Publications

2024    |   2023    |   2022    |   2021    |   2020    |   Before 2020    |  


2024

Siedentop B, Rüegg D, Bonhoeffer S, Chabas H
My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages.

2024, Proc Biol Sci, vol. 291, pp. 20232449
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2023

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Mulchandani R, Wang Y, Gilbert M, Van Boeckel TP
Global trends in antimicrobial use in food-producing animals: 2020 to 2030.

2023, PLOS Glob Public Health, vol. 3, pp. e0001305
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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.

2023, PLOS Glob Public Health, vol. 3, pp. e0002454
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Morgan A, Woolhouse M, Wagenaar J, Van Bunnik B
Modelling the effects of antibiotic usage in livestock on human salmonellosis.

2023, One Health, vol. 17, pp. 100639
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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.

2023, Proc Biol Sci, vol. 290, pp. 20231085
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Pathak A, Angst DC, León-Sampedro R, Hall A
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses.

2023, ISME J, vol. 17, pp. 1495-1503
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Witzany C, Rolff J, Regoes R, Igler C
The pharmacokinetic-pharmacodynamic modelling framework as a tool to predict drug resistance evolution.

2023, Microbiology, vol. 169
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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.

2023, PLoS Med, vol. 20, pp. e1004178
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Rozhonova H, Cano A, Gitschlag B, Rozhoňová H, Stoltzfus A, Mccandlish D, Payne J
Mutation bias and the predictability of evolution.

2023, Philos Trans R Soc Lond B Biol Sci, vol. 378, pp. 20220055
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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.

2023, Lancet Planet Health, vol. 7, pp. e291-e303
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Jagadesh S, Zhao C, Mulchandani R, Van Boeckel TP
Mapping Global Bushmeat Activities to Improve Zoonotic Spillover Surveillance by Using Geospatial Modeling.

2023, Emerg Infect Dis, vol. 29, pp. 742-750
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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.

2023, mSystems, vol. 8, pp. e0037722
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Crona K, Krug J, Srivastava M
Geometry of fitness landscapes: peaks, shapes and universal positive epistasis.

2023, J Math Biol, vol. 86, pp. 62
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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.

2023, Lancet Reg Health Eur, vol. 26, pp. 100563
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Fink J, Held N, Manhart M
Microbial population dynamics decouple growth response from environmental nutrient concentration.

2023, Proc Natl Acad Sci U S A, vol. 120, pp. e2207295120
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2022

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Ashcroft P, Lehtinen S, Bonhoeffer S
Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification.

2022, PLoS One, vol. 17, pp. e0263597
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Igler C
Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack.

2022, Virus Evol, vol. 8, pp. veac086
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Trubenova B, Trubenová B, Roizman D, Rolff J, Regoes R
Modeling Polygenic Antibiotic Resistance Evolution in Biofilms.

2022, Front Microbiol, vol. 13, pp. 916035
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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.

2022, Front Microbiol, vol. 13, pp. 812116
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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.

2022, PLoS One, vol. 17, pp. e0263789
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Trubenova B, Szép E, Trubenová B, Csilléry K
Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size.

2022, Mol Ecol Resour, vol. 22, pp. 2941-2955
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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.

2022, Sci Adv, vol. 8, pp. eabq8015
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Witzany C, Regoes R, Igler C
Assessing the relative importance of bacterial resistance, persistence and hyper-mutation for antibiotic treatment failure.

2022, Proc Biol Sci, vol. 289, pp. 20221300
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Guillemet M, Chabas H, Nicot A, Gatchich F, Ortega-Abboud E, Buus C, Hindhede L, Rousseau G, Bataillon T, Moineau S, Gandon S
Competition and coevolution drive the evolution and the diversification of CRISPR immunity.

2022, Nat Ecol Evol, vol. 6, pp. 1480-1488
DOI 

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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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.

2022, BMC Microbiol, vol. 22, pp. 253
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Rozhonova H, Rozhoňová H, Danciu D, Stark S, Rätsch G, Kahles A, Lehmann K
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing.

2022, Bioinformatics, vol. 38, pp. 4293-4300
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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 

Srivastava M, Payne J
On the incongruence of genotype-phenotype and fitness landscapes.

2022, PLoS Comput Biol, vol. 18, pp. e1010524
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Somerville V, Schowing T, Chabas H, Schmidt R, Von Ah U, Bruggmann R, Engel P
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities.

2022, Microbiome, vol. 10, pp. 137
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Huisman JS, Scire J, Angst DC, Li J, Neher R, Maathuis M, Bonhoeffer S, Stadler T
Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2.

2022, Elife, vol. 11, pp. e71345
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Chabas H, Müller V, Bonhoeffer S, Regoes R
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.

2022, PLoS Comput Biol, vol. 18, pp. e1010329
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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.

2022, Epidemics, vol. 39, pp. 100572
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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.

2022, Injury, vol. 53, pp. 1690-1698
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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.

2022, Environ Health Perspect, vol. 130, pp. 57011
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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 

Ashcroft P, Bonhoeffer S
Constrained optimization of divisional load in hierarchically organized tissues during homeostasis.

2022, J R Soc Interface, vol. 19, pp. 20210784
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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 

Rozhonova H, Cano A, Rozhoňová H, Stoltzfus A, Mccandlish D, Payne J
Mutation bias shapes the spectrum of adaptive substitutions.

2022, Proc Natl Acad Sci U S A, vol. 119, pp. e2119720119
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Igler C, Schwyter L, Gehrig D, Wendling C
Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates.

2022, Philos Trans R Soc Lond B Biol Sci, vol. 377, pp. 20200470
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Igler C, Huisman JS, Siedentop B, Bonhoeffer S, Lehtinen S
Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics.

2022, Philos Trans R Soc Lond B Biol Sci, vol. 377, pp. 20200478
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2021

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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.

2021, PLoS One, vol. 16, pp. e0252827
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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.

2021, Front Vet Sci, vol. 8, pp. 659051
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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.

2021, Front Public Health, vol. 9, pp. 607677
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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 

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.

2021, Elife, vol. 10, pp. e69744
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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.

2021, PLoS Comput Biol, vol. 17, pp. e1009679
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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.

2021, Epidemics, vol. 37, pp. 100480
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Jones M, Rivett D, Pascual Garcia A, Bell T
Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms.

