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Publications of all group members

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2012

Refardt, D
Real-time quantitative PCR to discriminate and quantify lambdoid bacteriophages of Escherichia coli K-12
Bacteriophage (2012) 2:-
Abstract

Refardt, D
Combining forces to target bacteria (invited commentary)
Evolutionary Applications (2012) --:-----
Abstract

Refardt, D, Ebert, D
The impact of infection on host competition and its relationship to parasite persistence in a Daphnia microparasite system
Evolutionary Ecology (2012) 26:95-107
Abstract Request reprint

Stadler, T, Degnan, J
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
ALGORITHMS FOR MOLECULAR BIOLOGY (2012) in press:-

Bokma, F, van den Brink, V, Stadler, T
Unexpectedly high extinction rate in recent hominins
EVOLUTION (2012) doi:10.1111/j.1558-5646.2012.01660.x:-

Cusimano, N, Stadler, T, Renner, S
A new method for handling missing species in diversification analysis applicable to randomly or non-randomly sampled phylogenies
SYSTEMATIC BIOLOGY (2012) doi:10.1093/sysbio/sys031:-

Leventhal, G, Kouyos, R, Stadler, T, von Wyl, V, Yerly, S, Boni, J, Cellerai, C, Klimkait, T, Gunthard, HF, Bonhoeffer, S
Inferring Epidemic Contact Structure from Phylogenetic Trees
PLOS COMPUTATIONAL BIOLOGY (2012) 8:-

Etienne, RS, Haegeman, B, Stadler, T, Aze, T, Pearson, PN, Purvis, A, Phillimore, AB
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012) 279:1300-1309

Mooers, A, Gascuel, O, Stadler, T, Li, H, Steel, M
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity
SYSTEMATIC BIOLOGY (2012) 61:195-203

Stadler, T, Steel, M
Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models
JOURNAL OF THEORETICAL BIOLOGY (2012) 297:33-40

Degnan, JH, Rosenberg, NA, Stadler, T
The probability distribution of ranked gene trees on a species tree
MATHEMATICAL BIOSCIENCES (2012) 235:45-55
Abstract

Stadler, T, Kouyos, R, von Wyl, V, Yerly, S, Boni, J, Burgisser, P, Klimkait, T, Joos, B, Rieder, P, Xie, D, Gunthard, HF, Drummond, AJ, Bonhoeffer, S
Estimating the Basic Reproductive Number from Viral Sequence Data
MOLECULAR BIOLOGY AND EVOLUTION (2012) 29:347-357
Abstract

2011

von Wyl, V, Kouyos, RD, Yerly, S, Boni, J, Shah, C, Burgisser, P, Klimkait, T, Weber, R, Hirschel, B, Cavassini, M, Staehelin, C, Battegay, M, Vernazza, PL, Bernasconi, E, Ledergerber, B, Bonhoeffer, S, Gunthard, HF
The Role of Migration and Domestic Transmission in the Spread of HIV-1 Non-B Subtypes in Switzerland
JOURNAL OF INFECTIOUS DISEASES (2011) 204:1095-1103
Abstract

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 (2011) 43:487-+
Abstract Request reprint
Supplementary Material

Kouyos, RD, zur Wiesch, PA, 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 (2011) 7:-
Abstract Request reprint

Kouyos, RD, zur Wiesch, PA, Bonhoeffer, S
Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards
PLOS COMPUTATIONAL BIOLOGY (2011) 7:-
Abstract Request reprint

zur Wiesch, PA, Kouyos, R, Engelstadter, J, Regoes, RR, Bonhoeffer, S
Population biological principles of drug-resistance evolution in infectious diseases
LANCET INFECTIOUS DISEASES (2011) 11:236-247
Abstract Request reprint

Mostowy, R, Kouyos, RD, Fouchet, D, Bonhoeffer, S
The Role of Recombination for the Coevolutionary Dynamics of HIV and the Immune Response
PLOS ONE (2011) 6:-
Abstract Request reprint

Takizawa, H, Regoes, RR, Boddupalli, CS, Bonhoeffer, S, Manz, MG
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation
JOURNAL OF EXPERIMENTAL MEDICINE (2011) 208:273-284
Abstract Request reprint

Kouyos, RD, von Wyl, V, Yerly, S, Boni, J, Rieder, P, Joos, B, Taffe, P, Shah, C, Burgisser, P, Klimkait, T, Weber, R, Hirschel, B, Cavassini, M, Rauch, A, Battegay, M, Vernazza, PL, Bernasconi, E, Ledergerber, B, Bonhoeffer, S, Gunthard, HF
Ambiguous Nucleotide Calls From Population-based Sequencing of HIV-1 are a Marker for Viral Diversity and the Age of Infection
CLINICAL INFECTIOUS DISEASES (2011) 52:532-539
Abstract Request reprint

Engelstadter, J, Sandrock, C, Vorburger, C
Contagious parthenogenesis, automixis, and a sex determination meltdown
Evolution (2011) in press:-
Abstract

Magnus, C, Regoes, RR
Restricted occupancy models for neutralization of HIV virions and populations
JOURNAL OF THEORETICAL BIOLOGY (2011) 283:192-202
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Rusert, P, Krarup, A, Magnus, C, Brandenberg, OF, Weber, J, Ehlert, AK, Regoes, RR, Guenthard, HF, Trkola, A
Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies
JOURNAL OF EXPERIMENTAL MEDICINE (2011) 208:1419-1433
Abstract Request reprint

