 533-6. PMID 16849212 DOI: 10.1098/rsif.2005.0072  1
2005 Althaus CL, Bonhoeffer S. Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1. Journal of Virology. 79: 13572-8. PMID 16227277 DOI: 10.1128/JVI.79.21.13572-13578.2005  1
2005 Brandin E, Broström C, Gille E, Bonhoeffer S, Albert J. Short communication: HIV type 2 dynamics. Aids Research and Human Retroviruses. 21: 608-10. PMID 16060831 DOI: 10.1089/aid.2005.21.608  1
2005 Pfeiffer T, Rutte C, Killingback T, Taborsky M, Bonhoeffer S. Evolution of cooperation by generalized reciprocity. Proceedings. Biological Sciences / the Royal Society. 272: 1115-20. PMID 16024372 DOI: 10.1098/rspb.2004.2988  1
2005 Pfeiffer T, Soyer OS, Bonhoeffer S. The evolution of connectivity in metabolic networks. Plos Biology. 3: e228. PMID 16000019 DOI: 10.1371/journal.pbio.0030228  1
2005 Regoes RR, Bonhoeffer S. The HIV coreceptor switch: a population dynamical perspective. Trends in Microbiology. 13: 269-77. PMID 15936659 DOI: 10.1016/j.tim.2005.04.005  1
2005 Müller V, Bonhoeffer S. Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation. Trends in Genetics : Tig. 21: 264-8. PMID 15851060 DOI: 10.1016/j.tig.2005.03.004  1
2005 Kreft JU, Bonhoeffer S. The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology (Reading, England). 151: 637-41. PMID 15758209 DOI: 10.1099/mic.0.27415-0  1
2005 Scherer A, Bonhoeffer S. Epitope down-modulation as a mechanism for the coexistence of competing T-cells. Journal of Theoretical Biology. 233: 379-90. PMID 15652147 DOI: 10.1016/j.jtbi.2004.10.018  1
2005 Funk GA, Jansen VA, Bonhoeffer S, Killingback T. Spatial models of virus-immune dynamics. Journal of Theoretical Biology. 233: 221-36. PMID 15619362 DOI: 10.1016/j.jtbi.2004.10.004  1
2005 Salathé M, Scherer A, Bonhoeffer S. Neutral drift and polymorphism in gene-for-gene systems Ecology Letters. 8: 925-932. DOI: 10.1111/j.1461-0248.2005.00794.x  1
2004 Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ. Evidence for positive epistasis in HIV-1. Science (New York, N.Y.). 306: 1547-50. PMID 15567861 DOI: 10.1126/science.1101786  1
2004 Ciuffi A, Bleiber G, Muñoz M, Martinez R, Loeuillet C, Rehr M, Fischer M, Günthard HF, 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. Journal of Virology. 78: 10747-54. PMID 15367641 DOI: 10.1128/JVI.78.19.10747-10754.2004  1
2004 Hersberger M, Bonhoeffer S, 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. Clinical and Experimental Immunology. 137: 566-9. PMID 15320907 DOI: 10.1111/j.1365-2249.2004.02574.x  1
2004 Pfeiffer T, Bonhoeffer S. Evolution of cross-feeding in microbial populations. The American Naturalist. 163: E126-35. PMID 15266392 DOI: 10.1086/383593  1
2004 Rusert P, Fischer M, Joos B, Leemann C, Kuster H, Flepp M, Bonhoeffer S, Günthard HF, Trkola A. Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol. Virology. 326: 113-29. PMID 15262500 DOI: 10.1016/j.virol.2004.05.022  1
2004 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 HF. Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point. Blood. 104: 1784-92. PMID 15187026 DOI: 10.1182/blood-2004-01-0251  1
2004 Bretscher MT, Althaus CL, Müller V, Bonhoeffer S. Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 26: 180-8. PMID 14745836 DOI: 10.1002/bies.10386  1
2004 Molinier J, Ries G, Bonhoeffer S, Hohn B. Interchromatid and interhomolog recombination in Arabidopsis thaliana. The Plant Cell. 16: 342-52. PMID 14729918 DOI: 10.1105/tpc.019042  1
2003 Müller V, Bonhoeffer S. Mathematical approaches in the study of viral kinetics and drug resistance in HIV-1 infection. Current Drug Targets. Infectious Disorders. 3: 329-44. PMID 14754433 DOI: 10.2174/1568005033481042  1