2021, Elife, vol. 10, pp. e71811
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Rozhonova H, Rozhoňová H, Payne J
Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation.

2021, Mol Biol Evol, vol. 38, pp. 5127-5133
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Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases.

2021, Microbiol Spectr, vol. 9, pp. e0049521
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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.

2021, Nat Commun, vol. 12, pp. 5384
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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.

2021, Emerg Infect Dis, vol. 27, pp. 2434-2444
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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.

2021, Nat Food, vol. 2, pp. 596-602
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Uecker H, Bonhoeffer S
Antibiotic treatment protocols revisited: the challenges of a conclusive assessment by mathematical modelling.

2021, J R Soc Interface, vol. 18, pp. 20210308
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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.

2021, BMJ Glob Health, vol. 6, pp. e004656
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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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Criscuolo N, Pires J, Zhao C, Van Boeckel TP
resistancebank.org, an open-access repository for surveys of antimicrobial resistance in animals.

2021, Sci Data, vol. 8, pp. 189
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Igler C, Rolff J, Regös RR
Multi-step vs. single-step resistance evolution under different drugs, pharmacokinetics, and treatment regimens.

2021, Elife, vol. 10, pp. e64116
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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 

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
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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''.

2021, Microbiome, vol. 9, pp. 73
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Rodríguez-Rojas A, Baeder D, Johnston P, Regös RR, Rolff J
Bacteria primed by antimicrobial peptides develop tolerance and persist.

2021, PLoS Pathog, vol. 17, pp. e1009443
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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
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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.

2021, ISME J, vol. 15, pp. 862-878
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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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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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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.

2021, Sci Transl Med, vol. 13
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Bouman J, Riou J, Bonhoeffer S, Regös RR
Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.

2021, PLoS Comput Biol, vol. 17, pp. e1008728
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On the relationship between serial interval, infectiousness profile and generation time.

2021, J R Soc Interface, vol. 18, pp. 20200756
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2020

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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.

2020, PLoS One, vol. 15, pp. e0243099
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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.

2020, Evol Ecol, vol. 34, pp. 339-359
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Bons E, Leemann C, Metzner K, Regös RR
Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history.

2020, PLoS Biol, vol. 18, pp. e3001010
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Schar D, Klein E, Laxminarayan R, Gilbert M, Van Boeckel TP
Global trends in antimicrobial use in aquaculture.

2020, Sci Rep, vol. 10, pp. 21878
PDF    DOI 

Tiseo K, Huber L, Gilbert M, Robinson T, Van Boeckel TP
Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030.

2020, Antibiotics (Basel), vol. 9, pp. E918
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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.

2020, PLoS Comput Biol, vol. 16, pp. e1008409
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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 

San Roman Rincon M, Wagner A
Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli.

2020, PLoS Comput Biol, vol. 16, pp. e1008433
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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.

2020, Antibiotics (Basel), vol. 9, pp. E662
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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.

2020, Sci Rep, vol. 10, pp. 14428
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Lin J, Manhart M, Amir A
Evolution of Microbial Growth Traits Under Serial Dilution.

2020, Genetics, vol. 215, pp. 767-777
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Villabona-Arenas C, Hall M, Lythgoe K, Gaffney S, Regös RR, Hué S, Atkins K
Number of HIV-1 founder variants is determined by the recency of the source partner infection.

2020, Science, vol. 369, pp. 103-108
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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 

Gorter F, Manhart M, Ackermann M
Understanding the evolution of interspecies interactions in microbial communities.

2020, Philos Trans R Soc Lond B Biol Sci, vol. 375, pp. 20190256
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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.

2020, Swiss Med Wkly, vol. 150, pp. w20277
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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.

2020, Sci Adv, vol. 6, pp. eaaz6137
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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 

Community-level signatures of ecological succession in natural bacterial communities.

2020, Nat Commun, vol. 11, pp. 2386
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Metabolically cohesive microbial consortia and ecosystem functioning.

2020, Philos Trans R Soc Lond B Biol Sci, vol. 375, pp. 20190245
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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.

2020, Mucosal Immunol, vol. 13, pp. 530-544
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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 

Ben-Ami F, Orlic C, Regös RR
Disentangling non-specific and specific transgenerational immune priming components in host-parasite interactions.

2020, Proc Biol Sci, vol. 287, pp. 20192386
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Sun L, Ashcroft P, Ackermann M, Bonhoeffer S
Stochastic Gene Expression Influences the Selection of Antibiotic Resistance Mutations.

2020, Mol Biol Evol, vol. 37, pp. 58-70
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Before 2020

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Igler C, Abedon S
Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.

2019, Front Microbiol, vol. 10, pp. 1171
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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.

2019, Glob Health Action, vol. 12, pp. 1697541
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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
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Kheir Gouda M, Manhart M, Balázsi G
Evolutionary regain of lost gene circuit function.

2019, Proc Natl Acad Sci U S A, vol. 116, pp. 25162-25171
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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
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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?

2019, BMC Infect Dis, vol. 19, pp. 1011
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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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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
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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 

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.

2019, Nature, vol. 573, pp. 276-280
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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.

2019, Science, vol. 365, pp. eaaw1944
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Trubenova B, Trubenová B, Hager R
Green beards in the light of indirect genetic effects.

2019, Ecol Evol, vol. 9, pp. 9597-9608
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Trubenova B, Trubenová B, Krejca M, Lehre P, Kötzing T
Surfing on the seascape: Adaptation in a changing environment.

2019, Evolution, vol. 73, pp. 1356-1374
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Bertels F, Leemann C, Metzner K, Regös RR
Parallel evolution of HIV-1 in a long-term experiment.

2019, Mol Biol Evol
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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
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Lehtinen S, Blanquart F, Lipsitch M, Fraser C, With The Maela Pneumococcal Collaboration C
On the evolutionary ecology of multidrug resistance in bacteria.

2019, PLoS Pathog, vol. 15, pp. e1007763
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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
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Chabas H, Nicot A, Meaden S, Westra E, Tremblay D, Pradier L, Lion S, Moineau S, Gandon S
Variability in the durability of CRISPR-Cas immunity.

2019, Philos Trans R Soc Lond B Biol Sci, vol. 374, pp. 20180097
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Lehtinen S
Co-colonisation and coexistence.

