Siedentop B, Kachalov V, Witzany C, Egger M, Kouyos R, Bonhoeffer S
The effect of combining antibiotics on resistance: A systematic review and meta-analysis.
Publications
453 publications in total
5 publications
None, Siedentop B, Losa Mediavilla C, Kouyos R, Bonhoeffer S, Chabas H
Assessing the Role of Bacterial Innate and Adaptive Immunity as Barriers to Conjugative Plasmids.
Siedentop B, Rüegg D, Bonhoeffer S, Chabas H
My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages.
15 publications
Schar D, Zhang Z, Pires J, Vrancken B, Suchard M, Lemey P, Ip M, Gilbert M, Van Boeckel TP, Dellicour S
Dispersal history and bidirectional human-fish host switching of invasive, hypervirulent Streptococcus agalactiae sequence type 283.
Mulchandani R, Wang Y, Gilbert M, Van Boeckel TP
Global trends in antimicrobial use in food-producing animals: 2020 to 2030.
Morgan A, Moran D, Van Boeckel TP
Taxation of veterinary antibiotics to reduce antimicrobial resistance.
Mendelsohn E, Ross N, Zambrana-Torrelio C, Van Boeckel TP, Laxminarayan R, Daszak P
Global patterns and correlates in the emergence of antimicrobial resistance in humans.
Balasubramanian R, Van Boeckel TP, Carmeli Y, Cosgrove S, Laxminarayan R
Global incidence in hospital-associated infections resistant to antibiotics: An analysis of point prevalence surveys from 99 countries.
Allel K, Day L, Hamilton A, Lin L, Furuya-Kanamori L, Moore C, Van Boeckel TP, Laxminarayan R, Yakob L
Global antimicrobial-resistance drivers: an ecological country-level study at the human-animal interface.
Iffland-Stettner A, Okano H, Gralka M, Guessous G, Amarnath K, Cordero O, Hwa T, Bonhoeffer S
A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01.
Jagadesh S, Zhao C, Mulchandani R, Van Boeckel TP
Mapping Global Bushmeat Activities to Improve Zoonotic Spillover Surveillance by Using Geospatial Modeling.
Van Boeckel TP, Babu Rajendran N, Arieti F, Mena-Benítez C, Galia L, Tebon M, Alvarez J, Gladstone B, Collineau L, De Angelis G, Duro R, Gaze W, Göpel S, Kanj S, Käsbohrer A, Limmathurotsakul D, Lopez De Abechuco E, Mazzolini E, Mutters N, Pezzani M, Presterl E, Renk H, Rodríguez-Baño J, Săndulescu O, Scali F, Skov R, Velavan T, Vuong C, Tacconelli E, Epi-Net One Health Consensus Working Group C
EPI-Net One Health reporting guideline for antimicrobial consumption and resistance surveillance data: a Delphi approach.
26 publications
Pascual Garcia A, Schwartzman J, Enke T, Iffland-Stettner A, Cordero O, Bonhoeffer S
Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles.
Delli Compagni R, Zhao C, Russo S, Van Boeckel TP
A hybrid Neural Network-SEIR model for forecasting intensive care occupancy in Switzerland during COVID-19 epidemics.
Ashcroft P, Lehtinen S, Bonhoeffer S
Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification.
Zheng D, Yin G, Liu M, Hou L, Yang Y, Van Boeckel TP, Zheng Y, Li Y
Global biogeography and projection of soil antibiotic resistance genes.
Huisman JS, Vaughan T, Egli A, Tschudin-Sutter S, Stadler T, Bonhoeffer S
The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.
2022, Philos Trans R Soc Lond B Biol Sci, vol. 377, pp. 20210245
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DOI
Pires J, Huber L, Hickman R, Dellicour S, Lunha K, Leangapichart T, Jiwakanon J, Magnusson U, Sunde M, Järhult J, Van Boeckel TP
Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand.
Trubenova B, Trubenová B, Roizman D, Moter A, Rolff J, Regoes R
Population genetics, biofilm recalcitrance, and antibiotic resistance evolution.
2022, Trends Microbiol, vol. 30, pp. 841-852
DOI
Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2.
Chabas H, Müller V, Bonhoeffer S, Regoes R
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.
Bouman J, Kadelka S, Stringhini S, Pennacchio F, Meyer B, Yerly S, Kaiser L, Guessous I, Azman A, Bonhoeffer S, Regoes R
Applying mixture model methods to SARS-CoV-2 serosurvey data from Geneva.
Huisman J, Benz F, Duxbury S, De Visser J, Hall A, Fischer E, Bonhoeffer S
Estimating plasmid conjugation rates: A new computational tool and a critical comparison of methods.
2022, Plasmid, vol. 121, pp. 102627
DOI
Whitaker J, Brunelli G, Van Boeckel TP, Dube A, Amoah A, Rickard R, Leather A, Davies J
Access to care following injury in Northern Malawi, a comparison of travel time estimates between Geographic Information System and community household reports.
Huisman JS, Scire J, Caduff L, Fernandez-Cassi X, Ganesanandamoorthy P, Kull A, Scheidegger A, Stachler E, Boehm A, Hughes B, Knudson A, Topol A, Wigginton K, Wolfe M, Kohn T, Ort C, Stadler T, Julian T
Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2.
Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases.
2022, J Antimicrob Chemother, vol. 77, pp. 646-655
DOI
Ashcroft P, Bonhoeffer S
Constrained optimization of divisional load in hierarchically organized tissues during homeostasis.
32 publications
Huber L, Hallenberg G, Lunha K, Leangapichart T, Jiwakanon J, Hickman R, Magnusson U, Sunde M, Järhult J, Van Boeckel TP
Geographic Drivers of Antimicrobial Use and Resistance in Pigs in Khon Kaen Province, Thailand.
Banholzer N, Van Weenen E, Lison A, Cenedese A, Seeliger A, Kratzwald B, Tschernutter D, Salles J, Bottrighi P, Lehtinen S, Feuerriegel S, Vach W
Estimating the effects of non-pharmaceutical interventions on the number of new infections with COVID-19 during the first epidemic wave.
Courcol J, Invernizzi C, Landry Z, Minisini M, Baumgartner D, Bonhoeffer S, Chabriw B, Clerc E, Daniels M, Getta P, Girod M, Kazala K, Markram H, Pasqualini A, Martínez-Pérez C, Peaudecerf F, Peaudecerf M, Pfreundt U, Roller B, Słomka J, Vasse M, Wheeler J, Metzger C, Stocker R, Schürmann F
ARC: An Open Web-Platform for Request/Supply Matching for a Prioritized and Controlled COVID-19 Response.
Bakkeren E, Herter J, Huisman JS, Steiger Y, Gül E, Newson J, Brachmann A, Piel J, Regoes R, Bonhoeffer S, Diard M, Hardt W
Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut.
Gostic K, Mcgough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar P, Hellewell J, Meakin S, Munday J, Bosse N, Sherrat K, Thompson R, White L, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S
Correction: Practical considerations for measuring the effective reproductive number, Rt.
Chen C, Nadeau S, Topolsky I, Manceau M, Huisman JS, Jablonski K, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, De Gouvea A, Moccia M, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis E, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus C, Beisel C, Beerenwinkel N, Ackermann M, Stadler T
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.
Manhart M, Bonhoeffer S
The search for universality in evolutionary landscapes: Comment on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics" by Susanna Manrubia, José A. Cuesta, et al.
2021, Phys Life Rev, vol. 39, pp. 76-78
DOI
Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases.
Jones M, Rivett D, Pascual Garcia A, Bell T
Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms.
Huber L, Agunos A, Gow S, Carson C, Van Boeckel TP
Reduction in Antimicrobial Use and Resistance to Salmonella, Campylobacter, and Escherichia coli in Broiler Chickens, Canada, 2013-2019.
Schar D, Zhao C, Wang Y, Larsson D, Gilbert M, Van Boeckel TP
Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia.
San Roman Rincon M, San Román M, Wagner A
Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling.
2021, Mol Ecol
DOI
Zhao C, Wang Y, Tiseo K, Pires J, Criscuolo N, Van Boeckel TP
Geographically targeted surveillance of livestock could help prioritize intervention against antimicrobial resistance in China.