2003 Trkola A, Kuster H, Leemann C, Ruprecht C, Joos B, Telenti A, Hirschel B, Weber R, Bonhoeffer S, Günthard HF. Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection. Journal of Virology. 77: 13146-55. PMID 14645571 DOI: 10.1128/JVI.77.24.13146-13155.2003  1
2003 Metzner KJ, Bonhoeffer S, 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. The Journal of Infectious Diseases. 188: 1433-43. PMID 14624368 DOI: 10.1086/379215  1
2003 Bonhoeffer S, Funk GA, Günthard HF, Fischer M, Müller V. Glancing behind virus load variation in HIV-1 infection. Trends in Microbiology. 11: 499-504. PMID 14607066 DOI: 10.1016/j.tim.2003.09.002  1
2003 Bandeira A, Faro J, Müller V, Bonhoeffer S. Quantitative constraints on the scope of negative selection: Robustness and weaknesses [3] (multiple letters) Trends in Immunology. 24: 172-175. PMID 12697445 DOI: 10.1016/S1471-4906(03)00055-3  1
2003 Müller V, Bonhoeffer S. Quantitative constraints on the scope of negative selection. Trends in Immunology. 24: 132-5. PMID 12615208 DOI: 10.1016/S1471-4906(03)00028-0  1
2003 Pfeiffer T, Bonhoeffer S. An evolutionary scenario for the transition to undifferentiated multicellularity. Proceedings of the National Academy of Sciences of the United States of America. 100: 1095-8. PMID 12547910 DOI: 10.1073/pnas.0335420100  1
2003 Brown MJF, Bonhoeffer S. On the evolution of claustral colony founding in ants Evolutionary Ecology Research. 5: 305-313.  1
2002 Bonhoeffer S, Sniegowski P. Virus evolution: the importance of being erroneous. Nature. 420: 367, 369. PMID 12459766 DOI: 10.1038/420367a  1
2002 Bonhoeffer S, Barbour AD, De Boer RJ. Procedures for reliable estimation of viral fitness from time-series data. Proceedings. Biological Sciences / the Royal Society. 269: 1887-93. PMID 12350250 DOI: 10.1098/rspb.2002.2097  1
2002 Regoes R, Bonhoeffer S. HIV coreceptor usage and drug treatment. Journal of Theoretical Biology. 217: 443-57. PMID 12234752 DOI: 10.1006/jtbi.2002.3049  1
2002 Müller V, Vigueras-Gómez JF, Bonhoeffer S. Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection Journal of Virology. 76: 8963-8965. PMID 12163616 DOI: 10.1128/JVI.76.17.8963-8965.2002  1
2002 Regoes RR, Ebert D, Bonhoeffer S. Dose-dependent infection rates of parasites produce the Allee effect in epidemiology Proceedings of the Royal Society B: Biological Sciences. 269: 271-279. PMID 11839196 DOI: 10.1098/rspb.2001.1816  1
2002 Regoes RR, Staprans SI, Feinberg MB, Bonhoeffer S. Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis Journal of Virology. 76: 2573-2578. PMID 11836438 DOI: 10.1128/jvi.76.5.2573-2578.2002  1
2002 Ortiz GM, Hu J, Goldwitz JA, Chandwani R, Larsson M, Bhardwaj N, Bonhoeffer S, 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 Journal of Virology. 76: 411-415. PMID 11739706 DOI: 10.1128/JVI.76.1.411-415.2002  1
2002 Pfeiffer T, Bonhoeffer S. Evolutionary consequences of tradeoffs between yield and rate of ATP production Zeitschrift Fur Physikalische Chemie. 216: 51-63.  1
2001 Betts MR, Ambrozak DR, Douek DC, Bonhoeffer S, 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 Journal of Virology. 75: 11983-11991. PMID 11711588 DOI: 10.1128/JVI.75.24.11983-11991.2001  1
2001 Ortiz GM, Wellons M, Brancato J, Vo HT, Zinn RL, Clarkson DE, Van Loon K, Bonhoeffer S, Miralles GD, Montefiori D, Bartlett JA, Nixon DF. Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects. Proceedings of the National Academy of Sciences of the United States of America. 98: 13288-93. PMID 11687611 DOI: 10.1073/pnas.221452198  1
