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Stochastic gene expression influences the selection of antibiotic resistance mutations.

Sun L, Ashcroft P, Ackermann M, Bonhoeffer S.

Mol Biol Evol. 2019 Aug 30. pii: msz199. doi: 10.1093/molbev/msz199. [Epub ahead of print]


Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut.

Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD.

Nature. 2019 Sep;573(7773):276-280. doi: 10.1038/s41586-019-1521-8. Epub 2019 Sep 4.


Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.

Frenoy A, Bonhoeffer S.

PLoS Biol. 2018 May 11;16(5):e2005056. doi: 10.1371/journal.pbio.2005056. eCollection 2018 May.


Assessing the public health impact of tolerance-based therapies with mathematical models.

Hozé N, Bonhoeffer S, Regoes R.

PLoS Comput Biol. 2018 May 4;14(5):e1006119. doi: 10.1371/journal.pcbi.1006119. eCollection 2018 May.


Effective polyploidy causes phenotypic delay and influences bacterial evolvability.

Sun L, Alexander HK, Bogos B, Kiviet DJ, Ackermann M, Bonhoeffer S.

PLoS Biol. 2018 Feb 22;16(2):e2004644. doi: 10.1371/journal.pbio.2004644. eCollection 2018 Feb.


Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.

Kühnert D, Kouyos R, Shirreff G, Pečerska J, Scherrer AU, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Stadler T, Bonhoeffer S; Swiss HIV Cohort Study.

PLoS Pathog. 2018 Feb 20;14(2):e1006895. doi: 10.1371/journal.ppat.1006895. eCollection 2018 Feb.


Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.

Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer AU, Müller V, Bonhoeffer S, Kouyos R, Regoes RR; Swiss HIV Cohort Study.

Mol Biol Evol. 2018 Jan 1;35(1):27-37. doi: 10.1093/molbev/msx246.


Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.

Ashcroft P, Manz MG, Bonhoeffer S.

PLoS Comput Biol. 2017 Oct 9;13(10):e1005803. doi: 10.1371/journal.pcbi.1005803. eCollection 2017 Oct.


Reducing antimicrobial use in food animals.

Van Boeckel TP, Glennon EE, Chen D, Gilbert M, Robinson TP, Grenfell BT, Levin SA, Bonhoeffer S, Laxminarayan R.

Science. 2017 Sep 29;357(6358):1350-1352. doi: 10.1126/science.aao1495. Epub 2017 Sep 28. No abstract available.


Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective.

Uecker H, Bonhoeffer S.

Math Biosci. 2017 Dec;294:85-91. doi: 10.1016/j.mbs.2017.09.002. Epub 2017 Sep 28.


Reversing resistance: different routes and common themes across pathogens.

Allen RC, Engelstädter J, Bonhoeffer S, McDonald BA, Hall AR.

Proc Biol Sci. 2017 Sep 27;284(1863). pii: 20171619. doi: 10.1098/rspb.2017.1619. Review.


Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies.

Tepekule B, Uecker H, Derungs I, Frenoy A, Bonhoeffer S.

PLoS Comput Biol. 2017 Sep 15;13(9):e1005745. doi: 10.1371/journal.pcbi.1005745. eCollection 2017 Sep.


Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.

Liechti JI, Leventhal GE, Bonhoeffer S.

PLoS Comput Biol. 2017 Aug 21;13(8):e1005704. doi: 10.1371/journal.pcbi.1005704. eCollection 2017 Aug.


Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study.

Fingerhuth SM, Low N, Bonhoeffer S, Althaus CL.

BMC Med. 2017 Jul 26;15(1):142. doi: 10.1186/s12916-017-0881-x.


An evolutionary perspective on the systems of adaptive immunity.

Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E.

Biol Rev Camb Philos Soc. 2018 Feb;93(1):505-528. doi: 10.1111/brv.12355. Epub 2017 Jul 26. Review.


Antibacterial effects of antiretrovirals, potential implications for microbiome studies in HIV.

Shilaih M, Angst DC, Marzel A, Bonhoeffer S, Günthard HF, Kouyos RD.

Antivir Ther. 2018;23(1):91-94. doi: 10.3851/IMP3173.


Short-term activity cycles impede information transmission in ant colonies.

Richardson TO, Liechti JI, Stroeymeyt N, Bonhoeffer S, Keller L.