Pascual Garcia A, Klein J, Villers J, Campillo-Funollet E, Sarkis C
Empowering the crowd: feasible strategies for epidemic management in high-density informal settlements. The case of COVID-19 in Northwest Syria.
Uecker H, Bonhoeffer S
Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling.
Hilty M, Moser A, David S, Wendel Garcia P, Capaldo G, Keiser S, Fumeaux T, Guerci P, Montomoli J, Van Boeckel TP, Jeitziner M, Que Y, Jakob S, Schüpbach R, Risc-19-Icu Investigators For Switzerland C
Near real-time observation reveals increased prevalence of young patients in the ICU during the emerging third SARS-CoV-2 wave in Switzerland.
2021, Swiss Med Wkly, vol. 151, pp. Swiss Med Wkly. 2021
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DOI
Criscuolo N, Pires J, Zhao C, Van Boeckel TP
resistancebank.org, an open-access repository for surveys of antimicrobial resistance in animals.
Evolutionary mechanisms that determine which bacterial genes are carried on plasmids.
Ramoneda J, Hawes I, Pascual Garcia A, Mackey T, Sumner D, Jungblut A
Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system.
2021, FEMS Microbiol Ecol, vol. 97, pp. fiab044
DOI
Angst DC, Tepekule B, Sun L, Bogos B, Bonhoeffer S
Comparing treatment strategies to reduce antibiotic resistance in an in vitro epidemiological setting.
2021, Proc Natl Acad Sci U S A, vol. 118, pp. e2023467118
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DOI
Nadeau S, Vaughan T, Scire J, Huisman JS, Stadler T
The origin and early spread of SARS-CoV-2 in Europe.
2021, Proc Natl Acad Sci U S A, vol. 118, pp. e2012008118
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DOI
Hangartner L, Beauparlant D, Rakasz E, Nedellec R, Hozé N, Mckenney K, Martins M, Seabright G, Allen J, Weiler A, Friedrich T, Regös RR, Crispin M, Burton D
Effector function does not contribute to protection from virus challenge by a highly potent HIV broadly neutralizing antibody in nonhuman primates.
Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework : Comment to ``A conceptual framework for the phylogenetically-constrained assembly of microbial communities''.
Ramirez Garcia A, Zhang J, Greppi A, Constancias F, Wortmann E, Wandres M, Hurley K, Pascual Garcia A, Ruscheweyh H, Sturla S, Lacroix C, Schwab C
Impact of manipulation of glycerol/diol dehydratase activity on intestinal microbiota ecology and metabolism.
2021, Environ Microbiol, vol. 23, pp. 1765-1779
DOI
Benz F, Huisman JS, Bakkeren E, Herter J, Stadler T, Ackermann M, Diard M, Egli A, Hall A, Hardt W, Bonhoeffer S
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo.
Luque Paz D, Ashcroft P, Skoda R
Myeloproliferative Neoplasms: The Long Wait for JAK2-Mutant Clone Expansion.
2021, Cell Stem Cell, vol. 28, pp. 359-361
DOI
Bouman J, Riou J, Bonhoeffer S, Regös RR
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.
Quantifying the impact of quarantine duration on COVID-19 transmission.
Lehtinen S, Ashcroft P, Bonhoeffer S
On the relationship between serial interval, infectiousness profile and generation time.
28 publications
Hallenberg G, Jiwakanon J, Angkititrakul S, Kang-Air S, Osbjer K, Lunha K, Sunde M, Järhult J, Van Boeckel TP, Rich K, Magnusson U
Antibiotic use in pig farms at different levels of intensification-Farmers' practices in northeastern Thailand.
Caudill V, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda E, Solis C, Cobey S, Bedford T, Carja O, Eggo R, Koelle K, Lythgoe K, Regös RR, Roy S, Allen N, Aviles M, Baker B, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan F, Chemel A, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow S, Hecht M, Hopp K, Hopson E, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez A, López A, Lorenzo F, Luu G, Mahoney A, Melton R, Nascimento G, Pradhananga A, Rodrigues N, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters E, Wong A, Pennings P
CpG-creating mutations are costly in many human viruses.
Schar D, Klein E, Laxminarayan R, Gilbert M, Van Boeckel TP
Global trends in antimicrobial use in aquaculture.
Gostic K, Mcgough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar P, Hellewell J, Meakin S, Munday J, Bosse N, Sherrat K, Thompson R, White L, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S
Practical considerations for measuring the effective reproductive number, Rt.
Tiseo K, Huber L, Gilbert M, Robinson T, Van Boeckel TP
Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030.
Nienhold R, Ashcroft P, Zmajkovic J, Rai S, Rao T, Drexler B, Meyer S, Lundberg P, Passweg J, Leković D, Čokić V, Bonhoeffer S, Skoda R
MPN patients with low mutant JAK2 allele burden show late expansion restricted to erythroid and megakaryocytic lineages.
2020, Blood, vol. 136, pp. 2591-2595
DOI
Witzany C, Bonhoeffer S, Rolff J
Is antimicrobial resistance evolution accelerating?
Lutscher F, Fink J, Zhu Y
Pushing the Boundaries: Models for the Spatial Spread of Ecosystem Engineers.
2020, Bull Math Biol, vol. 82, pp. 138
DOI
Lunha K, Leangapichart T, Jiwakanon J, Angkititrakul S, Sunde M, Järhult J, Ström Hallenberg G, Hickman R, Van Boeckel TP, Magnusson U
Antimicrobial Resistance in Fecal Escherichia coli from Humans and Pigs at Farms at Different Levels of Intensification.
Carroll L, Huisman JS, Wiedmann M
Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State.
Jacopin E, Lehtinen S, Débarre F, Blanquart F
Factors favouring the evolution of multidrug resistance in bacteria
2020, J R Soc Interface, vol. 17
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Von Wyl V, Bonhoeffer S, Bugnion E, Puhan M, Salathé M, Stadler T, Troncoso C, Vayena E, Low N
A research agenda for digital proximity tracing apps.
2020, Swiss Med Wkly, vol. 150, pp. w20324
DOI
COVID-19 infectivity profile correction.
2020, Swiss Med Wkly, vol. 150, pp. w20336
DOI
Zhao C, Tepekule B, Criscuolo N, Wendel Garcia P, Hilty M, Risc-Icu Consortium Investigators In Switzerland , Fumeaux T, Van Boeckel TP
icumonitoring.ch: a platform for short-term forecasting of intensive care unit occupancy during the COVID-19 epidemic in Switzerland.
Lehtinen S, Chewapreecha C, Lees J, Hanage W, Lipsitch M, Croucher N, Bentley S, Turner P, Fraser C, Mostowy R
Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae.
Garcia V, Bonhoeffer S, Fu F
Cancer-induced immunosuppression can enable effectiveness of immunotherapy through bistability generation: A mathematical and computational examination.
2020, J Theor Biol, vol. 492, pp. 110185
DOI
Pascual Garcia A, Bonhoeffer S, Bell T
Metabolically cohesive microbial consortia and ecosystem functioning.
2020, Philos Trans R Soc Lond B Biol Sci, vol. 375, pp. 20190245
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Pascual Garcia A, Bell T
Community-level signatures of ecological succession in natural bacterial communities.
Hausmann A, Böck D, Geiser P, Berthold D, Fattinger S, Furter M, Bouman J, Barthel-Scherrer M, Lang C, Bakkeren E, Kolinko I, Diard M, Bumann D, Slack E, Regös RR, Pilhofer M, Sellin M, Hardt W
Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression.
Laxminarayan R, Van Boeckel TP, Frost I, Kariuki S, Khan E, Limmathurotsakul D, Larsson D, Levy-Hara G, Mendelson M, Outterson K, Peacock S, Zhu Y
The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later.
2020, Lancet Infect Dis, vol. 20, pp. e51-e60
DOI
Jasinska W, Manhart M, Lerner J, Gauthier L, Serohijos A, Bershtein S
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution.
2020, Nat Ecol Evol, vol. 4, pp. 437-452
DOI
Sun L, Ashcroft P, Ackermann M, Bonhoeffer S
Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations.
347 publications
Mohsin M, Van Boeckel TP, Saleemi M, Umair M, Naseem M, He C, Khan A, Laxminarayan R
Excessive use of medically important antimicrobials in food animals in Pakistan: a five-year surveillance survey.