2019, Nat Ecol Evol, vol. 3, pp. 334-335
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Allen R, Angst DC, Hall A
Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics.

2019, Appl Environ Microbiol, vol. 85, pp. e02111-18
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Mcleod D, Day T
Social evolution under demographic stochasticity.

2019, PLoS Comput Biol, vol. 15, pp. e1006739
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A constructive approach to the epistemological problem of emergence in complex systems.

2018, PLoS One, vol. 13, pp. e0206489
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Trubenova B, Oliveto P, Paixão T, Pérez Heredia J, Sudholt D, Trubenová B
How to Escape Local Optima in Black Box Optimisation: When Non-elitism Outperforms Elitism.

2018, Algorithmica, vol. 80, pp. 1604-1633
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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 

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.

2018, Front Vet Sci, vol. 5, pp. 84
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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 

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.

2018, Sci Data, vol. 5, pp. 180227
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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
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Chabas H, Lion S, Nicot A, Meaden S, Van Houte S, Moineau S, Wahl L, Westra E, Gandon S
Evolutionary emergence of infectious diseases in heterogeneous host populations.

2018, PLoS Biol, vol. 16, pp. e2006738
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Bons E, Regös RR
Virus dynamics and phyloanatomy: Merging population dynamic and phylogenetic approaches.

2018, Immunol Rev, vol. 285, pp. 134-146
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Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, Buckling A, Westra E, Van Houte S
Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity.

2018, Cell, vol. 174, pp. 908-916.e12
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Manhart M, Shakhnovich E
Growth tradeoffs produce complex microbial communities on a single limiting resource.

2018, Nat Commun, vol. 9, pp. 3214
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Day T, Mcleod D
The Role of Phenotypic Plasticity in Moderating Evolutionary Conflict.

2018, Am Nat, vol. 192, pp. 230-240
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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
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Bons E, Bertels F, Regös RR
Estimating the mutational fitness effects distribution during early HIV infection.

2018, Virus Evol, vol. 4, pp. vey029
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San Roman Rincon M, San Román M, Wagner A
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment.

2018, PLoS Comput Biol, vol. 14, pp. e1006340
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Blanquart F, Lehtinen S, Lipsitch M, Fraser C
The evolution of antibiotic resistance in a structured host population.

2018, J R Soc Interface, vol. 15, pp. 20180040
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Frenoy A, Bonhoeffer S
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.

2018, PLoS Biol, vol. 16, pp. e2005056
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Hozé N, Bonhoeffer S, Regös RR
Assessing the public health impact of tolerance-based therapies with mathematical models.

2018, PLoS Comput Biol, vol. 14, pp. e1006119
PDF    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
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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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Yu G, Bäder DY, Regös RR, Rolff J
Predicting drug resistance evolution: insights from antimicrobial peptides and antibiotics.

2018, Proc Biol Sci, vol. 285
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Sun L, Alexander H, Bogos B, Kiviet D, Ackermann M, Bonhoeffer S
Effective polyploidy causes phenotypic delay and influences bacterial evolvability.

2018, PLoS Biol, vol. 16, pp. e2004644
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Manhart M, Adkar B, Shakhnovich E
Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection.

2018, Proc Biol Sci, vol. 285, pp. 20172459
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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 

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.

2018, BMJ Open, vol. 8, pp. e021823
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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.

2018, PLoS Pathog, vol. 14, pp. e1006895
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Goldschmidt F, Regös RR, Johnson D
Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community.

2018, ISME J, vol. 12, pp. 136-144
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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.

2018, Mol Biol Evol, vol. 35, pp. 27-37
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Barido-Sottani J, Bošková V, Plessis L, Kühnert D, Magnus C, Mitov V, Müller N, Pecerska J, Rasmussen D, Zhang C, Drummond A, Heath T, Pybus O, Vaughan T, Stadler T
Taming the BEAST-A Community Teaching Material Resource for BEAST 2.

2018, Syst Biol, vol. 67, pp. 170-174
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Gabel M, Regös RR, Graw F
More or less-On the influence of labelling strategies to infer cell population dynamics.

2017, PLoS One, vol. 12, pp. e0185523
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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
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Bruce J, Cooper G, Chabas H, West S, Griffin A
Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens.

2017, Evolution, vol. 71, pp. 2484-2495
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Ashcroft P, Manz M, Bonhoeffer S
Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.

2017, PLoS Comput Biol, vol. 13, pp. e1005803
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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.

2017, Science, vol. 357, pp. 1350-1352
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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.

2017, PLoS Comput Biol, vol. 13, pp. e1005745
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Allen R, Engelstädter J, Bonhoeffer S, Mcdonald B, Hall A
Reversing resistance: different routes and common themes across pathogens.

2017, Proc Biol Sci, vol. 284, pp. 20171619
PDF    DOI 

Goldschmidt F, Regös RR, Johnson D
Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

2017, ISME J, vol. 11, pp. 2112-2123
PDF    DOI 

Liechti J, Leventhal G, Bonhoeffer S
Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.

2017, PLoS Comput Biol, vol. 13, pp. e1005704
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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
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Fingerhuth S, Low N, Bonhoeffer S, Althaus C
Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study.

2017, BMC Med, vol. 15, pp. 142
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Brandenberg O, Magnus C, Rusert P, Günthard H, Regös RR, Trkola A
Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters.

2017, PLoS Pathog, vol. 13, pp. e1006313
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Richardson T, Liechti J, Stroeymeyt N, Bonhoeffer S, Keller L
Short-term activity cycles impede information transmission in ant colonies.

2017, PLoS Comput Biol, vol. 13, pp. e1005527
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Van Boeckel TP, Laxminarayan R
Correction to global antibiotic consumption data.

2017, Lancet Infect Dis, vol. 17, pp. 476-477
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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
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Blanquart F, Lehtinen S, Fraser C
An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae.

2017, Proc Biol Sci, vol. 284, pp. 20170679
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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
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Uecker H
Evolutionary rescue in randomly mating, selfing, and clonal populations.

2017, Evolution, vol. 71, pp. 845-858
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Moor K, Diard M, Sellin M, Felmy B, Wotzka S, Toska A, Bakkeren E, Arnoldini M, Bansept F, Co A, Völler T, Minola A, Fernandez-Rodriguez B, Agatic G, Barbieri S, Piccoli L, Casiraghi C, Corti D, Lanzavecchia A, Regös RR, Loverdo C, Stocker R, Brumley D, Hardt W, Slack E
High-avidity IgA protects the intestine by enchaining growing bacteria.