PLoS Comput Biol. 2017 May 10;13(5):e1005527. doi: 10.1371/journal.pcbi.1005527. eCollection 2017 May.


Emergence of Resistance to Fungicides: The Role of Fungicide Dose.

Mikaberidze A, Paveley N, Bonhoeffer S, van den Bosch F.

Phytopathology. 2017 May;107(5):545-560. doi: 10.1094/PHYTO-08-16-0297-R. Epub 2017 Mar 28.


Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load.

Alexander HK, Mayer SI, Bonhoeffer S.

Mol Biol Evol. 2017 Feb 1;34(2):419-436. doi: 10.1093/molbev/msw244.


Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1.

Polster R, Petropoulos CJ, Bonhoeffer S, Guillaume F.

Mol Biol Evol. 2016 Dec;33(12):3213-3225. Epub 2016 Sep 27.


Invasiveness of plant pathogens depends on the spatial scale of host distribution.

Mikaberidze A, Mundt CC, Bonhoeffer S.

Ecol Appl. 2016 Jun;26(4):1238-48.


Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners.

Fingerhuth SM, Bonhoeffer S, Low N, Althaus CL.

PLoS Pathog. 2016 May 19;12(5):e1005611. doi: 10.1371/journal.ppat.1005611. eCollection 2016 May.


How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

du Plessis L, Leventhal GE, Bonhoeffer S.

Mol Biol Evol. 2016 Sep;33(9):2454-68. doi: 10.1093/molbev/msw097. Epub 2016 May 14.


Potential Pitfalls in Estimating Viral Load Heritability.

Leventhal GE, Bonhoeffer S.

Trends Microbiol. 2016 Sep;24(9):687-698. doi: 10.1016/j.tim.2016.04.008. Epub 2016 May 12. Review.


A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs.

Legros M, Bonhoeffer S.

J R Soc Interface. 2016 Apr;13(117). pii: 20160148. doi: 10.1098/rsif.2016.0148. Epub 2016 Apr 13.


Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1.

Nagaraja P, Alexander HK, Bonhoeffer S, Dixit NM.

Epidemics. 2016 Mar;14:11-25. doi: 10.1016/j.epidem.2015.09.001. Epub 2015 Oct 18.


The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.

Cadosch D, Abel Zur Wiesch P, Kouyos R, Bonhoeffer S.

PLoS Comput Biol. 2016 Mar 11;12(3):e1004749. doi: 10.1371/journal.pcbi.1004749. eCollection 2016 Mar.


From "What Is?" to "What Isn't?" Computational Biology.

Nussinov R, Bonhoeffer S, Papin JA, Sporns O.

PLoS Comput Biol. 2015 Jul 2;11(7):e1004318. doi: 10.1371/journal.pcbi.1004318. eCollection 2015 Jul. No abstract available.


Eight challenges in phylodynamic inference.

Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T.

Epidemics. 2015 Mar;10:88-92. doi: 10.1016/j.epidem.2014.09.001. Epub 2014 Sep 16.


Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds.

Yang WL, Kouyos RD, Böni J, Yerly S, Klimkait T, Aubert V, Scherrer AU, Shilaih M, Hinkley T, Petropoulos C, Bonhoeffer S, Günthard HF; Swiss HIV Cohort Study (SHCS).

PLoS Pathog. 2015 Mar 23;11(3):e1004722. doi: 10.1371/journal.ppat.1004722. eCollection 2015 Mar.


Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy.

Fu F, Nowak MA, Bonhoeffer S.

PLoS Comput Biol. 2015 Mar 19;11(3):e1004142. doi: 10.1371/journal.pcbi.1004142. eCollection 2015 Mar.


High heritability is compatible with the broad distribution of set point viral load in HIV carriers.

Bonhoeffer S, Fraser C, Leventhal GE.

PLoS Pathog. 2015 Feb 6;11(2):e1004634. doi: 10.1371/journal.ppat.1004634. eCollection 2015 Feb.


Evolution and emergence of infectious diseases in theoretical and real-world networks.

Leventhal GE, Hill AL, Nowak MA, Bonhoeffer S.

Nat Commun. 2015 Jan 16;6:6101. doi: 10.1038/ncomms7101.


Contribution of recombination to the evolutionary history of HIV.

Vuilleumier S, Bonhoeffer S.