Do Couto Pires J, Kraemer J, Kuenzli E, Kasraian S, Tinguely R, Hatz C, Endimiani A, Hilty M
Gut microbiota dynamics in travelers returning from India colonized with extended-spectrum cephalosporin-resistant Enterobacteriaceae: A longitudinal study.
2019, Travel Med Infect Dis, vol. 27, pp. 72-80
DOI
Frost I, Van Boeckel TP, Pires J, Craig J, Laxminarayan R
Global geographic trends in antimicrobial resistance: the role of international travel.
2019, J Travel Med, vol. 26, pp. taz036
DOI
Silvester R, Pires J, Van Boeckel TP, Madhavan A, Balakrishnan Meenakshikutti A, Hatha M
Occurrence of β-Lactam Resistance Genes and Plasmid-Mediated Resistance Among Vibrios Isolated from Southwest Coast of India.
2019, Microb Drug Resist, vol. 25, pp. 1306-1315
DOI
Pascual Garcia A, Arenas M, Bastolla U
The Molecular Clock in the Evolution of Protein Structures.
2019, Syst Biol, vol. 68, pp. 987-1002
DOI
Knight G, Davies N, Colijn C, Coll F, Donker T, Gifford D, Glover R, Jit M, Klemm E, Lehtinen S, Lindsay J, Lipsitch M, Llewelyn M, Mateus A, Robotham J, Sharland M, Stekel D, Yakob L, Atkins K
Mathematical modelling for antibiotic resistance control policy: do we know enough?
Tepekule B, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota.
2019, Proc Natl Acad Sci U S A, vol. 116, pp. 23106-23116
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Bakkeren E, Huisman JS, Fattinger S, Hausmann A, Furter M, Egli A, Slack E, Sellin M, Bonhoeffer S, Regös RR, Diard M, Hardt W
Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut.
Van Boeckel TP, Do Couto Pires J, Silvester R, Zhao C, Song J, Criscuolo N, Gilbert M, Bonhoeffer S, Laxminarayan R
Global trends in antimicrobial resistance in animals in low- and middle-income countries.
Enke T, Datta M, Schwartzman J, Cermak N, Schmitz D, Barrere J, Pascual Garcia A, Cordero O
Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities.
2019, Curr Biol, vol. 29, pp. 1528-1535.e6
DOI
Mcleod D, Day T
Why is sterility virulence most common in sexually transmitted infections? Examining the role of epidemiology.
2019, Evolution, vol. 73, pp. 872-882
DOI
None, Pascual Garcia A
A constructive approach to the epistemological problem of emergence in complex systems.
Dhingra M, Artois J, Dellicour S, Lemey P, Dauphin G, Von Dobschuetz S, Van Boeckel TP, Castellan D, Morzaria S, Gilbert M
Geographical and Historical Patterns in the Emergences of Novel Highly Pathogenic Avian Influenza (HPAI) H5 and H7 Viruses in Poultry.
Shilaih M, Angst DC, Marzel A, Bonhoeffer S, Günthard H, Kouyos R
Antibacterial effects of antiretrovirals, potential implications for microbiome studies in HIV.
2018, Antivir Ther, vol. 23, pp. 91-94
DOI
Retkute R, Jewell C, Van Boeckel TP, Zhang G, Xiao X, Thanapongtharm W, Keeling M, Gilbert M, Tildesley M
Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control.
2018, Prev Vet Med, vol. 159, pp. 171-181
DOI
Igler C, Lagator M, Tkačik G, Bollback J, Guet C
Evolutionary potential of transcription factors for gene regulatory rewiring.
2018, Nat Ecol Evol, vol. 2, pp. 1633-1643
DOI
Gilbert M, Nicolas G, Cinardi G, Van Boeckel TP, Vanwambeke S, Wint G, Robinson T
Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010.
Bons E, Regös RR
Virus dynamics and phyloanatomy: Merging population dynamic and phylogenetic approaches.
2018, Immunol Rev, vol. 285, pp. 134-146
DOI
Rozhonova H, Zahradník J, Kolářová L, Pařízková H, Kolenko P, Schneider B
Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function.
2018, Fish Shellfish Immunol, vol. 79, pp. 140-152
DOI
Day T, Mcleod D
The Role of Phenotypic Plasticity in Moderating Evolutionary Conflict.
2018, Am Nat, vol. 192, pp. 230-240
DOI
Rozhonova H, Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P
Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia.
2018, Syst Appl Microbiol, vol. 41, pp. 184-190
DOI
Hozé N, Bonhoeffer S, Regös RR
Assessing the public health impact of tolerance-based therapies with mathematical models.
Frenoy A, Bonhoeffer S
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.
Klein E, Van Boeckel TP, Martinez E, Pant S, Gandra S, Levin S, Goossens H, Laxminarayan R
Global increase and geographic convergence in antibiotic consumption between 2000 and 2015.
2018, Proc Natl Acad Sci U S A, vol. 115, pp. E3463-E3470
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Stadler T, Meinel D, Aguilar-Bultet L, Huisman JS, Schindler R, Egli A, Seth-Smith H, Eichenberger L, Brodmann P, Hübner P, Bagutti C, Tschudin-Sutter S
Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.
Müller V, De Boer R, Bonhoeffer S, Szathmáry E
An evolutionary perspective on the systems of adaptive immunity.
2018, Biol Rev Camb Philos Soc, vol. 93, pp. 505-528
DOI
Kühnert D, Kouyos R, Shirreff G, Pečerska J, Scherrer A, Böni J, Yerly S, Klimkait T, Aubert V, Günthard H, Stadler T, Bonhoeffer S, Swiss Hiv Cohort Study C
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.
Sun L, Alexander H, Bogos B, Kiviet D, Ackermann M, Bonhoeffer S
Effective polyploidy causes phenotypic delay and influences bacterial evolvability.
Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard H, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer A, Müller V, Bonhoeffer S, Kouyos R, Regös RR, Swiss Hiv Cohort Study C
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.
Amigo I, Pascual Garcia A
Conflicts of interest in scientific publishing.
Uecker H, Bonhoeffer S
Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective.
2017, Math Biosci, vol. 294, pp. 85-91
DOI
Ashcroft P, Manz M, Bonhoeffer S
Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.
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.
Van Boeckel TP, Glennon E, Chen D, Gilbert M, Robinson T, Grenfell B, Levin S, Bonhoeffer S, Laxminarayan R
Reducing antimicrobial use in food animals.
Allen R, Engelstädter J, Bonhoeffer S, Mcdonald B, Hall A
Reversing resistance: different routes and common themes across pathogens.
Liechti J, Leventhal G, Bonhoeffer S
Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.
Fingerhuth S, Low N, Bonhoeffer S, Althaus C
Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study.
Frenoy A, Taddei F, Misevic D
Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals.
2017, Evolution, vol. 71, pp. 1802-1814
DOI
Richardson T, Liechti J, Stroeymeyt N, Bonhoeffer S, Keller L
Short-term activity cycles impede information transmission in ant colonies.
Van Boeckel TP, Laxminarayan R
Correction to global antibiotic consumption data.
Mikaberidze A, Paveley N, Bonhoeffer S, Van Den Bosch F
Emergence of Resistance to Fungicides: The Role of Fungicide Dose.
2017, Phytopathology, vol. 107, pp. 545-560
DOI
Ashcroft P, Smith C, Garrod M, Galla T
Effects of population growth on the success of invading mutants.
2017, J Theor Biol, vol. 420, pp. 232-240
DOI
Uecker H
Evolutionary rescue in randomly mating, selfing, and clonal populations.
2017, Evolution, vol. 71, pp. 845-858
DOI
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High-avidity IgA protects the intestine by enchaining growing bacteria.
2017, Nature, vol. 544, pp. 498-502
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Alexander H, Mayer S, Bonhoeffer S
Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load.
Robinson T, Bu D, Carrique-Mas J, Fèvre E, Gilbert M, Grace D, Hay S, Jiwakanon J, Kakkar M, Kariuki S, Laxminarayan R, Lubroth J, Magnusson U, Thi Ngoc P, Van Boeckel TP, Woolhouse M
Antibiotic resistance: mitigation opportunities in livestock sector development.