Mostowy, R, Engelstadter, J
The impact of environmental change on host-parasite coevolutionary dynamics
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011) 278:2283-2292
Abstract Request reprint

Refardt, D
Within-host competition determines reproductive success of temperate bacteriophages
ISME Journal (2011) 5:1451-1460
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Supplementary Material

Haag, KL, Larsson, JIR, Refardt, D, Ebert, D
Cytological and molecular description of Hamiltosporidium tvaerminnensis gen. et sp. nov., a microsporidian parasite of Daphnia magna, and establishment of Hamiltosporidium magnivora comb. nov.
Parasitology (2011) 138:447-462
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Graw, F, Richter, K, Oxenius, A, Regoes, RR
Comparison of cytotoxic T lymphocyte efficacy in acute and persistent lymphocytic choriomeningitis virus infection
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011) XXX:XXX-XXX
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Alizon, S, Luciani, F, Regoes, RR
Epidemiological and clinical consequences of within-host evolution
TRENDS IN MICROBIOLOGY (2011) 19:24-32
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Johnson, PLF, Kochin, BF, McAfee, MS, Stromnes, IM, Regoes, RR, Ahmed, R, Blattman, JN, Antia, R
Vaccination Alters the Balance between Protective Immunity, Exhaustion, Escape, and Death in Chronic Infections
JOURNAL OF VIROLOGY (2011) 85:5565-5570
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Ruprecht, CR, Krarup, A, Reynell, L, Mann, AM, Brandenberg, OF, Berlinger, L, Abela, IA, Regoes, RR, Gunthard, HF, Rusert, P, Trkola, A
MPER-specific antibodies induce gp120 shedding and irreversibly neutralize HIV-1
JOURNAL OF EXPERIMENTAL MEDICINE (2011) 208:439-454
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Meredith, RW, Janecka, JE, Gatesy, J, Ryder, OA, Fisher, CA, Teeling, EC, Goodbla, A, Eizirik, E, Simao, TLL, Stadler, T, Rabosky, DL, Honeycutt, RL, Flynn, JJ, Ingram, CM, Steiner, C, Williams, TL, Robinson, TJ, Burk-Herrick, A, Westerman, M, Ayoub, NA, Springer, MS, Murphy, WJ
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
SCIENCE (2011) 334:521-524
Abstract

Stadler, T
Simulating Trees with a Fixed Number of Extant Species
SYSTEMATIC BIOLOGY (2011) 60:676-684
Abstract

Stadler, T
Inferring speciation and extinction processes from extant species data
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011) 108:16145-16146

Hohna, S, Stadler, T, Ronquist, F, Britton, T
Inferring Speciation and Extinction Rates under Different Sampling Schemes
MOLECULAR BIOLOGY AND EVOLUTION (2011) 28:2577-2589
Abstract

Stadler, T
Inferring Epidemiological Parameters on the Basis of Allele Frequencies
GENETICS (2011) 188:663-672
Abstract

Stadler, T
Mammalian phylogeny reveals recent diversification rate shifts
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011) 108:6187-6192
Abstract

Hoorn, C, Wesselingh, FP, Ter Steege, H, Bermudez, MA, Mora, A, Sevink, J, Sanmartin, I, Sanchez-Meseguer, A, Anderson, CL, Figueiredo, JP, Jaramillo, C, Riff, D, Negri, FR, Hooghiemstra, H, Lundberg, J, Stadler, T, Sarkinen, T, Antonelli, A
Origins of Biodiversity Response
SCIENCE (2011) 331:399-400

2010

Takizawa, H, Boddupalli, CS, Regoes, RR, Bonhoeffer, S, Manz, MG
Hematopoietic Stem Cell Cycling Dynamics In Steady State and Upon Hematopoietic Challenge
BLOOD (2010) 116:253-253

Bonhoeffer, S, zur Wiesch, PA, Kouyos, RD
ROTATING ANTIBIOTICS DOES NOT MINIMIZE SELECTION FOR RESISTANCE
MATHEMATICAL BIOSCIENCES AND ENGINEERING (2010) 7:919-922 Request reprint

Alizon, S, von Wyl, V, Stadler, T, Kouyos, RD, Yerly, S, Hirschel, B, Boni, J, Shah, C, Klimkait, T, Furrer, H, Rauch, A, Vernazza, PL, Bernasconi, E, Battegay, M, Burgisser, P, Telenti, A, Gunthard, HF, Bonhoeffer, S
Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load
PLOS PATHOGENS (2010) 6:-
Abstract Request reprint

Mostowy, R, Salathe, M, Kouyos, RD, Bonhoeffer, S
ON THE EVOLUTION OF SEXUAL REPRODUCTION IN HOSTS COEVOLVING WITH MULTIPLE PARASITES
EVOLUTION (2010) 64:1644-1656
Abstract Request reprint

Kouyos, RD, von Wyl, V, Yerly, S, Boni, J, Taffe, P, Shah, C, Burgisser, P, Klimkait, T, Weber, R, Hirschel, B, Cavassini, M, Furrer, H, Battegay, M, Vernazza, PL, Bernasconi, E, Rickenbach, M, Ledergerber, B, Bonhoeffer, S, Gunthard, HF
Molecular Epidemiology Reveals Long-Term Changes in HIV Type 1 Subtype B Transmission in Switzerland
JOURNAL OF INFECTIOUS DISEASES (2010) 201:1488-1497
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zur Wiesch, PS, Engelstadter, J, Bonhoeffer, S
Compensation of Fitness Costs and Reversibility of Antibiotic Resistance Mutations
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2010) 54:2085-2095
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Kouyos, RD, von Wyl, V, Yerly, S, Boni, J, Rieder, P, Joos, B, Taffe, P, Shah, C, Burgisser, P, Klimkait, T, Weber, R, Hirschel, B, Cavassini, M, Rauch, A, Battegay, M, Vernazza, PL, Bernasconi, E, Ledergerber, B, Bonhoeffer, S, Gunthard, HF
Ambiguity in population-based sequencing of HIV-1 as a marker for the age of HIV infection
ANTIVIRAL THERAPY (2010) 15:A158-A158