2017, Nature, vol. 544, pp. 498-502
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Adkar B, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich E
Optimization of lag phase shapes the evolution of a bacterial enzyme.

2017, Nat Ecol Evol, vol. 1, pp. 149
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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.

2017, Mol Biol Evol, vol. 34, pp. 419-436
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Trubenova B, Heredia J, Trubenová B, Sudholt D, Paixão T
Selection Limits to Adaptive Walks on Correlated Landscapes.

2017, Genetics, vol. 205, pp. 803-825
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Lehtinen S, Blanquart F, Croucher N, Turner P, Lipsitch M, Fraser C
Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage.

2017, Proc Natl Acad Sci U S A, vol. 114, pp. 1075-1080
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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.

2017, Mol Biol Evol, vol. 34, pp. 185-203
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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: mitigation opportunities in livestock sector development.

2017, Animal, vol. 11, pp. 1-3
DOI 

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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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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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.

2016, Mol Biol Evol, vol. 33, pp. 3213-3225
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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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Leventhal GE, Bonhoeffer S
Potential Pitfalls in Estimating Viral Load Heritability.

2016, Trends Microbiol, vol. 24, pp. 687-698
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Du Plessis L, Leventhal GE, Bonhoeffer S
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

2016, Mol Biol Evol, vol. 33, pp. 2454-2468
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Chabas H, Van Houte S, Høyland-Kroghsbo N, Buckling A, Westra E
Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies.

2016, Proc Biol Sci, vol. 283, pp. 20160721
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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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Kühnert D, Stadler T, Vaughan T, Drummond A
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.

2016, Mol Biol Evol, vol. 33, pp. 2102-2116
PDF    DOI 

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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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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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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Bäder DY, Yu G, Hozé N, Rolff J, Regös RR
Antimicrobial combinations: Bliss independence and Loewe additivity derived from mechanistic multi-hit models.

2016, Philos Trans R Soc Lond B Biol Sci, vol. 371
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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.

2016, PLoS Pathog, vol. 12, pp. e1005611
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Van Houte S, Ekroth A, Broniewski J, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra E
The diversity-generating benefits of a prokaryotic adaptive immune system.

2016, Nature, vol. 532, pp. 385-388
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Legros M, Bonhoeffer S
A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs.

2016, J R Soc Interface, vol. 13, pp. 20160148
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Cadosch DR, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.

2016, PLoS Comput Biol, vol. 12, pp. e1004749
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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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Lagator M, Igler C, Moreno A, Guet C, Bollback J
Epistatic Interactions in the Arabinose Cis-Regulatory Element.

2016, Mol Biol Evol, vol. 33, pp. 761-769
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Garcia V, Feldman M, Regös RR
Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection.

2016, PLoS Comput Biol, vol. 12, pp. e1004721
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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.

2016, PLoS Med, vol. 13, pp. e1001958
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Yu G, Bäder DY, Regös RR, Rolff J
Combination Effects of Antimicrobial Peptides.

2016, Antimicrob Agents Chemother, vol. 60, pp. 1717-1724
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None, San Roman Rincon M, Payne J, None, None, Sib Swiss Institute Of Bioinformatics Members C
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

2016, Nucleic Acids Res, vol. 44, pp. D27-37
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Lam S, Dawson N, Das S, Sillitoe I, Ashford P, Lee D, Lehtinen S, Orengo C, Lees J
Gene3D: expanding the utility of domain assignments.

2016, Nucleic Acids Res, vol. 44, pp. D404-9
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Alexander HK, Lambert A, Stadler T
Quantifying Age-dependent Extinction from Species Phylogenies.

2016, Syst Biol, vol. 65, pp. 35-50
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Trubenova B, Trubenová B, Novak S, Hager R
Indirect genetic effects and the dynamics of social interactions.

2015, PLoS One, vol. 10, pp. e0126907
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Lehtinen S, Lees J, Bähler J, Shawe-Taylor J, Orengo C
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression.

2015, PLoS One, vol. 10, pp. e0134668
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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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Manhart M, Kion-Crosby W, Morozov A
Path statistics, memory, and coarse-graining of continuous-time random walks on networks.

2015, J Chem Phys, vol. 143, pp. 214106
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Novitsky V, Kühnert D, Moyo S, Widenfelt E, Okui L, Essex M
Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana.

2015, Epidemics, vol. 13, pp. 44-55
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Lehtinen S, Bähler J, Orengo C
Co-Expression Network Models Suggest that Stress Increases Tolerance to Mutations.

2015, Sci Rep, vol. 5, pp. 16726
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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.

2015, J Virol, vol. 89, pp. 8871-8879
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Mikaberidze A
Fitness Cost of Resistance: Impact on Management

2015, , pp. 77-89
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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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González C, Ray J, Manhart M, Adams R, Nevozhay D, Morozov A, Balázsi G
Stress-response balance drives the evolution of a network module and its host genome.

2015, Mol Syst Biol, vol. 11, pp. 827
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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.

2015, PLoS Pathog, vol. 11, pp. e1005047
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Weber De Melo V, Sheikh Ali H, Freise J, Kühnert D, Essbauer S, Mertens M, Wanka K, Drewes S, Ulrich R, Heckel G
Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus.

2015, Evol Appl, vol. 8, pp. 545-559
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Nussinov R, Bonhoeffer S, Papin J, Sporns O
From "What Is?" to "What Isn't?" Computational Biology.

2015, PLoS Comput Biol, vol. 11, pp. e1004318
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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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Stadler T, Vaughan T, Gavryushkin A, Guindon S, Kühnert D, Leventhal GE, Drummond A
How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

2015, Proc Biol Sci, vol. 282, pp. 20150420
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Gorter F, Hall AR, Buckling A, Scanlan P
Parasite host range and the evolution of host resistance.

2015, J Evol Biol, vol. 28, pp. 1119-1130
DOI 

Garcia V, Richter K, Graw F, Oxenius A, Regös RR
Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities.

2015, PLoS Comput Biol, vol. 11, pp. e1004178
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Rahnamaeian M, Cytryńska M, Zdybicka-Barabas A, Dobslaff K, Wiesner J, Twyman R, Zuchner T, Sadd B, Regös RR, Schmid-Hempel P, Vilcinskas A
Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria.