2017, Animal, vol. 11, pp. 1-3
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Kühnert D, Hodcroft E, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain A, Joy J, Kendall M, Kühnert D, Leventhal G, Liang R, Plazzotta G, Poon A, Rasmussen D, Stadler T, Volz E, Weis C, Leigh Brown A, Fraser C, Pangea-Hiv Consortium C
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Kaiser P, Regös RR, Hardt W
Population Dynamics Analysis of Ciprofloxacin-Persistent S. Typhimurium Cells in a Mouse Model for Salmonella Diarrhea.
2016, Methods Mol Biol, vol. 1333, pp. 189-203
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Polster R, Petropoulos C, Bonhoeffer S, Guillaume F
Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1.
Arora N, Schuenemann V, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D, Bos K, Davis L, Mikalová L, Bruisten S, Komericki P, French P, Grant P, Pando M, Vaulet L, Fermepin M, Martinez A, Centurion Lara A, Giacani L, Norris S, Šmajs D, Bosshard P, González-Candelas F, Nieselt K, Krause J, Bagheri H
Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster.
2016, Nat Microbiol, vol. 2, pp. 16245
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Rusert P, Kouyos R, Kadelka C, Ebner H, Schanz M, Huber M, Braun D, Hozé N, Scherrer A, Magnus C, Weber J, Uhr T, Cippa V, Thorball C, Kuster H, Cavassini M, Bernasconi E, Hoffmann M, Calmy A, Battegay M, Rauch A, Yerly S, Aubert V, Klimkait T, Böni J, Fellay J, Regös RR, Günthard H, Trkola A, Swiss Hiv Cohort Study C
Determinants of HIV-1 broadly neutralizing antibody induction.
2016, Nat Med, vol. 22, pp. 1260-1267
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Du Plessis L, Leventhal GE, Bonhoeffer S
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
Leventhal GE, Bonhoeffer S
Potential Pitfalls in Estimating Viral Load Heritability.
2016, Trends Microbiol, vol. 24, pp. 687-698
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Delva W, Leventhal GE, Helleringer S
Connecting the dots: network data and models in HIV epidemiology.
2016, AIDS, vol. 30, pp. 2009-2020
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Stewart E, Hagerty C, Mikaberidze A, Mundt C, Zhong Z, Mcdonald B
An Improved Method for Measuring Quantitative Resistance to the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis.
2016, Phytopathology, vol. 106, pp. 782-788
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Robinson T, Bu D, Carrique-Mas J, Fèvre E, Gilbert M, Grace D, Hay S, Jiwakanon J, Kakkar M, Kariuki S, Laxminarayan R, Lubroth J, Magnusson U, Thi Ngoc P, Van Boeckel TP, Woolhouse M
Antibiotic resistance is the quintessential One Health issue.
2016, Trans R Soc Trop Med Hyg, vol. 110, pp. 377-380
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Mikaberidze A, Mundt C, Bonhoeffer S
Invasiveness of plant pathogens depends on the spatial scale of host distribution.
2016, Ecol Appl, vol. 26, pp. 1238-1248
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Fingerhuth S , Bonhoeffer S, Low N, Althaus C
Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners.
Legros M, Bonhoeffer S
A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs.
Cadosch DR, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.
Nagaraja P, Alexander HK, Bonhoeffer S, Dixit N
Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1.
2016, Epidemics, vol. 14, pp. 11-25
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Takahashi S, Liao Q, Van Boeckel TP, Xing W, Sun J, Hsiao V, Metcalf C, Chang Z, Liu F, Zhang J, Wu J, Cowling B, Leung G, Farrar J, Van Doorn H, Grenfell B, Yu H
Hand, Foot, and Mouth Disease in China: Modeling Epidemic Dynamics of Enterovirus Serotypes and Implications for Vaccination.
Regös RR, Magnus C
The role of chance in primate lentiviral infectivity: from protomer to host organism.
2015, Prog Mol Biol Transl Sci, vol. 129, pp. 327-351
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Tazzyman S, Bonhoeffer S
Why There Are No Essential Genes on Plasmids.
2015, Mol Biol Evol, vol. 32, pp. 3079-3088
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Brandenberg O, Magnus C, Regös RR, Trkola A
The HIV-1 Entry Process: A Stoichiometric View.
2015, Trends Microbiol, vol. 23, pp. 763-774
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Trubenova B, Paixão T, Badkobeh G, Barton N, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenová B
Toward a unifying framework for evolutionary processes.
2015, J Theor Biol, vol. 383, pp. 28-43
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Geoghegan J, Tan L, Kühnert D, Halpin R, Lin X, Simenauer A, Akopov A, Das S, Stockwell T, Shrivastava S, Ngoc N, Uyen L, Tuyen N, Thanh T, Hang V, Qui P, Hung N, Khanh T, Thinh L, Nhan L, Van H, Viet D, Tuan H, Viet H, Hien T, Chau N, Thwaites G, Grenfell B, Stadler T, Wentworth D, Holmes E, Van Doorn H
Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.
Mikaberidze A, Mcdonald B, Bonhoeffer S
Developing smarter host mixtures to control plant disease
2015, Plant Pathol, vol. 64, pp. 996-1004
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Nussinov R, Bonhoeffer S, Papin J, Sporns O
From "What Is?" to "What Isn't?" Computational Biology.
Maier L, Diard M, Sellin M, Chouffane E, Trautwein-Weidner K, Periaswamy B, Slack E, Dolowschiak T, Stecher B, Loverdo C, Regös RR, Hardt W
Correction: Granulocytes Impose a Tight Bottleneck upon the Gut Luminal Pathogen Population during Salmonella Typhimurium Colitis.
Scanlan P, Hall AR, Blackshields G, Friman V, Davis M, Goldberg J, Buckling A
Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations.
2015, Mol Biol Evol, vol. 32, pp. 1425-1435
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Manhart M, Morozov A
Scaling properties of evolutionary paths in a biophysical model of protein adaptation.
2015, Phys Biol, vol. 12, pp. 045001
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Parasite host range and the evolution of host resistance.
2015, J Evol Biol, vol. 28, pp. 1119-1130
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Sadd B, Barribeau S, Bloch G, De Graaf D, Dearden P, Elsik C, Gadau J, Grimmelikhuijzen C, Hasselmann M, Lozier J, Robertson H, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse R, Bornberg-Bauer E, Klasberg S, Bennett A, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam G, Beckers M, Beye M, Biewer M, Bitondi M, Blaxter M, Bourke A, Brown M, Buechel S, Cameron R, Cappelle K, Carolan J, Christiaens O, Ciborowski K, Clarke D, Colgan T, Collins D, Cridge A, Dalmay T, Dreier S, Du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas F, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann F, Irvine F, Jermiin L, Johnson C, Johnson R, Jones A, Kadowaki T, Kidner J, Koch V, Köhler A, Kraus F, Lattorff H, Leask M, Lockett G, Mallon E, Antonio D, Marxer M, Meeus I, Moritz R, Nair A, Näpflin K, Nissen I, Niu J, Nunes F, Oakeshott J, Osborne A, Otte M, Pinheiro D, Rossié N, Rueppell O, Santos C, Schmid-Hempel R, Schmitt B, Schulte C, Simões Z, Soares M, Swevers L, Winnebeck E, Wolschin F, Yu N, Zdobnov E, Aqrawi P, Blankenburg K, Coyle M, Francisco L, Hernandez A, Holder M, Hudson M, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee S, Mata R, Mathew T, Newsham I, Ngo R, Okwuonu G, Pham C, Pu L, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden K, Wu Y, Debyser G, Devreese B, Asher C, Blommaert J, Chipman A, Chittka L, Fouks B, Liu J, O'Neill M, Sumner S, Puiu D, Qu J, Salzberg S, Scherer S, Muzny D, Richards S, Robinson G, Gibbs R, Schmid-Hempel P, Worley K
The genomes of two key bumblebee species with primitive eusocial organization.
Barribeau S, Sadd B, Du Plessis L, Brown M, Buechel S, Cappelle K, Carolan J, Christiaens O, Colgan T, Erler S, Evans J, Helbing S, Karaus E, Lattorff H, Marxer M, Meeus I, Näpflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse R, Yu N, Zdobnov E, Schmid-Hempel P
A depauperate immune repertoire precedes evolution of sociality in bees.