Engelstadter, J
The effective size of populations infected with cytoplasmic sex-ratio distorters
Genetics (2010) 186:309-320
Abstract

Nor, I, Hermelin, D., Charlat, S., Engelstadter, J, Reuter, M., Duron, O., Sagott, M.-F.
Mod/Resc parsimony inference
Combinatorial Pattern Matching. Lecture Notes in Computer Science (2010) 6129:202-213
Abstract

Schulz zur Wiesch, P, Engelstadter, J, Bonhoeffer, S
Compensation of Fitness Costs and Reversibility of Antibiotic Resistance Mutations
Antimicrobial Agents and Chemotherapy (2010) 54:2085-2095
Abstract Request reprint

Graw, F, Magnus, C, Regoes, RR
Theoretical analysis of the evolution of immune memory
BMC EVOLUTIONARY BIOLOGY (2010) 10:-
Abstract Request reprint

Magnus, C, Regoes, RR
Estimating the Stoichiometry of HIV Neutralization
PLOS COMPUTATIONAL BIOLOGY (2010) 6:e1000713-
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Refardt, D, Rainey, PB
Tuning a genetic switch: Experimental evolution and natural variation of prophage induction
Evolution (2010) 64:1086-1097
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Supplementary Material

Regoes, RR
Population genetics meets cancer genomics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010) 107:18241-18242
Abstract Request reprint

Kouyos, RD, Gordon, SN, Staprans, SI, Silvestri, G, Regoes, RR
Similar Impact of CD8+T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys
PLOS COMPUTATIONAL BIOLOGY (2010) 6:-
Abstract Request reprint

Stadler, T
Sampling-through-time in birth-death trees
JOURNAL OF THEORETICAL BIOLOGY (2010) 267:396-404
Abstract

Hoorn, C, Wesselingh, FP, ter Steege, H, Bermudez, MA, Mora, A, Sevink, J, Sanmartin, I, Sanchez-Meseguer, A, Anderson, CL, Figueiredo, JP, Jaramillo, C, Riff, D, Negri, FR, Hooghiemstra, H, Lundberg, J, Stadler, T, Sarkinen, T, Antonelli, A
Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity
SCIENCE (2010) 330:927-931
Abstract

Linz, S, Semple, C, Stadler, T
Analyzing and reconstructing reticulation networks under timing constraints
JOURNAL OF MATHEMATICAL BIOLOGY (2010) 61:715-737
Abstract

Hartmann, K, Wong, D, Stadler, T
Sampling Trees from Evolutionary Models
SYSTEMATIC BIOLOGY (2010) 59:465-476
Abstract

Trajanovski, S, Albrecht, C, Schreiber, K, Schultheiss, R, Stadler, T, Benke, M, Wilke, T
Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus Dina (Hirudinea: Erpobdellidae) in Lake Ohrid
BIOGEOSCIENCES (2010) 7:3387-3402
Abstract

2009

Novak, M, Pfeiffer, T, Ackermann, M, Bonhoeffer, S
Bacterial growth properties at low optical densities
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2009) 96:267-274
Abstract Request reprint

Misevic, D, Kouyos, RD, Bonhoeffer, S
Predicting the Evolution of Sex on Complex Fitness Landscapes
PLOS COMPUTATIONAL BIOLOGY (2009) 5:-
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Engelstadter, J, Bonhoeffer, S
Red Queen Dynamics with Non-Standard Fitness Interactions
PLOS COMPUTATIONAL BIOLOGY (2009) 5:-
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Salathe, M, Kouyos, RD, Bonhoeffer, S
On the Causes of Selection for Recombination Underlying the Red Queen Hypothesis
AMERICAN NATURALIST (2009) 174:S31-S42
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Muller, V, von Wyl, V, Yerly, S, Boni, J, Klimkait, T, Burgisser, P, Ledergerber, B, Gunthard, HF, Bonhoeffer, S
African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study
AIDS (2009) 23:1269-1276
Abstract

Magnus, C, Rusert, P, Bonhoeffer, S, Trkola, A, Regoes, RR
Estimating the Stoichiometry of Human Immunodeficiency Virus Entry
JOURNAL OF VIROLOGY (2009) 83:1523-1531
Abstract Request reprint

Kouyos, RD, Salathe, M, Otto, SP, Bonhoeffer, S
The role of epistasis on the evolution of recombination in host-parasite coevolution
THEORETICAL POPULATION BIOLOGY (2009) 75:1-13
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Engelstadter, J, Hurst, GDD
The ecology and evolution of microbes that manipulate host reproduction
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS (2009) 140:127-149
Abstract