2015, Proc Biol Sci, vol. 282, pp. 20150293
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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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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.

2015, Genome Biol, vol. 16, pp. 83
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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.

2015, Genome Biol, vol. 16, pp. 76
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Tazzyman S, Hall A
Lytic phages obscure the cost of antibiotic resistance in Escherichia coli.

2015, ISME J, vol. 9, pp. 809-820
PDF    DOI 

Fu F, Nowak M, Bonhoeffer S
Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy.

2015, PLoS Comput Biol, vol. 11, pp. e1004142
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Hall AR, Angst DC, Schiessl K, Ackermann M
Costs of antibiotic resistance - separating trait effects and selective effects.

2015, Evol Appl, vol. 8, pp. 261-272
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Vuilleumier S, Bonhoeffer S
Contribution of recombination to the evolutionary history of HIV.

2015, Curr Opin HIV AIDS, vol. 10, pp. 84-89
DOI 

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.

2015, PLoS Pathog, vol. 11, pp. e1004722
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Frost S, Pybus O, Gog J, Viboud C, Bonhoeffer S, Bedford T
Eight challenges in phylodynamic inference.

2015, Epidemics, vol. 10, pp. 88-92
DOI 

Johnson S, Bergthaler A, Graw F, Flatz L, Bonilla W, Siegrist C, Lambert P, Regös RR, Pinschewer D
Protective efficacy of individual CD8+ T cell specificities in chronic viral infection.

2015, J Immunol, vol. 194, pp. 1755-1762
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Bonhoeffer S, Fraser C, Leventhal GE
High heritability is compatible with the broad distribution of set point viral load in HIV carriers.

2015, PLoS Pathog, vol. 11, pp. e1004634
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Manhart M, Morozov A
Protein folding and binding can emerge as evolutionary spandrels through structural coupling.

2015, Proc Natl Acad Sci U S A, vol. 112, pp. 1797-1802
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Sillitoe I, Lewis T, Cuff A, Das S, Ashford P, Dawson N, Furnham N, Laskowski R, Lee D, Lees J, Lehtinen S, Studer R, Thornton J, Orengo C
CATH: comprehensive structural and functional annotations for genome sequences.

2015, Nucleic Acids Res, vol. 43, pp. D376-81
PDF    DOI 

Leventhal GE, Hill A, Nowak M, Bonhoeffer S
Evolution and emergence of infectious diseases in theoretical and real-world networks.

2015, Nat Commun, vol. 6, pp. 6101
PDF    DOI 

Brandenberg O, Magnus C, Rusert P, Regös RR, Trkola A
Different infectivity of HIV-1 strains is linked to number of envelope trimers required for entry.

2015, PLoS Pathog, vol. 11, pp. e1004595
PDF    DOI 

Garcia V, Regös RR
The Effect of Interference on the CD8(+) T Cell Escape Rates in HIV.

2014, Front Immunol, vol. 5, pp. 661
PDF    DOI 

Trubenova B, Trubenová B, Hager R
Social Selection and Indirect Genetic Effects in Structured populations.

2014, Evol Biol, vol. 41, pp. 123-133
PDF    DOI 

Pinho R, Garcia V, Feldman M
Phenotype accessibility and noise in random threshold gene regulatory networks.

2014, PLoS One, vol. 10, pp. e0119972
PDF    DOI 

Alexander HK, Martin G, Martin O, Bonhoeffer S
Evolutionary rescue: linking theory for conservation and medicine.

2014, Evol Appl, vol. 7, pp. 1161-1179
PDF    DOI 

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.

2014, PLoS Pathog, vol. 10, pp. e1004557
PDF    DOI 

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?

2014, Proc Biol Sci, vol. 281, pp. 20140566
PDF    DOI 

Garcia V
Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks

2014, PLoS Comp Biol
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Lopez Pascua L, Hall AR, Best A, Morgan A, Boots M, Buckling A
Higher resources decrease fluctuating selection during host-parasite coevolution.

2014, Ecol Lett, vol. 17, pp. 1380-1388
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Boskova V, Bonhoeffer S, Stadler T
Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models.

2014, PLoS Comput Biol, vol. 10, pp. e1003913
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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
DOI 

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
DOI 

Brandenberg O, Rusert P, Magnus C, Weber J, Böni J, Günthard H, Regös RR, Trkola A
Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain's exceptional capacity for sequence variation.

2014, Retrovirology, vol. 11, pp. 75
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Regös RR, Mclaren P, Battegay M, Bernasconi E, Calmy A, Günthard H, Hoffmann M, Rauch A, Telenti A, Fellay J, Swiss Hiv Cohort Study C
Disentangling human tolerance and resistance against HIV.

2014, PLoS Biol, vol. 12, pp. e1001951
PDF    DOI 

Graw F, Regös RR
Predicting the impact of CD8+ T cell polyfunctionality on HIV disease progression.

2014, J Virol, vol. 88, pp. 10134-10145
PDF    DOI 

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
PDF    DOI 

Haldane A, Manhart M, Morozov A
Biophysical fitness landscapes for transcription factor binding sites.

2014, PLoS Comput Biol, vol. 10, pp. e1003683
PDF    DOI 

Tazzyman S, Bonhoeffer S
Plasmids and evolutionary rescue by drug resistance.

2014, Evolution, vol. 68, pp. 2066-2078
DOI 

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
DOI 

Hall A, Angst D
Costs of antibiotic resistance - separating trait effects and selective

2014, Evol Appl
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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
DOI 

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

2014, PLoS Pathog, vol. 10, pp. e1004225
PDF    DOI 

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.

2014, PLoS Genet, vol. 10, pp. e1004439
PDF    DOI 

San Roman Rincon M, San Román M, Cancela H, Acerenza L
Source and regulation of flux variability in Escherichia coli.

2014, BMC Syst Biol, vol. 8, pp. 67
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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
DOI 

Kühnert D, Stadler T, Vaughan T, Drummond A
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.

2014, J R Soc Interface, vol. 11, pp. 20131106
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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
DOI 

Leventhal GE, Dünner R, Barribeau S
Delayed virulence and limited costs promote fecundity compensation upon infection.

2014, Am Nat, vol. 183, pp. 480-493
DOI 

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth T, Alizon S, Bonhoeffer S
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.