Vuilleumier S, Bonhoeffer S
Contribution of recombination to the evolutionary history of HIV.
2015, Curr Opin HIV AIDS, vol. 10, pp. 84-89
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Fu F, Nowak M, Bonhoeffer S
Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy.
Frost S, Pybus O, Gog J, Viboud C, Bonhoeffer S, Bedford T
Eight challenges in phylodynamic inference.
2015, Epidemics, vol. 10, pp. 88-92
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Yang W, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer A, Shilaih M, Hinkley T, Petropoulos C, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study (Shcs) C
Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds.
Bonhoeffer S, Fraser C, Leventhal GE
High heritability is compatible with the broad distribution of set point viral load in HIV carriers.
Leventhal GE, Hill A, Nowak M, Bonhoeffer S
Evolution and emergence of infectious diseases in theoretical and real-world networks.
Alexander HK, Martin G, Martin O, Bonhoeffer S
Evolutionary rescue: linking theory for conservation and medicine.
Maier L, Diard M, Sellin M, Chouffane E, Trautwein-Weidner K, Periaswamy B, Slack E, Dolowschiak T, Stecher B, Loverdo C, Regös RR, Hardt W
Granulocytes impose a tight bottleneck upon the gut luminal pathogen population during Salmonella typhimurium colitis.
Kouyos R, Metcalf C, Birger R, Klein E, Abel Zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich T, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt L, Read A, Smith D, Standley C, Wale N, Grenfell B
The path of least resistance: aggressive or moderate treatment?
Boskova V, Bonhoeffer S, Stadler T
Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models.
Hall AR, Corno G
Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater.
2014, FEMS Microbiol Ecol, vol. 90, pp. 168-174
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Stadler T, Kühnert D, Rasmussen D, Du Plessis L
Insights into the early epidemic spread of ebola in sierra leone provided by viral sequence data.
2014, PLoS Curr, vol. 6, pp. ecurrents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a2
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Ocampo P, 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.
2014, Antimicrob Agents Chemother, vol. 58, pp. 4573-4582
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Lambert A, Alexander HK, Stadler T
Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics.
2014, J Theor Biol, vol. 352, pp. 60-70
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Tazzyman S, Bonhoeffer S
Plasmids and evolutionary rescue by drug resistance.
2014, Evolution, vol. 68, pp. 2066-2078
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Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos C, Engelstädter J, Bonhoeffer S
Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1.
Avila D, Keiser O, Egger M, Kouyos R, Böni J, Yerly S, Klimkait T, Vernazza P, Aubert V, Rauch A, Bonhoeffer S, Günthard H, Stadler T, Spycher B, Swiss Hiv Cohort Study C
Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.
2014, Am J Epidemiol, vol. 179, pp. 1514-1525
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Abel Zur Wiesch P, Kouyos R, Abel S, Viechtbauer W, Bonhoeffer S
Cycling empirical antibiotic therapy in hospitals: meta-analysis and models.
Trubenova B, Shimizu H, Woodcock S, Wilkin M, Trubenová B, Monk N, Baron M
Compensatory flux changes within an endocytic trafficking network maintain thermal robustness of Notch signaling.
2014, Cell, vol. 157, pp. 1160-1174
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Mikaberidze A, Mcdonald B, Bonhoeffer S
Can high-risk fungicides be used in mixtures without selecting for fungicide resistance?
2014, Phytopathology, vol. 104, pp. 324-331
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Leventhal GE, Dünner R, Barribeau S
Delayed virulence and limited costs promote fecundity compensation upon infection.
2014, Am Nat, vol. 183, pp. 480-493
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Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth T, Alizon S, Bonhoeffer S
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.
Leventhal GE, Günthard H, Bonhoeffer S, Stadler T
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.
Hool A, Leventhal GE, Bonhoeffer S
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution.
2013, Epidemics, vol. 5, pp. 174-180
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Tazzyman S, Bonhoeffer S
Fixation probability of mobile genetic elements such as plasmids.
2013, Theor Popul Biol, vol. 90, pp. 49-55
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Magnus C, Brandenberg O, Rusert P, Trkola A, Regös RR
Mathematical models: a key to understanding HIV envelope interactions?
2013, J Immunol Methods, vol. 398-399, pp. 1-18
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Hall AR
Genotype-by-environment interactions due to antibiotic resistance and adaptation in Escherichia coli.
2013, J Evol Biol, vol. 26, pp. 1655-1664
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Manhart M, Morozov A
Path-based approach to random walks on networks characterizes how proteins evolve new functions.
2013, Phys Rev Lett, vol. 111, pp. 088102
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Lehtinen S, Marsellach F, Codlin S, Schmidt A, Clément-Ziza M, Beyer A, Bähler J, Orengo C, Pancaldi V
Stress induces remodelling of yeast interaction and co-expression networks.
2013, Mol Biosyst, vol. 9, pp. 1697-1707
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Oña L, Kouyos R, Lachmann M, Bonhoeffer S
On the role of resonance in drug failure under HIV treatment interruption.
Stadler T, Bonhoeffer S
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.
2013, Philos Trans R Soc Lond B Biol Sci, vol. 368, pp. 20120198
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Saenz R, Bonhoeffer S
Nested model reveals potential amplification of an HIV epidemic due to drug resistance.
2013, Epidemics, vol. 5, pp. 34-43
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Diard M, Garcia V, Maier L, Remus-Emsermann M, Regös RR, Ackermann M, Hardt W
Stabilization of cooperative virulence by the expression of an avirulent phenotype.
2013, Nature, vol. 494, pp. 353-356
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Stadler T, Kühnert D, Bonhoeffer S, Drummond A
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).
2013, Proc Natl Acad Sci U S A, vol. 110, pp. 228-233
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Kouyos R, Leventhal GE, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Bonhoeffer S
Exploring the complexity of the HIV-1 fitness landscape.
Legros MP, Bonhoeffer S
Evolution of drug resistance in malaria parasites.
Leventhal GE, Kouyos R, Stadler T, Wyl V, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard H, Bonhoeffer S
Inferring epidemic contact structure from phylogenetic trees.
Mostowy R, Kouyos R, Hoof I, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Keşmir C, Bonhoeffer S
Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.
Arnoldini M, Mostowy R, Bonhoeffer S, Ackermann M
Evolution of stress response in the face of unreliable environmental signals.
Alexander HK, Bonhoeffer S
Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics.
2012, Epidemics, vol. 4, pp. 187-202
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Moslonka-Lefebvre M, Bonhoeffer S, Alizon S
Weighting for sex acts to understand the spread of STI on networks.
2012, J Theor Biol, vol. 311, pp. 46-53
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Cadosch DR, Bonhoeffer S, Kouyos R
Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV.
Stadler T, Kouyos R, Von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard H, Drummond A, Bonhoeffer S, Swiss Hiv Cohort Study C
Estimating the basic reproductive number from viral sequence data.
2012, Mol Biol Evol, vol. 29, pp. 347-357
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Sinka M, Rubio-Palis Y, Manguin S, Patil A, Temperley W, Gething P, Van Boeckel TP, Kabaria C, Harbach R, Hay S
Correction: The dominant vectors of human malaria in the Americas: occurrence data, distribution maps and bionomic précis.
Graw F, Magnus C, Regoes R
Correction: Theoretical analysis of the evolution of immune memory.
2011, BMC Evol Biol, vol. 11, pp. 54-54
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Kouyos R, Von Wyl V, Hinkley T, Petropoulos C, Haddad M, Whitcomb J, Böni J, Yerly S, Cellerai C, Klimkait T, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Assessing predicted HIV-1 replicative capacity in a clinical setting.
Von Wyl V, Kouyos R, Yerly S, Böni J, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Staehelin C, Battegay M, Vernazza P, Bernasconi E, Ledergerber B, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study C
The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland.
2011, J Infect Dis, vol. 204, pp. 1095-1103
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Magnus C, Regös RR
Restricted occupancy models for neutralization of HIV virions and populations.
2011, J Theor Biol, vol. 283, pp. 192-202
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Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb J, Petropoulos C, Bonhoeffer S
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase.
2011, Nat Genet, vol. 43, pp. 487-489
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Kouyos R, 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.