Engelstadter, J, Telschow, A
Cytoplasmic incompatibility and host population structure
HEREDITY (2009) 103:196-207
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Engelstadter, J, Bonhoeffer, S
Red Queen Dynamics with Non-Standard Fitness Interactions
PLOS COMPUTATIONAL BIOLOGY (2009) 5:e1000469-
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Engelstadter, J, Hurst, GDD
What Use Are Male Hosts? The Dynamics of Maternally Inherited Bacteria Showing Sexual Transmission or Male Killing
AMERICAN NATURALIST (2009) 173:E159-E170
Abstract

Yeaman, S, Guillaume, F
Predicting adaptation under migration load: the role of genetic skew
Evolution (2009) 63:2926-2938
Abstract

Whitlock, MC, Guillaume, F
Testing for Spatially Divergent Selection: Comparing Q(ST) to F(ST)
Genetics (2009) 183:1055-1063
Abstract

Guillaume, F, Perrin, N
Inbreeding Load, Bet Hedging, and the Evolution of Sex-Biased Dispersal
American Naturalist (2009) 173:536-541
Abstract

Jaquiery, J, Guillaume, F, Perrin, N
Predicting the Deleterious Effects of Mutation Load in Fragmented Populations
Conservation Biology (2009) 23:207-218
Abstract

Graw, F , Regoes, RR
Investigating CTL mediated killing with a 3D cellular automaton
PLOS COMPUTATIONAL BIOLOGY (2009) 5:e1000466-
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Stadler, T
On incomplete sampling under birth-death models and connections to the sampling-based coalescent
JOURNAL OF THEORETICAL BIOLOGY (2009) 261:58-66
Abstract

Ford, D, Matsen, FA, Stadler, T
A Method for Investigating Relative Timing Information on Phylogenetic Trees
SYSTEMATIC BIOLOGY (2009) 58:167-183
Abstract

2008

Salathe, M, Bonhoeffer, S
The effect of opinion clustering on disease outbreaks
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2008) 5:1505-1508
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Salathe, M, Kouyos, RD, Bonhoeffer, S
The state of affairs in the kingdom of the Red Queen
TRENDS IN ECOLOGY & EVOLUTION (2008) 23:439-445
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Salathe, M, Kouyos, RD, Regoes, RR, Bonhoeffer, S
Rapid parasite adaptation drives selection for high recombination rates
EVOLUTION (2008) 62:295-300
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Engelstadter, J
Constraints on the evolution of asexual reproduction
BIOESSAYS (2008) 30:1138-1150
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Engelstadter, J, Telschow, A, Yamamura, N
Coexistence of cytoplasmic incompatibility and male-killing-inducing endosymbionts, and their impact on host gene flow
THEORETICAL POPULATION BIOLOGY (2008) 73:125-133
Abstract

Duron, O, Hurst, GDD, Hornett, EA, Josling, JA, Engelstadter, J
High incidence of the maternally inherited bacterium Cardinium in spiders
MOLECULAR ECOLOGY (2008) 17:1427-1437
Abstract

Engelstadter, J, Haig, D
Sexual antagonism and the evolution of X chromosome inactivation
EVOLUTION (2008) 62:2097-2104
Abstract

Engelstadter, J
Muller's Ratchet and the Degeneration of Y Chromosomes: A Simulation Study
GENETICS (2008) 180:957-967
Abstract

Neuenschwander, S, Hospital, F, Guillaume, F, Goudet, J
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Bioinformatics (2008) 24:1552-1553
Abstract

Reuter, M, Lehmann, L, Guillaume, F
The spread of incompatibility-inducing parasites in sub-divided host populations
BMC Evolutionary Biology (2008) 8:-
Abstract

Refardt, D, Decaestecker, E, Johnson, PTJ, Vávra, J
Morphology, molecular phylogeny, and ecology of Binucleata daphniae n. g., n. sp (Fungi: Microsporidia), a parasite of Daphnia magna Straus, 1820 (Crustacea: Branchiopoda)
Journal of Eukaryotic Microbiology (2008) 55:393-408
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Fouchet, D, Regoes, R
A Population Dynamics Analysis of the Interaction between Adaptive Regulatory T Cells and Antigen Presenting Cells
PLoS ONE (2008) 3:e2306-
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2007

Kouyos, RD, Salathe, M, Bonhoeffer, S
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations
BMC EVOLUTIONARY BIOLOGY (2007) 7:-
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Debarre, 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 (2007) 4:893-906
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Kouyos, RD, Silander, OK, Bonhoeffer, S
Epistasis between deleterious mutations and the evolution of recombination
TRENDS IN ECOLOGY & EVOLUTION (2007) 22:308-315
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Engelstadter, J, Hurst, GDD
The impact of male-killing bacteria on host evolutionary processes
GENETICS (2007) 175:245-254
Abstract

Engelstadter, J, Hammerstein, P, Hurst, GDD
The evolution of endosymbiont density in doubly infected host species
JOURNAL OF EVOLUTIONARY BIOLOGY (2007) 20:685-695
Abstract

Guillaume, F, Whitlock, MC
Effects of migration on the genetic covariance matrix
Evolution (2007) 61:2398-2409
Abstract

Refardt, D, Ebert, D
Inference of parasite local adaptation using two different fitness components
Journal of Evolutionary Biology (2007) 20:921-929
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Refardt, D, Mouton, L
Reverse arrangement of rRNA subunits in the microsporidium Glugoides intestinalis
Journal of Eukaryotic Microbiology (2007) 54:83-85
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Regoes, RR, Yates, A, Antia, R
Mathematical models of cytotoxic T-lymphocyte killing
IMMUNOLOGY AND CELL BIOLOGY (2007) 85:274-279
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Regoes, RR, Barber, DL, Ahmed, R, Antia, R
Estimation of the rate of killing by cytotoxic T lymphocytes in vivo
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007) 104:1599-1603
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2006