2014, Science, vol. 343, pp. 1243727
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Barribeau S, Sadd B, Du Plessis L, Schmid-Hempel P
Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system.

2014, Proc Natl Acad Sci U S A, vol. 111, pp. 3496-3501
PDF    DOI 

Kaiser P, Regös RR, Dolowschiak T, Wotzka S, Lengefeld J, Slack E, Grant A, Ackermann M, Hardt W
Cecum lymph node dendritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment.

2014, PLoS Biol, vol. 12, pp. e1001793
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Leventhal GE, Günthard H, Bonhoeffer S, Stadler T
Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.

2014, Mol Biol Evol, vol. 31, pp. 6-17
PDF    DOI 

Seich Al Basatena N, Chatzimichalis K, Graw F, Frost S, Regös RR, Asquith B
Can non-lytic CD8+ T cells drive HIV-1 escape?

2013, PLoS Pathog, vol. 9, pp. e1003656
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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
DOI 

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
DOI 

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
DOI 

Kaiser P, Slack E, Grant A, Hardt W, Regös RR
Lymph node colonization dynamics after oral Salmonella Typhimurium infection in mice.

2013, PLoS Pathog, vol. 9, pp. e1003532
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Angst DC, Hall AR
The cost of antibiotic resistance depends on evolutionary history in Escherichia coli.

2013, BMC Evol Biol, vol. 13, pp. 163
PDF    DOI 

Hall AR
Genotype-by-environment interactions due to antibiotic resistance and adaptation in Escherichia coli.

2013, J Evol Biol, vol. 26, pp. 1655-1664
DOI 

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
DOI 

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
DOI 

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

2013, Theor Biol Med Model, vol. 10, pp. 44
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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
DOI 

Inglis R, Hall AR, Buckling A
The role of 'soaking' in spiteful toxin production in Pseudomonas aeruginosa.

2013, Biol Lett, vol. 9, pp. 20120569
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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
DOI 

Regös RR, Hamblin S, Tanaka M
Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed.

2013, Proc Biol Sci, vol. 280, pp. 20122047
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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
PDF    DOI 

Trubenova B, Trubenová B, Hager R
Phenotypic and evolutionary consequences of social behaviours: interactions among individuals affect direct genetic effects.

2012, PLoS One, vol. 7, pp. e46273
PDF    DOI 

Legros MP, Bonhoeffer S
Evolution of drug resistance in malaria parasites.

2012, Malar J, vol. 11, pp. P63-P63
PDF    DOI 

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.

2012, PLoS Comput Biol, vol. 8, pp. e1002413
PDF    DOI 

Magnus C, Regös RR
Analysis of the subunit stoichiometries in viral entry.

2012, PLoS One, vol. 7, pp. e33441
PDF    DOI 

Regös RR
The role of exposure history on HIV acquisition: insights from repeated low-dose challenge studies.

2012, PLoS Comput Biol, vol. 8, pp. e1002767
PDF    DOI 

Graw F, Regös RR
Influence of the fibroblastic reticular network on cell-cell interactions in lymphoid organs.

2012, PLoS Comput Biol, vol. 8, pp. e1002436
PDF    DOI 

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.

2012, PLoS Comput Biol, vol. 8, pp. e1002525
PDF    DOI 

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

2012, PLoS Comput Biol, vol. 8, pp. e1002627
PDF    DOI 

Kouyos R, Leventhal GE, Hinkley T, Haddad M, Whitcomb J, Petropoulos C, Bonhoeffer S
Exploring the complexity of the HIV-1 fitness landscape.

2012, PLoS Genet, vol. 8, pp. e1002551
PDF    DOI 

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
DOI 

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
DOI 

Näsvall J, Sun L, Roth J, Andersson D
Real-time evolution of new genes by innovation, amplification, and divergence.

2012, Science, vol. 338, pp. 384-387
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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.

2012, J R Soc Interface, vol. 9, pp. 2309-2320
PDF    DOI 

Manhart M, Haldane A, Morozov A
A universal scaling law determines time reversibility and steady state of substitutions under selection.

2012, Theor Popul Biol, vol. 82, pp. 66-76
PDF    DOI 

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
DOI 

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.

2011, Parasit Vectors, vol. 4, pp. 210-210
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Graw F, Magnus C, Regoes R
Correction: Theoretical analysis of the evolution of immune memory.

2011, BMC Evol Biol, vol. 11, pp. 54-54
PDF   

Graw F, Richter K, Oxenius A, Regös RR
Comparison of cytotoxic T lymphocyte efficacy in acute and persistent lymphocytic choriomeningitis virus infection.

2011, Proc Biol Sci, vol. 278, pp. 3395-3402
PDF    DOI 

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.

2011, PLoS Pathog, vol. 7, pp. e1002321
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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
DOI 

Magnus C, Regös RR
Restricted occupancy models for neutralization of HIV virions and populations.

2011, J Theor Biol, vol. 283, pp. 192-202
DOI 

Rusert P, Krarup A, Magnus C, Brandenberg O, Weber J, Ehlert A, Regös RR, Günthard H, Trkola A
Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies.

2011, J Exp Med, vol. 208, pp. 1419-1433
PDF    DOI 

Johnson P, Kochin B, Mcafee M, Stromnes I, Regös RR, Ahmed R, Blattman J, Antia R
Vaccination alters the balance between protective immunity, exhaustion, escape, and death in chronic infections.

2011, J Virol, vol. 85, pp. 5565-5570
PDF    DOI 

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
DOI 

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.

2011, PLoS Pathog, vol. 7, pp. e1001334
PDF    DOI 

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

2011, PLoS Comput Biol, vol. 7, pp. e1001094
PDF    DOI 

Ruprecht C, Krarup A, Reynell L, Mann A, Brandenberg O, Berlinger L, Abela I, Regös RR, Günthard H, Rusert P, Trkola A
MPER-specific antibodies induce gp120 shedding and irreversibly neutralize HIV-1.

2011, J Exp Med, vol. 208, pp. 439-454
PDF    DOI 

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
DOI 

Takizawa H, Regös RR, Boddupalli C, Bonhoeffer S, Manz M
Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.

2011, J Exp Med, vol. 208, pp. 273-284
PDF    DOI 

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.