Kouyos R, Abel Zur Wiesch P, Bonhoeffer S
Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards.
Zur Wiesch P, Kouyos R, Engelstädter J, Regös RR, Bonhoeffer S
Population biological principles of drug-resistance evolution in infectious diseases.
2011, Lancet Infect Dis, vol. 11, pp. 236-247
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Takizawa H, Regös RR, Boddupalli C, Bonhoeffer S, Manz M
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.
Kouyos R, Von Wyl V, Yerly S, Böni J, Rieder P, Joos B, Taffé P, Shah C, Bürgisser P, Klimkait T, Weber R, Hirschel B, Cavassini M, Rauch A, Battegay M, Vernazza P, Bernasconi E, Ledergerber B, Bonhoeffer S, Günthard H, Swiss Hiv Cohort Study C
Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection.
Mostowy R, Kouyos R, Fouchet D, Bonhoeffer S
The role of recombination for the coevolutionary dynamics of HIV and the immune response.
Alizon S, Luciani F, Regös RR
Epidemiological and clinical consequences of within-host evolution.
2011, Trends Microbiol, vol. 19, pp. 24-32
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Graw F, Magnus C, Regös RR
Correction: Theoretical analysis of the evolution of immune memory
2011, BMC Evol Biol, vol. 11, pp. 54-54
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Sinka M, Bangs M, Manguin S, Coetzee M, Mbogo C, Hemingway J, Patil A, Temperley W, Gething P, Kabaria C, Okara R, Van Boeckel TP, Godfray H, Harbach R, Hay S
The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis.
Bonhoeffer S, Wiesch P, Kouyos R
Rotating antibiotics does not minimize selection for resistance.
2010, Math Biosci Eng, vol. 7, pp. 919-922
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Alizon S, Von Wyl V, Stadler T, Kouyos R, Yerly S, Hirschel B, Böni J, Shah C, Klimkait T, Furrer H, Rauch A, Vernazza P, Bernasconi E, Battegay M, Bürgisser P, Telenti A, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.
Sinka M, Rubio-Palis Y, Manguin S, Patil A, Temperley W, Gething P, Van Boeckel TP, Kabaria C, Harbach R, Hay S
The dominant Anopheles vectors of human malaria in the Americas: occurrence data, distribution maps and bionomic précis.
Martins J, Chappey C, Haddad M, Whitcomb J, Stawiski E, Petropoulos C, Bonhoeffer S
Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments.
2010, Epidemics, vol. 2, pp. 85-91
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Mostowy R, Salathé M, Kouyos R, Bonhoeffer S
On the evolution of sexual reproduction in hosts coevolving with multiple parasites.
2010, Evolution, vol. 64, pp. 1644-1656
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Kouyos R, 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 P, Bernasconi E, Rickenbach M, Ledergerber B, Bonhoeffer S, Günthard H
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland.
2010, J Infect Dis, vol. 201, pp. 1488-1497
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Schulz Zur Wiesch P, Engelstädter J, Bonhoeffer S
Compensation of fitness costs and reversibility of antibiotic resistance mutations.
2010, Antimicrob Agents Chemother, vol. 54, pp. 2085-2095
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Ben-Ami F, Ebert D, Regös RR
Pathogen dose infectivity curves as a method to analyze the distribution of host susceptibility: a quantitative assessment of maternal effects after food stress and pathogen exposure.
2010, Am Nat, vol. 175, pp. 106-115
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Novak M, Pfeiffer T, Ackermann M, Bonhoeffer S
Bacterial growth properties at low optical densities.
2009, Antonie Van Leeuwenhoek, vol. 96, pp. 267-274
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Misevic D, Kouyos R, Bonhoeffer S
Predicting the evolution of sex on complex fitness landscapes.
Engelstädter J, Bonhoeffer S
Red Queen dynamics with non-standard fitness interactions.
Salathé M, Kouyos R, Bonhoeffer S
On the causes of selection for recombination underlying the red queen hypothesis.
Müller V, Von Wyl V, Yerly S, Böni J, Klimkait T, Bürgisser P, Ledergerber B, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study.
2009, AIDS, vol. 23, pp. 1269-1276
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Von Wyl V, Yerly S, Bürgisser P, Klimkait T, Battegay M, Bernasconi E, Cavassini M, Furrer H, Hirschel B, Vernazza P, Francioli P, Bonhoeffer S, Ledergerber B, Günthard H, Swiss Hiv Cohort Study C
Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland.
2009, Clin Infect Dis, vol. 48, pp. 979-987
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Kouyos R, Fouchet D, Bonhoeffer S
Recombination and drug resistance in HIV: population dynamics and stochasticity.
2009, Epidemics, vol. 1, pp. 58-69
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Bonhoeffer S, Ferguson N, Heesterbeek H, Korber B
Research on infectious disease dynamics. Introduction.
2009, Epidemics, vol. 1, pp. 1
Magnus C, Rusert P, Bonhoeffer S, Trkola A, Regös RR
Estimating the stoichiometry of human immunodeficiency virus entry.
Kouyos R, Salathé M, Otto S, Bonhoeffer S
The role of epistasis on the evolution of recombination in host-parasite coevolution.
2009, Theor Popul Biol, vol. 75, pp. 1-13
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Salathé M, Bonhoeffer S
The effect of opinion clustering on disease outbreaks.
Salathé M, Kouyos R, Bonhoeffer S
The state of affairs in the kingdom of the Red Queen.
2008, Trends Ecol Evol, vol. 23, pp. 439-445
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Marconi V, Bonhoeffer S, Paredes R, Lu J, Hoh R, Martin J, Deeks S, Kuritzkes D
Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide.
2008, J Acquir Immune Defic Syndr, vol. 48, pp. 572-576
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Salathé M, Kouyos R, Regös RR, Bonhoeffer S
Rapid parasite adaptation drives selection for high recombination rates.
2008, Evolution, vol. 62, pp. 295-300
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Kouyos R, Salathé M, Bonhoeffer S
The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations.
Débarre F, Bonhoeffer S, Regös RR
The effect of population structure on the emergence of drug resistance during influenza pandemics.
Kouyos R, Silander O, Bonhoeffer S
Epistasis between deleterious mutations and the evolution of recombination.
2007, Trends Ecol Evol, vol. 22, pp. 308-315
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Handel A, Regös RR, Antia R
Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance
2007, PLoS Comput Biol, vol. 3
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Kouyos R, Althaus C, Bonhoeffer S
Stochastic or deterministic: what is the effective population size of HIV-1?
2006, Trends Microbiol, vol. 14, pp. 507-511
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Soyer O, Bonhoeffer S
Evolution of complexity in signaling pathways.
2006, Proc Natl Acad Sci U S A, vol. 103, pp. 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.
Funk G, Oxenius A, Fischer M, Opravil M, Joos B, Flepp M, Weber R, Günthard H, 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.
2006, J Med Virol, vol. 78, pp. 1141-1146
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Scherer A, Salathé M, Bonhoeffer S
High epitope expression levels increase competition between T cells.
Salathé M, Salathé R, Schmid-Hempel P, Bonhoeffer S
Mutation accumulation in space and the maintenance of sexual reproduction.
2006, Ecol Lett, vol. 9, pp. 941-946
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Novak M, Pfeiffer T, Lenski R, Sauer U, Bonhoeffer S
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli.
2006, Am Nat, vol. 168, pp. 242-251
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Regös RR, Bowen E, Cope A, Gor D, Hassan-Walker A, Prentice H, Johnson M, Sweny P, Burroughs A, Griffiths P, Bonhoeffer S, Emery V
Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis.
Soyer O, Pfeiffer T, Bonhoeffer S
Simulating the evolution of signal transduction pathways.
2006, J Theor Biol, vol. 241, pp. 223-232
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Kouyos R, Otto S, Bonhoeffer S
Effect of varying epistasis on the evolution of recombination.
Müller V, Ledergerber B, Perrin L, Klimkait T, Furrer H, Telenti A, Bernasconi E, Vernazza P, Günthard H, Bonhoeffer S, Swiss Hiv Cohort Study C
Stable virulence levels in the HIV epidemic of Switzerland over two decades.
2006, AIDS, vol. 20, pp. 889-894
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Salathé M, Ackermann M, Bonhoeffer S
The effect of multifunctionality on the rate of evolution in yeast.