2001 García F, Plana M, Ortiz GM, Bonhoeffer S, 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. Aids (London, England). 15: F29-40. PMID 11416735 DOI: 10.1097/00002030-200106150-00002  1
2001 Funk GA, Fischer M, Joos B, Opravil M, Günthard HF, Ledergerber B, Bonhoeffer S. Quantification of in vivo replicative capacity of HIV-1 in different compartments of infected cells Journal of Acquired Immune Deficiency Syndromes. 26: 397-404. PMID 11391158  1
2001 Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways Science. 292: 504-507. PMID 11283355  1
2000 Bonhoeffer S, Rembiszewski M, Ortiz GM, Nixon DF. Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection Aids. 14: 2313-2322. PMID 11089619 DOI: 10.1097/00002030-200010200-00012  1
2000 Jin X, Ogg G, Bonhoeffer S, 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 Molecular Medicine (Cambridge, Mass.). 6: 803-809. PMID 11071274  1
2000 Regoes RR, Nowak MA, Bonhoeffer S. Evolution of virulence in a heterogeneous host population Evolution. 54: 64-71. PMID 10937184 DOI: 10.1111/j.0014-3820.2000.tb00008.x  1
2000 Ribeiro RM, Bonhoeffer S. Production of resistant HIV mutants during antiretroviral therapy Proceedings of the National Academy of Sciences of the United States of America. 97: 7681-7686. PMID 10884399 DOI: 10.1073/pnas.97.14.7681  1
2000 Bonhoeffer S, Mohri H, Ho D, Perelson AS. Quantification of cell turnover kinetics using 5-bromo-2'-deoxyuridine Journal of Immunology. 164: 5049-5054. PMID 10799860  1
2000 Binley JM, Clas B, Gettie A, Vesanen M, Montefiori DC, Sawyer L, Booth J, Lewis M, Marx PA, Bonhoeffer S, 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 Virology. 270: 237-249. PMID 10772996 DOI: 10.1006/viro.2000.0254  1
2000 Jin X, Demoitie MA, Donahoe SM, Ogg GS, Bonhoeffer S, Kakimoto WM, Gillespie G, Moss PA, Dyer W, Kurilla MG, Riddell SR, Downie J, Sullivan JS, McMichael AJ, Workman C, et al. High frequency of cytomegalovirus-specific cytotoxic T-effector cells in HLA-A*0201-positive subjects during multiple viral coinfectious Journal of Infectious Diseases. 181: 165-175. PMID 10608763 DOI: 10.1086/315201  1
1999 Ramratnam B, Bonhoeffer S, 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. Lancet (London, England). 354: 1782-5. PMID 10577640 DOI: 10.1016/S0140-6736(99)02035-8  1
1999 Ortiz GM, Nixon DF, Trkola A, Binley J, Jin X, Bonhoeffer S, Kuebler PJ, Donahoe SM, Demoitie MA, Kakimoto WM, Ketas T, Clas B, Heymann JJ, Zhang L, Cao Y, et al. HIV-1-specific immune responses in subjects who temporarily contain virus replication after discontinuation of highly active antiretroviral therapy. The Journal of Clinical Investigation. 104: R13-8. PMID 10491418 DOI: 10.1172/JCI7371  1
1999 Parkin NT, Lie YS, Hellmann N, Markowitz M, Bonhoeffer S, Ho DD, Petropoulos CJ. Phenotypic changes in drug susceptibility associated with failure of human immunodeficiency virus type 1 (HIV-1) triple combination therapy Journal of Infectious Diseases. 180: 865-870. PMID 10438382 DOI: 10.1086/314928  1
1999 Nixon DF, Douek D, Kuebler PJ, Jin X, Vesanen M, Bonhoeffer S, 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 Immunology Letters. 66: 219-228. PMID 10203058 DOI: 10.1016/S0165-2478(98)00162-X  1
1999 Ribeiro RM, Bonhoeffer S. A stochastic model for primary HIV infection: Optimal timing of therapy Aids. 13: 351-357. PMID 10199225 DOI: 10.1097/00002030-199902250-00007  1
