ETH - Theoretical Biology - Publications Sebastian Bonhoeffer

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Publications Sebastian Bonhoeffer

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

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
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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

von Wyl, V, Yerly, S, Boni, J, Burgisser, P, Klimkait, T, Battegay, M, Bernasconi, E, Cavassini, M, Furrer, H, Hirschel, B, Vernazza, PL, Francioli, P, Bonhoeffer, S, Ledergerber, B, Gunthard, HF
Long-Term Trends of HIV Type 1 Drug Resistance Prevalence among Antiretroviral Treatment-Experienced Patients in Switzerland
CLINICAL INFECTIOUS DISEASES (2009) 48:979-987
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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
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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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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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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
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES (2008) 48:572-576
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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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Bonhoeffer, S
Evidence for positive epistasis in HIV-1 (vol 306, pg 1547, 2004)
SCIENCE (2008) 320:746-746 Request reprint

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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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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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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Brandin, E, Thorstensson, R, Bonhoeffer, S, Albert, J
Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy
JOURNAL OF VIROLOGY (2006) 80:9861-9864
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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
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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
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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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von Wyl, V, Yerly, S, Boni, J, Schupbach, J, Burgisser, P, Klimkait, T, Rickenbach, M, Perrin, L, Bonhoeffer, S, Ledergerber, B, Gunthard, H
Prevalence of HIV-1 drug resistance in Switzerland between 1999 and 2004: no trend for an increase
ANTIVIRAL THERAPY (2006) 11:S117-S117

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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Brandin, E, Brostrom, C, Gille, E, Bonhoeffer, S, Albert, J
HIV type 2 dynamics
AIDS RESEARCH AND HUMAN RETROVIRUSES (2005) 21:608-610
Abstract

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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Kreft, JU, Bonhoeffer, S
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off
MICROBIOLOGY-SGM (2005) 151:637-641 Request reprint

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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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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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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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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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
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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
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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

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