2006, Mol Biol Evol, vol. 23, pp. 721-722
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Regös RR, Bonhoeffer S
Emergence of drug-resistant influenza virus: population dynamical considerations.
2006, Science, vol. 312, pp. 389-391
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Soyer O, Salathé M, Bonhoeffer S
Signal transduction networks: topology, response and biochemical processes.
2006, J Theor Biol, vol. 238, pp. 416-425
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Salathé M, May R, Bonhoeffer S
The evolution of network topology by selective removal.
Althaus C, Bonhoeffer S
Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1.
Salathé M, Scherer A, Bonhoeffer S
Neutral drift and polymorphism in gene-for-gene systems.
2005, Ecol Lett, vol. 8, pp. 925-932
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Brandin E, Broström C, Gille E, Bonhoeffer S, Albert J
Short communication: HIV type 2 dynamics.
2005, AIDS Res Hum Retroviruses, vol. 21, pp. 608-610
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Pfeiffer T, Soyer O, Bonhoeffer S
The evolution of connectivity in metabolic networks.
Regös RR, Bonhoeffer S
The HIV coreceptor switch: a population dynamical perspective.
2005, Trends Microbiol, vol. 13, pp. 269-277
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Pfeiffer T, Rutte C, Killingback T, Taborsky M, Bonhoeffer S
Evolution of cooperation by generalized reciprocity.
Müller V, Bonhoeffer S
Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation.
2005, Trends Genet, vol. 21, pp. 264-268
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Scherer A, Bonhoeffer S
Epitope down-modulation as a mechanism for the coexistence of competing T-cells.
2005, J Theor Biol, vol. 233, pp. 379-390
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Funk G, Jansen V, Bonhoeffer S, Killingback T
Spatial models of virus-immune dynamics.
2005, J Theor Biol, vol. 233, pp. 221-236
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Kreft J, Bonhoeffer S
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off.
2005, Microbiology, vol. 151, pp. 637-641
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Bonhoeffer S, Chappey C, Parkin N, Whitcomb J, Petropoulos C
Evidence for positive epistasis in HIV-1.
2004, Science, vol. 306, pp. 1547-1550
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Ciuffi A, Bleiber G, Muñoz M, Martinez R, Loeuillet C, Rehr M, Fischer M, Günthard H, 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.
Hersberger M, Bonhoeffer S, Rampini S, Opravil M, Marti-Jaun J, Telenti A, Hänseler E, Ledergerber B, Speck R, Swiss Hiv Cohort Study C
CCTTT-repeat polymorphism of the inducible nitric oxide synthase is not associated with HIV pathogenesis.
2004, Clin Exp Immunol, vol. 137, pp. 566-569
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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, Günthard H, Swiss Hiv Cohort Study C
Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point.
2004, Blood, vol. 104, pp. 1784-1792
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Rusert P, Fischer M, Joos B, Leemann C, Kuster H, Flepp M, Bonhoeffer S, Günthard H, Trkola A
Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol.
2004, Virology, vol. 326, pp. 113-129
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Pfeiffer T, Bonhoeffer S
Evolution of cross-feeding in microbial populations.
2004, Am Nat, vol. 163, pp. E126-35
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Molinier J, Ries G, Bonhoeffer S, Hohn B
Interchromatid and interhomolog recombination in Arabidopsis thaliana.
2004, Plant Cell, vol. 16, pp. 342-352
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Bretscher M, Althaus C, Müller V, Bonhoeffer S
Recombination in HIV and the evolution of drug resistance: for better or for worse?
2004, Bioessays, vol. 26, pp. 180-188
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Müller V, Bonhoeffer S
Mathematical approaches in the study of viral kinetics and drug resistance in HIV-1 infection.
2003, Curr Drug Targets Infect Disord, vol. 3, pp. 329-344
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Trkola A, Kuster H, Leemann C, Ruprecht C, Joos B, Telenti A, Hirschel B, Weber R, Bonhoeffer S, Günthard H, Swiss Hiv Cohot Study C
Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection.
Bonhoeffer S, Funk G, Günthard H, Fischer M, Müller V
Glancing behind virus load variation in HIV-1 infection.
2003, Trends Microbiol, vol. 11, pp. 499-504
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Metzner K, Bonhoeffer S, Fischer M, Karanicolas R, Allers K, Joos B, Weber R, Hirschel B, Kostrikis L, Günthard H, Swiss Hiv Cohort Study C
Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions.
2003, J Infect Dis, vol. 188, pp. 1433-1443
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Müller V, Bonhoeffer S
Response to Bandeira and Faro: Closing the circle of constraints.
2003, Trends Immunol, vol. 24, pp. 173-175
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Müller V, Bonhoeffer S
Quantitative constraints on the scope of negative selection.
2003, Trends Immunol, vol. 24, pp. 132-135
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Pfeiffer T, Bonhoeffer S
An evolutionary scenario for the transition to undifferentiated multicellularity.
2003, Proc Natl Acad Sci U S A, vol. 100, pp. 1095-1098
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Bonhoeffer S, Sniegowski P
Virus evolution: the importance of being erroneous.
2002, Nature, vol. 420, pp. 367, 369
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Müller V, Vigueras-Gómez J, Bonhoeffer S
Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection.
Bonhoeffer S, Barbour A, De Boer R
Procedures for reliable estimation of viral fitness from time-series data.
Regös RR, Bonhoeffer S
HIV coreceptor usage and drug treatment.
2002, J Theor Biol, vol. 217, pp. 443-457
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Regös RR, Staprans S, Feinberg M, Bonhoeffer S
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis.
Regös RR, Ebert D, Bonhoeffer S
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology.
Ortiz G, Hu J, Goldwitz J, Chandwani R, Larsson M, Bhardwaj N, Bonhoeffer S, Ramratnam B, Zhang L, Markowitz M, Nixon D
Residual viral replication during antiretroviral therapy boosts human immunodeficiency virus type 1-specific CD8+ T-cell responses in subjects treated early after infection.
Betts M, Ambrozak D, Douek D, Bonhoeffer S, Brenchley J, Casazza J, Koup R, Picker L
Analysis of total human immunodeficiency virus (HIV)-specific CD4(+) and CD8(+) T-cell responses: relationship to viral load in untreated HIV infection.
Ortiz G, Wellons M, Brancato J, Vo H, Zinn R, Clarkson D, Van Loon K, Bonhoeffer S, Miralles G, Montefiori D, Bartlett J, Nixon D
Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects.
2001, Proc Natl Acad Sci U S A, vol. 98, pp. 13288-13293
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García F, Plana M, Ortiz G, Bonhoeffer S, Soriano A, Vidal C, Cruceta A, Arnedo M, Gil C, Pantaleo G, Pumarola T, Gallart T, Nixon D, Miró J, Gatell J
The virological and immunological consequences of structured treatment interruptions in chronic HIV-1 infection.
2001, AIDS, vol. 15, pp. F29-40
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Funk G, Fischer M, Joos B, Opravil M, Günthard H, Ledergerber B, Bonhoeffer S
Quantification of in vivo replicative capacity of HIV-1 in different compartments of infected cells.
2001, J Acquir Immune Defic Syndr, vol. 26, pp. 397-404
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Pfeiffer T, Schuster S, Bonhoeffer S
Cooperation and competition in the evolution of ATP-producing pathways.
2001, Science, vol. 292, pp. 504-507
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Bonhoeffer S, Rembiszewski M, Ortiz G, Nixon D
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection.
2000, AIDS, vol. 14, pp. 2313-2322
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Jin X, Ogg G, Bonhoeffer S, Safrit J, Vesanen M, Bauer D, Chen D, Cao Y, Demoitie M, Zhang L, Markowitz M, Nixon D, Mcmichael A, Ho D
An antigenic threshold for maintaining human immunodeficiency virus type 1-specific cytotoxic T lymphocytes.
Ribeiro R, Bonhoeffer S
Production of resistant HIV mutants during antiretroviral therapy.
2000, Proc Natl Acad Sci U S A, vol. 97, pp. 7681-7686
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Bonhoeffer S, Mohri H, Ho D, Perelson A
Quantification of cell turnover kinetics using 5-bromo-2'-deoxyuridine.