Kouyos, RD, Althaus, CL, Bonhoeffer, S
Stochastic or deterministic: what is the effective population size of HIV-1?
TRENDS IN MICROBIOLOGY (2006) 14:507-511
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Soyer, OS, Bonhoeffer, S
Evolution of complexity in signaling pathways
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006) 103:16337-16342
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Funk, GA, Oxenius, A, Fischer, M, Opravil, M, Joos, B, Flepp, M, Weber, R, Gunthard, HF, Bonhoeffer, S
HIV replication elicits little cytopathic effects little cytopathic effects in vivo: Analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death
JOURNAL OF MEDICAL VIROLOGY (2006) 78:1141-1146
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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 OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006) 273:1961-1967
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Salathe, M, Salathe, R, Schmid-Hempel, P, Bonhoeffer, S
Mutation accumulation in space and the maintenance of sexual reproduction
ECOLOGY LETTERS (2006) 9:941-946
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Scherer, A, Salathe, M, Bonhoeffer, S
High epitope expression levels increase competition between T cells
PLOS COMPUTATIONAL BIOLOGY (2006) 2:948-958
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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
AMERICAN NATURALIST (2006) 168:242-251
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Soyer, OS, Pfeiffer, T, Bonhoeffer, S
Simulating the evolution of signal transduction pathways
JOURNAL OF THEORETICAL BIOLOGY (2006) 241:223-232
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Kouyos, RD, Otto, SP, Bonhoeffer, S
Effect of varying epistasis on the evolution of recombination
GENETICS (2006) 173:589-597
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Bonhoeffer, S, Chappey, C, Parkin, NT, Whitcomb, JM, Petropoulos, CJ
Response to comment on "Evidence for positive epistasis in HIV-1''
SCIENCE (2006) 312:- Request reprint

Regoes, RR, Bonhoeffer, S
Emergence of drug-resistant influenza virus: Population dynamical considerations
SCIENCE (2006) 312:389-391
Abstract Request reprint
Supplementary Material Programs

Muller, V, Ledergerber, B, Perrin, L, Klimkait, T, Furrer, H, Telenti, A, Bernasconi, E, Vernazza, P, Gunthard, HF, Gunthard, F, Bonhoeffer, S
Stable virulence levels in the HIV epidemic of Switzerland over two decades
AIDS (2006) 20:889-894
Abstract Request reprint

Salathe, M, Ackermann, M, Bonhoeffer, S
The effect of multifunctionality on the rate of evolution in yeast
MOLECULAR BIOLOGY AND EVOLUTION (2006) 23:721-722
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Soyer, OS, Salathe, M, Bonhoeffer, S
Signal transduction networks: Topology, response and biochemical processes
JOURNAL OF THEORETICAL BIOLOGY (2006) 238:416-425
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Guillaume, F, Rougemont, J
Nemo: an evolutionary and population genetics programming framework
Bioinformatics (2006) 22:2556-2557
Abstract

Guillaume, F, Perrin, N
Joint evolution of dispersal and inbreeding load
Genetics (2006) 173:497-509
Abstract

Bull, JJ, Regoes, RR
Pharmacodynarnics of non-replicating viruses, bacteriocins and lysins
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006) 273:2703-2712
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Yates, A, Antia, R, Regoes, RR
How do pathogen evolution and host heterogeneity interact in disease emergence?
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006) 273:3075-3083
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2005

Salathe, M, May, RM, Bonhoeffer, S
The evolution of network topology by selective removal
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2005) 2:533-536
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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 (2005) 79:13572-13578
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Salathe, M, Scherer, A, Bonhoeffer, S
Neutral drift and polymorphism in gene-for-gene systems
ECOLOGY LETTERS (2005) 8:925-932
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Pfeiffer, T, Soyer, OS, Bonhoeffer, S
The evolution of connectivity in metabolic networks
PLOS BIOLOGY (2005) 3:1269-1275
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Pfeiffer, T, Rutte, C, Killingback, T, Taborsky, M, Bonhoeffer, S
Evolution of cooperation by generalized reciprocity
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2005) 272:1115-1120
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Regoes, RR, Bonhoeffer, S
The HIV coreceptor switch: a population dynamical perspective
TRENDS IN MICROBIOLOGY (2005) 13:269-277
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Supplementary Material Programs

Muller, V, Bonhoeffer, S
Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation
TRENDS IN GENETICS (2005) 21:264-268
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Scherer, A, Bonhoeffer, S
Epitope down-modulation as a mechanism for the coexistence of competing T-cells
JOURNAL OF THEORETICAL BIOLOGY (2005) 233:379-390
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Funk, GA, Jansen, VAA, Bonhoeffer, S, Killingback, T
Spatial models of virus-immune dynamics
JOURNAL OF THEORETICAL BIOLOGY (2005) 233:221-236
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2004

Bonhoeffer, S, Chappey, C, Parkin, NT, Whitcomb, JM, Petropoulos, CJ
Evidence for positive epistasis in HIV-1
SCIENCE (2004) 306:1547-1550
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Supplementary Material