1999 Levin BR, Lipsitch M, Bonhoeffer S. Population biology, evolution, and infectious disease: convergence and synthesis. Science (New York, N.Y.). 283: 806-9. PMID 9933155 DOI: 10.1126/science.283.5403.806  1
1999 Zhang L, Dailey PJ, He T, Gettie A, Bonhoeffer S, Perelson AS, Ho DD. Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques Journal of Virology. 73: 855-860. PMID 9847402  1
1999 Ogg GS, Jin X, Bonhoeffer S, 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-specifiic effector cytotoxic T lymphocytes after combination antiretroviral therapy Journal of Virology. 73: 797-800. PMID 9847391  1
1998 Bonhoeffer S. Models of viral kinetics and drug resistance in HIV-1 infection Aids Patient Care and Stds. 12: 769-774. PMID 11362021  1
1998 Connor RI, Montefiori DC, Binley JM, Moore JP, Bonhoeffer S, 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 Journal of Virology. 72: 7501-7509. PMID 9696847  1
1998 Morris L, Binley JM, Clas BA, Bonhoeffer S, 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 Journal of Experimental Medicine. 188: 233-245. PMID 9670036 DOI: 10.1084/jem.188.2.233  1
1998 Ribeiro RM, Bonhoeffer S, Nowak MA. The frequency of resistant mutant virus before antiviral therapy Aids. 12: 461-465. PMID 9543443 DOI: 10.1097/00002030-199805000-00006  1
1998 Ogg GS, Jin X, Bonhoeffer S, 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 Science. 279: 2103-2106. PMID 9516110 DOI: 10.1126/science.279.5359.2103  1
1998 Levin BR, Antia R, Berliner E, Bloland P, Bonhoeffer S, Cohen M, DeRouin T, Fields PI, Jafari H, Jernigan D, Lipsitch M, McGowan JE, Mead P, Nowak M, Porco T, et al. Resistance to antimicrobial chemotherapy: a prescription for research and action. The American Journal of the Medical Sciences. 315: 87-94. PMID 9472907 DOI: 10.1097/00000441-199802000-00004  1
1998 Mohri H, Bonhoeffer S, Monard S, Perelson AS, Ho DD. Rapid turnover of T lymphocytes in SIV-infected rhesus macaques Science. 279: 1223-1227. PMID 9469816 DOI: 10.1126/science.279.5354.1223  1
1998 Levin B, Antia R, Berllner E, Bloland P, Bonhoeffer S, Cohen M, Derouin T, Fields P, Jafari H, Jernigan D, Lipsitch M, Mcgowan J, Nowak M, Porco T, Sykora P, et al. Resistance to Antimicrobial Chemotherapy: A Prescription for Research and Action The American Journal of the Medical Sciences. 315: 87-94. DOI: 10.1016/S0002-9629(15)40282-4  0.6
1997 Bonhoeffer S, Lipsitch M, Levin BR. Evaluating treatment protocols to prevent antibiotic resistance. Proceedings of the National Academy of Sciences of the United States of America. 94: 12106-11. PMID 9342370 DOI: 10.1073/pnas.94.22.12106  1
1997 Bittner B, Bonhoeffer S, Nowak MA. Virus load and antigenic diversity Bulletin of Mathematical Biology. 59: 881-896. PMID 9281903 DOI: 10.1007/BF02459997  1
1997 Bonhoeffer S, May RM, Shaw GM, Nowak MA. Virus dynamics and drug therapy. Proceedings of the National Academy of Sciences of the United States of America. 94: 6971-6. PMID 9192676 DOI: 10.1073/pnas.94.13.6971  1
1997 Bonhoeffer S, Nowak MA. Pre-existence and emergence of drug resistance in HIV-1 infection Proceedings of the Royal Society B: Biological Sciences. 264: 631-637. PMID 9178534 DOI: 10.1098/rspb.1997.0089  1
1997 Bonhoeffer S, Coffin JM, Nowak MA. Human immunodeficiency virus drug therapy and virus load. Journal of Virology. 71: 3275-8. PMID 9060694  1
1997 Nowak MA, Bonhoeffer S, Shaw GM, May RM. Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations. Journal of Theoretical Biology. 184: 203-17. PMID 9059598 DOI: 10.1006/jtbi.1996.0307  1
1996 Bonhoeffer S, Herz AV, Boerlijst MC, Nee S, Nowak MA, May RM. Explaining "linguistic features" of noncoding DNA. Science (New York, N.Y.). 271: 14b-5b. PMID 17798153 DOI: 10.1126/science.271.5245.14b  0.96