2011, Clin Infect Dis, vol. 52, pp. 532-539
PDF    DOI 

Mostowy R, Kouyos R, Fouchet D, Bonhoeffer S
The role of recombination for the coevolutionary dynamics of HIV and the immune response.

2011, PLoS One, vol. 6, pp. e16052
PDF    DOI 

Alizon S, Luciani F, Regös RR
Epidemiological and clinical consequences of within-host evolution.

2011, Trends Microbiol, vol. 19, pp. 24-32
DOI 

Graw F, Magnus C, Regös RR
Correction: Theoretical analysis of the evolution of immune memory

2011, BMC Evol Biol, vol. 11, pp. 54-54
PDF   

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.

2010, Parasit Vectors, vol. 3, pp. 117
PDF    DOI 

Graw F, Magnus C, Regös RR
Theoretical analysis of the evolution of immune memory.

2010, BMC Evol Biol, vol. 10, pp. 380
PDF    DOI 

Bonhoeffer S, Wiesch P, Kouyos R
Rotating antibiotics does not minimize selection for resistance.

2010, Math Biosci Eng, vol. 7, pp. 919-922
DOI 

Regös RR
Population genetics meets cancer genomics.

2010, Proc Natl Acad Sci U S A, vol. 107, pp. 18241-18242
PDF    DOI 

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.

2010, PLoS Pathog, vol. 6, pp. e1001123
PDF    DOI 

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.

2010, Parasit Vectors, vol. 3, pp. 72
PDF    DOI 

Kouyos R, Gordon S, Staprans S, Silvestri G, Regös RR
Similar impact of CD8+ T cell responses on early virus dynamics during SIV infections of rhesus macaques and sooty mangabeys.

2010, PLoS Comput Biol, vol. 6
PDF    DOI 

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
DOI 

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
DOI 

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
DOI 

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
PDF    DOI 

Magnus C, Regös RR
Estimating the stoichiometry of HIV neutralization.

2010, PLoS Comput Biol, vol. 6, pp. e1000713
PDF    DOI 

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
DOI 

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

2009, Antonie Van Leeuwenhoek, vol. 96, pp. 267-274
DOI 

Misevic D, Kouyos R, Bonhoeffer S
Predicting the evolution of sex on complex fitness landscapes.

2009, PLoS Comput Biol, vol. 5, pp. e1000510
PDF    DOI 

Engelstädter J, Bonhoeffer S
Red Queen dynamics with non-standard fitness interactions.

2009, PLoS Comput Biol, vol. 5, pp. e1000469
PDF    DOI 

Graw F, Regös RR
Investigating CTL mediated killing with a 3D cellular automaton.

2009, PLoS Comput Biol, vol. 5, pp. e1000466
PDF    DOI 

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

2009, Am Nat, vol. 174 Suppl 1, pp. S31-42
PDF    DOI 

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
DOI 

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
DOI 

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

2009, Epidemics, vol. 1, pp. 58-69
DOI 

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.

2009, J Virol, vol. 83, pp. 1523-1531
PDF    DOI 

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
DOI 

Salathé M, Bonhoeffer S
The effect of opinion clustering on disease outbreaks.

2008, J R Soc Interface, vol. 5, pp. 1505-1508
PDF    DOI 

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
PDF    DOI 

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
DOI 

Fouchet D, Regös RR
A population dynamics analysis of the interaction between adaptive regulatory T cells and antigen presenting cells.

2008, PLoS One, vol. 3, pp. e2306
PDF    DOI 

Ben-Ami F, Regös RR, Ebert D
A quantitative test of the relationship between parasite dose and infection probability across different host-parasite combinations.

2008, Proc Biol Sci, vol. 275, pp. 853-859
PDF    DOI 

Salathé M, Kouyos R, Regös RR, Bonhoeffer S
Rapid parasite adaptation drives selection for high recombination rates.

2008, Evolution, vol. 62, pp. 295-300
DOI 

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

2007, BMC Evol Biol, vol. 7, pp. 211
PDF    DOI 

Débarre F, Bonhoeffer S, Regös RR
The effect of population structure on the emergence of drug resistance during influenza pandemics.

2007, J R Soc Interface, vol. 4, pp. 893-906
PDF    DOI 

Kouyos R, Silander O, Bonhoeffer S
Epistasis between deleterious mutations and the evolution of recombination.

2007, Trends Ecol Evol, vol. 22, pp. 308-315
DOI 

Handel A, Regös RR, Antia R
Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance

2007, PLoS Comput Biol, vol. 3
PDF   

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
DOI 

Bull J, Regös RR
Pharmacodynamics of non-replicating viruses, bacteriocins and lysins.

2006, Proc Biol Sci, vol. 273, pp. 2703-2712
PDF    DOI 

Soyer O, Bonhoeffer S
Evolution of complexity in signaling pathways.

2006, Proc Natl Acad Sci U S A, vol. 103, pp. 16337-16342
PDF    DOI 

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

2006, J Virol, vol. 80, pp. 9861-9864
PDF    DOI 

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
DOI 

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
DOI 

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.

2006, Proc Biol Sci, vol. 273, pp. 1961-1967
PDF    DOI 

Scherer A, Salathé M, Bonhoeffer S
High epitope expression levels increase competition between T cells.

2006, PLoS Comput Biol, vol. 2, pp. e109
PDF    DOI 

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
DOI 

Soyer O, Pfeiffer T, Bonhoeffer S
Simulating the evolution of signal transduction pathways.

2006, J Theor Biol, vol. 241, pp. 223-232
DOI 

Kouyos R, Otto S, Bonhoeffer S
Effect of varying epistasis on the evolution of recombination.

2006, Genetics, vol. 173, pp. 589-597
PDF    DOI 

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
DOI 

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
DOI 

Regös RR, Bonhoeffer S
Emergence of drug-resistant influenza virus: population dynamical considerations.

2006, Science, vol. 312, pp. 389-391
DOI 

Soyer O, Salathé M, Bonhoeffer S
Signal transduction networks: topology, response and biochemical processes.

2006, J Theor Biol, vol. 238, pp. 416-425
DOI 

Salathé M, May R, Bonhoeffer S
The evolution of network topology by selective removal.

2005, J R Soc Interface, vol. 2, pp. 533-536
PDF    DOI 

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

2005, J Virol, vol. 79, pp. 13572-13578
PDF    DOI 

Salathé M, Scherer A, Bonhoeffer S
Neutral drift and polymorphism in gene-for-gene systems.