Ciuffi, A, Bleiber, G, Munoz, M, Martinez, R, Loeuillet, C, Rehr, M, Fischer, M, Gunthard, 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 (2004) 78:10747-10754
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Trkola, A, Kuster, H, Leemann, C, Oxenius, A, Fagard, C, Furrer, H, Battegay, M, Vernazza, P, Bernasconi, E, Weber, R, Hirschel, B, Bonhoeffer, S, Gunthard, HF
Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point
BLOOD (2004) 104:1784-1792
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Hersberger, M, Bonhoeffer, S, Rampini, SK, Opravil, M, Marti-Jaun, J, Telenti, A, Hanseler, E, Ledergerber, B, Speck, RF
CCTTT-repeat polymorphism of the inducible nitric oxide synthase is not associated with HIV pathogenesis
CLINICAL AND EXPERIMENTAL IMMUNOLOGY (2004) 137:566-569
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Rusert, P, Fischer, M, Joos, B, Leemann, C, Kuster, H, Flepp, M, Bonhoeffer, S, Gunthard, HF, Trkola, A
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol
VIROLOGY (2004) 326:113-129
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Petropoulos, CJ, Huang, W, Toma, J, Fransen, S, Bonhoeffer, S, Whitcomb, JM
Resistance to HIV-1 entry inhibitors may occur by multiple molecular mechanisms
ANTIVIRAL THERAPY (2004) 9:U35-U35

Pfeiffer, T, Bonhoeffer, S
Evolution of cross-feeding in microbial populations
AMERICAN NATURALIST (2004) 163:E126-E135
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Bretscher, MT, Althaus, CL, Muller, V, Bonhoeffer, S
Recombination in HIV and the evolution of drug resistance: for better or for worse?
BIOESSAYS (2004) 26:180-188
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Molinier, J, Ries, G, Bonhoeffer, S, Hohn, B
Interchromatid and interhomolog recombination in Arabidopsis thaliana
PLANT CELL (2004) 16:342-352
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Giorgi, MS, Arlettaz, R, Guillaume, F, Nussle, S, Ossola, C, Vogel, P, Christe, P
Causal mechanisms underlying host specificity in bat ectoparasites
Oecologia (2004) 138:648-654
Abstract

Mucklow, PT, Vizoso, DB, Jensen, KH, Refardt, D, Ebert, D
Variation in phenoloxidase activity and its relation to parasite resistance within and between populations of Daphnia magna
Proceedings of the Royal Society B - Biological Sciences (2004) 271:1175-1183
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Canning, EU, Refardt, D, Vossbrinck, CR, Okamura, B, Curry, A
Correction for genus Bryonosema (Microsporidia, Pseudonosematidae)
European Journal of Protistology (2004) 40:69-69 Request reprint

2003

Trkola, A, Kuster, H, Leemann, C, Ruprecht, C, Joos, B, Telenti, A, Hirschel, B, Weber, R, Bonhoeffer, S, Gunthard, HF
Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection
JOURNAL OF VIROLOGY (2003) 77:13146-13155
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Metzner, KJ, Bonhoeffer, S, Fischer, M, Karanicolas, R, Allers, K, Joos, B, Weber, R, Hirschel, B, Kostrikis, LG, Gunthard, HF
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions
JOURNAL OF INFECTIOUS DISEASES (2003) 188:1433-1443
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Bonhoeffer, S, Funk, GA, Gunthard, HF, Fischer, M, Muller, V
Glancing behind virus load variation in HIV-1 infection
TRENDS IN MICROBIOLOGY (2003) 11:499-504
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Gunthard, H, Joos, B, Kuster, H, Fischer, M, Leemann, C, Boni, J, Oxenius, A, Fagard, C, Hirschel, B, Wong, J, Phillips, R, Bonhoeffer, S, Weber, R, Trkola, A
Virus characteristics predict viraemia control after cessation of antiretroviral therapy
ANTIVIRAL THERAPY (2003) 8:U63-U63

Muller, V, Bonhoeffer, S
Response to Bandeira and Faro: Closing the circle of constraints
TRENDS IN IMMUNOLOGY (2003) 24:173-175 Request reprint

Muller, V, Bonhoeffer, S
Quantitative constraints on the scope of negative selection.
TRENDS IN IMMUNOLOGY (2003) 24:132-135
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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 (2003) 100:1095-1098
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Brown, MJF, Bonhoeffer, S
On the evolution of claustral colony founding in ants
EVOLUTIONARY ECOLOGY RESEARCH (2003) 5:305-313
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Regoes, RR, Hottinger, JW, Sygnarski, L, Ebert, D
The infection rate of Daphnia magna by Pasteuria ramosa conforms with the mass-action principle
EPIDEMIOLOGY AND INFECTION (2003) 131:957-966
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Antia, R, Regoes, RR, Koella, JC, Bergstrom, CT
The role of evolution in the emergence of infectious diseases
NATURE (2003) 426:658-661
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2002

Bonhoeffer, S, Sniegowski, P
Virus evolution - The importance of being erroneous
NATURE (2002) 420:367-+ Request reprint