1996 Nowak MA, Anderson RM, Boerlijst MC, Bonhoeffer S, May RM, McMichael AJ. HIV-1 evolution and disease progression. Science (New York, N.Y.). 274: 1008-11. PMID 8966557 DOI: 10.1126/science.274.5289.1008  0.96
1996 Bonhoeffer S, Lenski RE, Ebert D. The curse of the pharaoh: the evolution of virulence in pathogens with long living propagules. Proceedings. Biological Sciences / the Royal Society. 263: 715-21. PMID 8763793 DOI: 10.1098/rspb.1996.0107  1
1996 Herz AV, Bonhoeffer S, Anderson RM, May RM, Nowak MA. Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay. Proceedings of the National Academy of Sciences of the United States of America. 93: 7247-51. PMID 8692977 DOI: 10.1073/pnas.93.14.7247  1
1996 Nowak MA, Bonhoeffer S, Hill AM, Boehme R, Thomas HC, McDade H. Viral dynamics in hepatitis B virus infection. Proceedings of the National Academy of Sciences of the United States of America. 93: 4398-402. PMID 8633078 DOI: 10.1073/pnas.93.9.4398  1
1996 Bonhoeffer S, Herz AV, Boerlijst MC, Nee S, Nowak MA, May RM. Explaining "linguistic features" of noncoding DNA. Science (New York, N.Y.). 271: 14-5. PMID 8539587  1
1996 Mukherji A, Rajan V, Slagle JR. Robustness of cooperation. Nature. 379: 125-6. PMID 8538761 DOI: 10.1038/379125b0  1
1996 Boerlijst MC, Bonhoeffer S, Nowak MA. Viral quasi-species and recombination Proceedings of the Royal Society B: Biological Sciences. 263: 1577-1584.  1
1995 Nowak MA, Bonhoeffer S, Loveday C, Balfe P, Semple M, Kaye S, Tenant-Flowers M, Tedder R. HIV results in the frame. Results confirmed Nature. 375: 193. PMID 7746311 DOI: 10.1038/375193a0  1
1995 Bonhoeffer S, Nowak MA. Can live attenuated virus work as post-exposure treatment? Immunology Today. 16: 131-135. PMID 7718085 DOI: 10.1016/0167-5699(95)80129-4  1
1995 Bonhoeffer S, Holmes EC, Nowak MA. Causes of HIV diversity [3] Nature. 376: 125. PMID 7603560 DOI: 10.1038/376125a0  1
1995 Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, Saag MS, Shaw GM. Viral dynamics in human immunodeficiency virus type 1 infection Nature. 373: 117-122. PMID 7529365 DOI: 10.1038/373117a0  1
1995 Nowak MA, Bonhoeffer S, Loveday C, Balfe P, Semple M, Kaye S, Tenant-Flowers M, Tedder R. Results confirmed [3] Nature. 375: 193.  1
1995 Nowak MA, Bonhoeffer S, Loveday C, Balfe P, Semple M, Kaye S, Tenant-Flowers M, Tedder R. HIV results in the frame [1] Nature. 375: 193.  1
1994 Nowak MA, Bonhoeffer S, May RM. Spatial games and the maintenance of cooperation. Proceedings of the National Academy of Sciences of the United States of America. 91: 4877-81. PMID 8197150 DOI: 10.1073/pnas.91.11.4877  1
1994 Bonhoeffer S, Nowak MA. Intra-host versus inter-host selection: Viral strategies of immune function impairment Proceedings of the National Academy of Sciences of the United States of America. 91: 8062-8066. PMID 8058757 DOI: 10.1073/pnas.91.17.8062  1
1994 Bonhoeffer S, Nowak MA. Mutation and the evolution of virulence Proceedings of the Royal Society B: Biological Sciences. 258: 133-140. DOI: 10.1098/rspb.1994.0153  1
1993 Bonhoeffer S, McCaskill JS, Stadler PF, Schuster P. RNA multi-structure landscapes - A study based on temperature dependent partition functions European Biophysics Journal. 22: 13-24. PMID 7685689 DOI: 10.1007/BF00205808  1
1993 Bonhoeffer S, Stadler PF. Error thresholds on correlated fitness landscapes Journal of Theoretical Biology. 164: 359-372. DOI: 10.1006/jtbi.1993.1160  1
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