Curr Opin HIV AIDS. 2015 Mar;10(2):84-9. doi: 10.1097/COH.0000000000000137. Review.


Evolutionary rescue: linking theory for conservation and medicine.

Alexander HK, Martin G, Martin OY, Bonhoeffer S.

Evol Appl. 2014 Dec;7(10):1161-79. doi: 10.1111/eva.12221. Epub 2014 Oct 15. Review.


Why There Are No Essential Genes on Plasmids.

Tazzyman SJ, Bonhoeffer S.

Mol Biol Evol. 2015 Dec;32(12):3079-88. doi: 10.1093/molbev/msu293. Epub 2014 Dec 23.


Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models.

Boskova V, Bonhoeffer S, Stadler T.

PLoS Comput Biol. 2014 Nov 6;10(11):e1003913. doi: 10.1371/journal.pcbi.1003913. eCollection 2014 Nov.


The path of least resistance: aggressive or moderate treatment?

Kouyos RD, Metcalf CJ, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt LC, Read AF, Smith DL, Standley C, Wale N, Grenfell B.

Proc Biol Sci. 2014 Nov 7;281(1794):20140566. doi: 10.1098/rspb.2014.0566.


Cycling empirical antibiotic therapy in hospitals: meta-analysis and models.

Abel zur Wiesch P, Kouyos R, Abel S, Viechtbauer W, Bonhoeffer S.

PLoS Pathog. 2014 Jun 26;10(6):e1004225. doi: 10.1371/journal.ppat.1004225. eCollection 2014 Jun.


Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1.

Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, Engelstädter J, Bonhoeffer S.

PLoS Genet. 2014 Jun 26;10(6):e1004439. doi: 10.1371/journal.pgen.1004439. eCollection 2014 Jun.


Antagonism between bacteriostatic and bactericidal antibiotics is prevalent.

Ocampo PS, Lázár V, Papp B, Arnoldini M, Abel zur Wiesch P, Busa-Fekete R, Fekete G, Pál C, Ackermann M, Bonhoeffer S.

Antimicrob Agents Chemother. 2014 Aug;58(8):4573-82. doi: 10.1128/AAC.02463-14. Epub 2014 May 27.


Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.

Avila D, Keiser O, Egger M, Kouyos R, Böni J, Yerly S, Klimkait T, Vernazza PL, Aubert V, Rauch A, Bonhoeffer S, Günthard HF, Stadler T, Spycher BD; Swiss HIV Cohort Study.

Am J Epidemiol. 2014 Jun 15;179(12):1514-25. doi: 10.1093/aje/kwu076. Epub 2014 May 12.


Plasmids and evolutionary rescue by drug resistance.

Tazzyman SJ, Bonhoeffer S.

Evolution. 2014 Jul;68(7):2066-78. doi: 10.1111/evo.12423. Epub 2014 May 21.


Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S.

Science. 2014 Mar 21;343(6177):1243727. doi: 10.1126/science.1243727. Review.


Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution.

Hool A, Leventhal GE, Bonhoeffer S.

Epidemics. 2013 Dec;5(4):174-80. doi: 10.1016/j.epidem.2013.09.002. Epub 2013 Sep 23.


Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.

Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T.

Mol Biol Evol. 2014 Jan;31(1):6-17. doi: 10.1093/molbev/mst172. Epub 2013 Oct 1.


Fixation probability of mobile genetic elements such as plasmids.

Tazzyman SJ, Bonhoeffer S.

Theor Popul Biol. 2013 Dec;90:49-55. doi: 10.1016/j.tpb.2013.09.012. Epub 2013 Sep 27.


Can high-risk fungicides be used in mixtures without selecting for fungicide resistance?

Mikaberidze A, McDonald BA, Bonhoeffer S.

Phytopathology. 2014 Apr;104(4):324-31. doi: 10.1094/PHYTO-07-13-0204-R.


On the role of resonance in drug failure under HIV treatment interruption.

Oña L, Kouyos RD, Lachmann M, Bonhoeffer S.

Theor Biol Med Model. 2013 Jul 11;10:44. doi: 10.1186/1742-4682-10-44.


Nested model reveals potential amplification of an HIV epidemic due to drug resistance.

Saenz RA, Bonhoeffer S.

Epidemics. 2013 Mar;5(1):34-43. doi: 10.1016/j.epidem.2012.11.002. Epub 2012 Nov 17.


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