Bonhoeffer, S, Barbour, AD, De Boer, RJ
Procedures for reliable estimation of viral fitness from time-series data
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (2002) 269:1887-1893
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Muller, V, Vigueras-Gomez, JF, Bonhoeffer, S
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection
JOURNAL OF VIROLOGY (2002) 76:8963-8965
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Regoes, RR, Bonhoeffer, S
HIV coreceptor usage and drug treatment
JOURNAL OF THEORETICAL BIOLOGY (2002) 217:443-457
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Regoes, RR, Staprans, SI, Feinberg, MB, Bonhoeffer, S
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis
JOURNAL OF VIROLOGY (2002) 76:2573-2578
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Regoes, RR, Ebert, D, Bonhoeffer, S
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (2002) 269:271-279
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Ortiz, GM, Hu, J, Goldwitz, JA, Chandwani, R, Larsson, M, Bhardwaj, N, Bonhoeffer, S, Ramratnam, B, Zhang, LQ, 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 (2002) 76:411-415
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Metzner, KJ, Bonhoeffer, S, Fischer, M, Karanicolas, R, Weber, R, Hirschel, B, Kostrikis, LG, Gunthard, HF
Detection of minor populations of drug-resistant viruses in patients undergoing structured treatment interruptions
ANTIVIRAL THERAPY (2002) 7:S96-S96 Request reprint

Pfeiffer, T, Bonhoeffer, S
Evolutionary consequences of tradeoffs between yield and rate of ATP production
ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS (2002) 216:51-63
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Canning, EU, Refardt, D, Vossbrinck, CR, Okamura, B, Curry, A
New diplokaryotic microsporidia (Phylum Microsporidia) from freshwater bryozoans (Bryozoa, Phylactolaemata)
European Journal of Protistology (2002) 38:247-265
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Refardt, D, Canning, EU, Mathis, A, Cheney, SA, Lafranchi-Tristem, NJ, Ebert, D
Small subunit ribosomal DNA phylogeny of microsporidia that infect Daphnia (Crustacea : Cladocera)
Parasitology (2002) 124:381-389
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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 (2001) 75:11983-11991
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Ortiz, GM, Wellons, M, Brancato, J, Vo, HTT, 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 (2001) 98:13288-13293
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Pfeiffer, T, Schuster, S, Bonhoeffer, S
Cooperation and competition in the evolution of ATP-producing pathways (vol 292, pg 504, 2001)
SCIENCE (2001) 293:1436-1436 Request reprint

Garcia, 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, Miro, JM, Gatell, JM
The virological and immunological consequences of structured treatment interruptions in chronic HIV-1 infection
AIDS (2001) 15:F29-F40
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Pfeiffer, T, Schuster, S, Bonhoeffer, S
Cooperation and competition in the evolution of ATP-producing pathways
SCIENCE (2001) 292:504-507
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Funk, GA, Fischer, M, Joos, B, Opravil, M, Gunthard, 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 (2001) 26:397-404
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Canning, EU, Curry, A, Cheney, SA, Lafranchi-Tristem, NJ, Ebert, D, Refardt, D, Killick-Kendrick, M, Killick-Kendrick, R
Flabelliforma montana (Phylum Microsporidia) from Phlebotomus ariasi (Diptera, Psychodidae): ultrastructural observations and phylogenetic relationships
European Journal of Protistology (2001) 37:207-221
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2000

Bonhoeffer, S, Rembiszewski, M, Ortiz, GM, Nixon, DF
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection
AIDS (2000) 14:2313-2322
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Jin, X, Ogg, G, Bonhoeffer, S, Safrit, J, Vesanen, M, Bauer, D, Chen, D, Cao, YZ, Demoitie, MA, Zhang, LQ, Markowitz, M, Nixon, D, McMichael, A, Ho, DD
An antigenic threshold for maintaining human immunodeficiency virus type 1-specific cytotoxic T lymphocytes
MOLECULAR MEDICINE (2000) 6:803-809
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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 (2000) 97:7681-7686
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Bonhoeffer, S, Mohri, H, Ho, D, Perelson, AS
Quantification of cell turnover kinetics using 5-bromo-2 '-deoxyuridine
JOURNAL OF IMMUNOLOGY (2000) 164:5049-5054
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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 (2000) 270:237-249
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Regoes, RR, Nowak, MA, Bonhoeffer, S
Evolution of virulence in a heterogeneous host population
EVOLUTION (2000) 54:64-71
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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, Nixon, DF
High frequency of cytomegalovirus-specific cytotoxic T-effector cells in HLA-A*0201-positive subjects during multiple viral coinfections
JOURNAL OF INFECTIOUS DISEASES (2000) 181:165-175
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1999

Ramratnam, B, Bonhoeffer, S, Binley, J, Hurley, A, Zhang, LQ, 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 (1999) 354:1782-1785
Abstract Request reprint

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 (1999) 180:865-870
Abstract Request reprint

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, LQ, Cao, YZ, 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
JOURNAL OF CLINICAL INVESTIGATION (1999) 104:R13-R18
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Nixon, DF, Douek, D, Kuebler, PJ, Jin, X, Vesanen, M, Bonhoeffer, S, Cao, YZ, 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 (1999) 66:219-228
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Ribeiro, RM, Bonhoeffer, S
A stochastic model for primary HIV infection: optimal timing of therapy
AIDS (1999) 13:351-357
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Levin, BR, Lipsitch, M, Bonhoeffer, S
Evolution and disease - Population biology, evolution, and infectious disease: Convergence and synthesis
SCIENCE (1999) 283:806-809
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Bonhoeffer, S
Turning points - A random walk from the cello to the lab
CURRENT BIOLOGY (1999) 9:R5-R5 Request reprint

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-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy
JOURNAL OF VIROLOGY (1999) 73:797-800
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Zhang, LQ, 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 (1999) 73:855-860
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1998