2000, J Immunol, vol. 164, pp. 5049-5054
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Binley J, Clas B, Gettie A, Vesanen M, Montefiori D, Sawyer L, Booth J, Lewis M, Marx P, Bonhoeffer S, Moore J
Passive infusion of immune serum into simian immunodeficiency virus-infected rhesus macaques undergoing a rapid disease course has minimal effect on plasma viremia.
2000, Virology, vol. 270, pp. 237-249
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Regös RR, Nowak M, Bonhoeffer S
Evolution of virulence in a heterogeneous host population.
2000, Evolution, vol. 54, pp. 64-71
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Jin , Demoitie , Donahoe , Ogg G, Bonhoeffer S, Kakimoto , Gillespie , Moss , Dyer , Kurilla , Riddell , Downie , Sullivan , Mcmichael , Workman , Nixon
High frequency of cytomegalovirus-specific cytotoxic T-effector cells in HLA-A*0201-positive subjects during multiple viral coinfections.
2000, J Infect Dis, vol. 181, pp. 165-175
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Ramratnam B, Bonhoeffer S, Binley J, Hurley A, Zhang L, Mittler J, Markowitz M, Moore J, Perelson A, Ho D
Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis.
1999, Lancet, vol. 354, pp. 1782-1785
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Parkin N, Lie Y, Hellmann N, Markowitz M, Bonhoeffer S, Ho D, Petropoulos C
Phenotypic changes in drug susceptibility associated with failure of human immunodeficiency virus type 1 (HIV-1) triple combination therapy.
1999, J Infect Dis, vol. 180, pp. 865-870
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Ortiz G, Nixon D, Trkola A, Binley J, Jin X, Bonhoeffer S, Kuebler P, Donahoe S, Demoitie M, Kakimoto W, Ketas T, Clas B, Heymann J, Zhang L, Cao Y, Hurley A, Moore J, Ho D, Markowitz M
HIV-1-specific immune responses in subjects who temporarily contain virus replication after discontinuation of highly active antiretroviral therapy.
Nixon D, Douek D, Kuebler P, Jin X, Vesanen M, Bonhoeffer S, Cao Y, Koup R, Ho D, Markowitz M
Molecular tracking of an Human Immunodeficiency Virus nef specific cytotoxic T-cell clone shows persistence of clone-specific T-cell receptor DNA but not mRNA following early combination antiretroviral therapy.
1999, Immunol Lett, vol. 66, pp. 219-228
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Levin B, Lipsitch M, Bonhoeffer S
Population biology, evolution, and infectious disease: convergence and synthesis.
1999, Science, vol. 283, pp. 806-809
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Ribeiro R, Bonhoeffer S
A stochastic model for primary HIV infection: optimal timing of therapy.
1999, AIDS, vol. 13, pp. 351-357
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Ogg G, Jin X, Bonhoeffer S, Moss P, Nowak M, Monard S, Segal J, Cao Y, Rowland-Jones S, Hurley A, Markowitz M, Ho D, Mcmichael A, Nixon D
Decay kinetics of human immunodeficiency virus-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy.
Zhang L, Dailey P, He T, Gettie A, Bonhoeffer S, Perelson A, Ho D
Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques.
Models of viral kinetics and drug resistance in HIV-1 infection.
1998, AIDS Patient Care STDS, vol. 12, pp. 769-774
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Connor R, Montefiori D, Binley J, Moore J, Bonhoeffer S, Gettie A, Fenamore E, Sheridan K, Ho D, Dailey P, Marx P
Temporal analyses of virus replication, immune responses, and efficacy in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine.
Morris L, Binley J, Clas B, Bonhoeffer S, Astill T, Kost R, Hurley A, Cao Y, Markowitz M, Ho D, Moore J
HIV-1 antigen-specific and -nonspecific B cell responses are sensitive to combination antiretroviral therapy.
Ogg G, Jin X, Bonhoeffer S, Dunbar P, Nowak M, Monard S, Segal J, Cao Y, Rowland-Jones S, Cerundolo V, Hurley A, Markowitz M, Ho D, Nixon D, Mcmichael A
Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA.
1998, Science, vol. 279, pp. 2103-2106
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Ribeiro R, Bonhoeffer S, Nowak M
The frequency of resistant mutant virus before antiviral therapy.
1998, AIDS, vol. 12, pp. 461-465
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Levin B, Antia R, Berliner E, Bloland P, Bonhoeffer S, Cohen M, Derouin T, Fields P, Jafari H, Jernigan D, Lipsitch M, Mcgowan J, Mead P, Nowak M, Porco T, Sykora P, Simonsen L, Spitznagel J, Tauxe R, Tenover F
Resistance to antimicrobial chemotherapy: a prescription for research and action.
1998, Am J Med Sci, vol. 315, pp. 87-94
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Mohri H, Bonhoeffer S, Monard S, Perelson A, Ho D
Rapid turnover of T lymphocytes in SIV-infected rhesus macaques.
1998, Science, vol. 279, pp. 1223-1227
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Bonhoeffer S, Lipsitch M, Levin B
Evaluating treatment protocols to prevent antibiotic resistance.
1997, Proc Natl Acad Sci U S A, vol. 94, pp. 12106-12111
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Bittner B, Bonhoeffer S, Nowak M
Virus load and antigenic diversity.
1997, Bull Math Biol, vol. 59, pp. 881-896
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Bonhoeffer S, May R, Shaw G, Nowak M
Virus dynamics and drug therapy.
1997, Proc Natl Acad Sci U S A, vol. 94, pp. 6971-6976
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Bonhoeffer S, Nowak M
Pre-existence and emergence of drug resistance in HIV-1 infection.
Bonhoeffer S, Coffin J, Nowak M
Human immunodeficiency virus drug therapy and virus load.
Nowak M, Bonhoeffer S, Shaw G, May R
Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations.
1997, J Theor Biol, vol. 184, pp. 203-217
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Nowak M, Anderson R, Boerlijst M, Bonhoeffer S, May R, Mcmichael A
HIV-1 evolution and disease progression.
1996, Science, vol. 274, pp. 1008-1011
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Herz A, Bonhoeffer S, Anderson R, May R, Nowak M
Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay.
1996, Proc Natl Acad Sci U S A, vol. 93, pp. 7247-7251
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Bonhoeffer S, Lenski R, Ebert D
The curse of the pharaoh: the evolution of virulence in pathogens with long living propagules.
1996, Proc Biol Sci, vol. 263, pp. 715-721
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Nowak M, Bonhoeffer S, Hill A, Boehme R, Thomas H, Mcdade H
Viral dynamics in hepatitis B virus infection.
1996, Proc Natl Acad Sci U S A, vol. 93, pp. 4398-4402
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Bonhoeffer S, Herz , Boerlijst , Nee , Nowak , May
No signs of hidden language in noncoding DNA.
1996, Phys Rev Lett, vol. 76, pp. 1977
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Bonhoeffer S, Herz , Boerlijst , Nee , Nowak , May
Explaining "linguistic features" of noncoding DNA.
1996, Science, vol. 271, pp. 14-15
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Nowak M, Bonhoeffer S, Loveday C, Balfe P, Semple M, Kaye S, Tenant-Flowers M, Tedder R
HIV results in the frame. Results confirmed.
1995, Nature, vol. 375, pp. 193
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Bonhoeffer S, Nowak M
Can live attenuated virus work as post-exposure treatment?
1995, Immunol Today, vol. 16, pp. 131-135
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Wei , Ghosh , Taylor , Johnson , Emini , Deutsch , Lifson , Bonhoeffer S, Nowak , Hahn
Viral dynamics in human immunodeficiency virus type 1 infection.
1995, Nature, vol. 373, pp. 117-122
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Bonhoeffer S, Nowak M
Intra-host versus inter-host selection: viral strategies of immune function impairment.
1994, Proc Natl Acad Sci U S A, vol. 91, pp. 8062-8066
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Nowak M, Bonhoeffer S, May R
Spatial games and the maintenance of cooperation.
1994, Proc Natl Acad Sci U S A, vol. 91, pp. 4877-4881
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Bonhoeffer S, Mccaskill J, Stadler P, Schuster P
RNA multi-structure landscapes. A study based on temperature dependent partition functions.
1993, Eur Biophys J, vol. 22, pp. 13-24
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