2005, Ecol Lett, vol. 8, pp. 925-932
DOI 

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
DOI 

Pfeiffer T, Soyer O, Bonhoeffer S
The evolution of connectivity in metabolic networks.

2005, PLoS Biol, vol. 3, pp. e228
PDF    DOI 

Regös RR, Bonhoeffer S
The HIV coreceptor switch: a population dynamical perspective.

2005, Trends Microbiol, vol. 13, pp. 269-277
DOI 

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

2005, Proc Biol Sci, vol. 272, pp. 1115-1120
PDF    DOI 

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
DOI 

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
DOI 

Funk G, Jansen V, Bonhoeffer S, Killingback T
Spatial models of virus-immune dynamics.

2005, J Theor Biol, vol. 233, pp. 221-236
DOI 

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
DOI 

Bonhoeffer S, Chappey C, Parkin N, Whitcomb J, Petropoulos C
Evidence for positive epistasis in HIV-1.

2004, Science, vol. 306, pp. 1547-1550
DOI 

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.

2004, J Virol, vol. 78, pp. 10747-10754
PDF    DOI 

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
DOI 

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
DOI 

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
DOI 

Pfeiffer T, Bonhoeffer S
Evolution of cross-feeding in microbial populations.

2004, Am Nat, vol. 163, pp. E126-35
DOI 

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

2004, Plant Cell, vol. 16, pp. 342-352
DOI 

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
DOI 

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
DOI 

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.

2003, J Virol, vol. 77, pp. 13146-13155
PDF    DOI 

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
DOI 

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
DOI 

Müller V, Bonhoeffer S
Response to Bandeira and Faro: Closing the circle of constraints.

2003, Trends Immunol, vol. 24, pp. 173-175
DOI 

Müller V, Bonhoeffer S
Quantitative constraints on the scope of negative selection.

2003, Trends Immunol, vol. 24, pp. 132-135
DOI 

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
PDF    DOI 

Bonhoeffer S, Sniegowski P
Virus evolution: the importance of being erroneous.

2002, Nature, vol. 420, pp. 367, 369
DOI 

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

2002, J Virol, vol. 76, pp. 8963-8965
PDF    DOI 

Bonhoeffer S, Barbour A, De Boer R
Procedures for reliable estimation of viral fitness from time-series data.

2002, Proc Biol Sci, vol. 269, pp. 1887-1893
PDF    DOI 

Regös RR, Bonhoeffer S
HIV coreceptor usage and drug treatment.

2002, J Theor Biol, vol. 217, pp. 443-457
DOI 

Regös RR, Staprans S, Feinberg M, Bonhoeffer S
Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis.

2002, J Virol, vol. 76, pp. 2573-2578
PDF    DOI 

Regös RR, Ebert D, Bonhoeffer S
Dose-dependent infection rates of parasites produce the Allee effect in epidemiology.

2002, Proc Biol Sci, vol. 269, pp. 271-279
PDF    DOI 

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.

2002, J Virol, vol. 76, pp. 411-415
PDF    DOI 

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.

2001, J Virol, vol. 75, pp. 11983-11991
PDF    DOI 

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
PDF    DOI 

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
DOI 

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
DOI 

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

2001, Science, vol. 292, pp. 504-507
DOI 

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
DOI 

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.

2000, Mol Med, vol. 6, pp. 803-809
PDF    DOI 

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
PDF    DOI 

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
DOI 

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
DOI 

Regös RR, Nowak M, Bonhoeffer S
Evolution of virulence in a heterogeneous host population.

2000, Evolution, vol. 54, pp. 64-71
DOI 

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
DOI 

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
DOI 

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
DOI 

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.

1999, J Clin Invest, vol. 104, pp. R13-8
PDF    DOI 

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
DOI 

Levin B, Lipsitch M, Bonhoeffer S
Population biology, evolution, and infectious disease: convergence and synthesis.

1999, Science, vol. 283, pp. 806-809
DOI 

Ribeiro R, Bonhoeffer S
A stochastic model for primary HIV infection: optimal timing of therapy.

1999, AIDS, vol. 13, pp. 351-357
DOI 

A random walk from the cello to the lab

1999, Curr Biol, vol. 9, pp. R5
DOI 

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.

1999, J Virol, vol. 73, pp. 797-800
PDF    DOI 

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.

1999, J Virol, vol. 73, pp. 855-860
PDF    DOI 

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

1998, AIDS Patient Care STDS, vol. 12, pp. 769-774
DOI 

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.

1998, J Virol, vol. 72, pp. 7501-7509
PDF    DOI 

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.

1998, J Exp Med, vol. 188, pp. 233-245
PDF    DOI 

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
DOI 

Ribeiro R, Bonhoeffer S, Nowak M
The frequency of resistant mutant virus before antiviral therapy.

1998, AIDS, vol. 12, pp. 461-465
DOI 

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
DOI 

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
DOI 

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
PDF    DOI 

Bittner B, Bonhoeffer S, Nowak M
Virus load and antigenic diversity.

1997, Bull Math Biol, vol. 59, pp. 881-896
DOI 

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
PDF    DOI 

Bonhoeffer S, Nowak M
Pre-existence and emergence of drug resistance in HIV-1 infection.

1997, Proc Biol Sci, vol. 264, pp. 631-637
PDF    DOI 

Bonhoeffer S, Coffin J, Nowak M
Human immunodeficiency virus drug therapy and virus load.

1997, J Virol, vol. 71, pp. 3275-3278
PDF    DOI 

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
DOI 

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
DOI 

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
PDF    DOI 

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
DOI 

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
DOI 

Bonhoeffer S, Herz , Boerlijst , Nee , Nowak , May
Explaining "linguistic features" of noncoding DNA.

1996, Science, vol. 271, pp. 14-15
DOI 

Bonhoeffer S, Holmes E, Nowak M
Causes of HIV diversity.

1995, Nature, vol. 376, pp. 125
DOI 

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
DOI 

Bonhoeffer S, Nowak M
Can live attenuated virus work as post-exposure treatment?

1995, Immunol Today, vol. 16, pp. 131-135
DOI 

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
DOI 

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
PDF    DOI 

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
PDF    DOI 

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
DOI 

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