Bonhoeffer, S
Models of viral kinetics and drug resistance in HIV-1 infection
AIDS PATIENT CARE AND STDS (1998) 12:769-774
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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 (1998) 72:7501-7509
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Morris, L, Binley, JM, Clas, BA, Bonhoeffer, S, Astill, TP, Kost, R, Hurley, A, Cao, YZ, 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 (1998) 188:233-245
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Ogg, GS, Jin, X, Bonhoeffer, S, Dunbar, PR, Nowak, MA, Monard, S, Segal, JP, Cao, YZ, 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 (1998) 279:2103-2106
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Ribeiro, RM, Bonhoeffer, S, Nowak, MA
The frequency of resistant mutant virus before antiviral therapy
AIDS (1998) 12:461-465
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Mohri, H, Bonhoeffer, S, Monard, S, Perelson, AS, Ho, DD
Rapid turnover of T lymphocytes in SIV-infected rhesus macaques
SCIENCE (1998) 279:1223-1227
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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, Sykora, P, Simonsen, L, Spitznagel, J, Tauxe, R, Tenover, F
Resistance to antimicrobial chemotherapy: A prescription for research and action
AMERICAN JOURNAL OF THE MEDICAL SCIENCES (1998) 315:87-94
Abstract

Regoes, RR, Wodarz, D, Nowak, MA
Virus dynamics: the effect of target cell limitation and immune responses on virus evolution
JOURNAL OF THEORETICAL BIOLOGY (1998) 191:451-462
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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 (1997) 94:12106-12111
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Bittner, B, Bonhoeffer, S, Nowak, MA
Virus load and antigenic diversity
BULLETIN OF MATHEMATICAL BIOLOGY (1997) 59:881-896
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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 (1997) 94:6971-6976
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Bonhoeffer, S, Nowak, MA
Pre-existence and emergence of drug resistance in HIV-1 infection
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (1997) 264:631-637
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Bonhoeffer, S, Coffin, JM, Nowak, MA
Human immunodeficiency virus drug therapy and virus load
JOURNAL OF VIROLOGY (1997) 71:3275-3278
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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 (1997) 184:205-219
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1996

Boerlijst, MC, Bonhoeffer, S, Nowak, MA
Viral quasi-species and recombination
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (1996) 263:1577-1584
Abstract Request reprint

Nowak, MA, Anderson, RM, Boerlijst, MC, Bonhoeffer, S, May, RM, McMichael, AJ
HIV-1 evolution and disease progression
SCIENCE (1996) 274:1008-1010 Request reprint

Herz, AVM, 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 (1996) 93:7247-7251
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Bonhoeffer, S, Lenski, RE, Ebert, D
The curse of the pharaoh: The evolution of virulence in pathogens with long living propagules
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (1996) 263:715-721
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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 (1996) 93:4398-4402
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Bonhoeffer, S, Herz, AVM, Boerlijst, MC, Nee, S, Nowak, MA, May, RM
No signs of hidden language in noncoding DNA
PHYSICAL REVIEW LETTERS (1996) 76:1977-1977 Request reprint

Nowak, MA, Bonhoeffer, S, May, RM
Robustness of cooperation - Reply
NATURE (1996) 379:126-126 Request reprint

Bonhoeffer, S, Herz, AVM, Boerlijst, MC, Nee, S, Nowak, MA, May, RM
Explaining ''linguistic features'' of noncoding DNA
SCIENCE (1996) 271:14-15 Request reprint

1995

BONHOEFFER, S, HOLMES, EC, NOWAK, MA
CAUSES OF HIV DIVERSITY
NATURE (1995) 376:125-125 Request reprint

NOWAK, MA, BONHOEFFER, S, LOVEDAY, C, BALFE, P, SEMPLE, M, KAYE, S, TENANTFLOWERS, M, TEDDER, R
HIV RESULTS IN THE FRAME - RESULTS CONFIRMED
NATURE (1995) 375:193-193 Request reprint

BONHOEFFER, S, NOWAK, MA
CAN LIVE ATTENUATED VIRUS WORK AS POSTEXPOSURE TREATMENT
IMMUNOLOGY TODAY (1995) 16:131-135
Abstract Request reprint

WEI, XP, 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 (1995) 373:117-122
Abstract Request reprint

Bonhoeffer, S, Holmes, EC, Nowak, MA
Varying selection pressure in HIV-1 infection
JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY (1995) 10:85-85

1994

BONHOEFFER, S, NOWAK, MA
MUTATION AND THE EVOLUTION OF VIRULENCE
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (1994) 258:133-140
Abstract Request reprint

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 (1994) 91:8062-8066
Abstract Request reprint

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 (1994) 91:4877-4881
Abstract Request reprint

NOWAK, MA, BONHOEFFER, S, MAY, RM
MORE SPATIAL GAMES
INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS (1994) 4:33-56
Abstract Request reprint

HOFACKER, IL, FONTANA, W, STADLER, PF, BONHOEFFER, LS, TACKER, M, SCHUSTER, P
FAST FOLDING AND COMPARISON OF RNA SECONDARY STRUCTURES
MONATSHEFTE FUR CHEMIE (1994) 125:167-188
Abstract

1993

BONHOEFFER, S, STADLER, PF
ERROR THRESHOLDS ON CORRELATED FITNESS LANDSCAPES
JOURNAL OF THEORETICAL BIOLOGY (1993) 164:359-372 Request reprint

BONHOEFFER, S, MCCASKILL, JS, STADLER, PF, SCHUSTER, P
RNA MULTISTRUCTURE LANDSCAPES - A STUDY BASED ON TEMPERATURE-DEPENDENT PARTITION-FUNCTIONS
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (1993) 22:13-24
Abstract Request reprint

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