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Estimating the mutational fitness effects distribution during early HIV infection.

Bons E, Bertels F, Regoes RR.

Virus Evol. 2018 Oct 4;4(2):vey029. doi: 10.1093/ve/vey029. eCollection 2018 Jul.


Virus dynamics and phyloanatomy: Merging population dynamic and phylogenetic approaches.

Bons E, Regoes RR.

Immunol Rev. 2018 Sep;285(1):134-146. doi: 10.1111/imr.12688.


Predicting drug resistance evolution: insights from antimicrobial peptides and antibiotics.

Yu G, Baeder DY, Regoes RR, Rolff J.

Proc Biol Sci. 2018 Mar 14;285(1874). pii: 20172687. doi: 10.1098/rspb.2017.2687.


More or less-On the influence of labelling strategies to infer cell population dynamics.

Gabel M, Regoes RR, Graw F.

PLoS One. 2017 Oct 18;12(10):e0185523. doi: 10.1371/journal.pone.0185523. eCollection 2017.


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.


Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community.

Goldschmidt F, Regoes RR, Johnson DR.

ISME J. 2018 Jan;12(1):136-144. doi: 10.1038/ismej.2017.147. Epub 2017 Sep 15.


Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

Goldschmidt F, Regoes RR, Johnson DR.

ISME J. 2017 Sep;11(9):2112-2123. doi: 10.1038/ismej.2017.76. Epub 2017 May 23.


Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters.

Brandenberg OF, Magnus C, Rusert P, Günthard HF, Regoes RR, Trkola A.

PLoS Pathog. 2017 May 4;13(5):e1006313. doi: 10.1371/journal.ppat.1006313. eCollection 2017 May.


High-avidity IgA protects the intestine by enchaining growing bacteria.

Moor K, Diard M, Sellin ME, Felmy B, Wotzka SY, Toska A, Bakkeren E, Arnoldini M, Bansept F, Co AD, Völler T, Minola A, Fernandez-Rodriguez B, Agatic G, Barbieri S, Piccoli L, Casiraghi C, Corti D, Lanzavecchia A, Regoes RR, Loverdo C, Stocker R, Brumley DR, Hardt WD, Slack E.

Nature. 2017 Apr 27;544(7651):498-502. doi: 10.1038/nature22058. Epub 2017 Apr 12.


Determinants of HIV-1 broadly neutralizing antibody induction.

Rusert P, Kouyos RD, Kadelka C, Ebner H, Schanz M, Huber M, Braun DL, Hozé N, Scherrer A, Magnus C, Weber J, Uhr T, Cippa V, Thorball CW, Kuster H, Cavassini M, Bernasconi E, Hoffmann M, Calmy A, Battegay M, Rauch A, Yerly S, Aubert V, Klimkait T, Böni J, Fellay J, Regoes RR, Günthard HF, Trkola A; Swiss HIV Cohort Study.

Nat Med. 2016 Nov;22(11):1260-1267. doi: 10.1038/nm.4187. Epub 2016 Sep 26.


Antimicrobial combinations: Bliss independence and Loewe additivity derived from mechanistic multi-hit models.

Baeder DY, Yu G, Hozé N, Rolff J, Regoes RR.

Philos Trans R Soc Lond B Biol Sci. 2016 May 26;371(1695). pii: 20150294. doi: 10.1098/rstb.2015.0294.


Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection.

Garcia V, Feldman MW, Regoes RR.

PLoS Comput Biol. 2016 Feb 1;12(2):e1004721. doi: 10.1371/journal.pcbi.1004721. eCollection 2016 Feb.


Combination Effects of Antimicrobial Peptides.

Yu G, Baeder DY, Regoes RR, Rolff J.

Antimicrob Agents Chemother. 2016 Jan 4;60(3):1717-24. doi: 10.1128/AAC.02434-15.


The HIV-1 Entry Process: A Stoichiometric View.

Brandenberg OF, Magnus C, Regoes RR, Trkola A.

Trends Microbiol. 2015 Dec;23(12):763-774. doi: 10.1016/j.tim.2015.09.003. Epub 2015 Nov 2. Review.


Population Dynamics Analysis of Ciprofloxacin-Persistent S. Typhimurium Cells in a Mouse Model for Salmonella Diarrhea.

Kaiser P, Regoes RR, Hardt WD.

Methods Mol Biol. 2016;1333:189-203. doi: 10.1007/978-1-4939-2854-5_16.


Correction: Granulocytes Impose a Tight Bottleneck upon the Gut Luminal Pathogen Population during Salmonella Typhimurium Colitis.

Maier L, Diard M, Sellin ME, Chouffane ES, Trautwein-Weidner K, Periaswamy B, Slack E, Dolowschiak T, Stecher B, Loverdo C, Regoes RR, Hardt WD.

PLoS Pathog. 2015 Jul 17;11(7):e1005047. doi: 10.1371/journal.ppat.1005047. eCollection 2015 Jul. No abstract available.


Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities.

Garcia V, Richter K, Graw F, Oxenius A, Regoes RR.

PLoS Comput Biol. 2015 May 1;11(5):e1004178. doi: 10.1371/journal.pcbi.1004178. eCollection 2015 May.


Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria.

Rahnamaeian M, Cytryńska M, Zdybicka-Barabas A, Dobslaff K, Wiesner J, Twyman RM, Zuchner T, Sadd BM, Regoes RR, Schmid-Hempel P, Vilcinskas A.

Proc Biol Sci. 2015 May 7;282(1806):20150293. doi: 10.1098/rspb.2015.0293.


The Effect of Interference on the CD8(+) T Cell Escape Rates in HIV.

Garcia V, Regoes RR.

Front Immunol. 2015 Jan 13;5:661. doi: 10.3389/fimmu.2014.00661. eCollection 2014.


The role of chance in primate lentiviral infectivity: from protomer to host organism.

Regoes RR, Magnus C.

Prog Mol Biol Transl Sci. 2015;129:327-51. doi: 10.1016/bs.pmbts.2014.10.013. Epub 2014 Dec 29. Review.


Different infectivity of HIV-1 strains is linked to number of envelope trimers required for entry.

Brandenberg OF, Magnus C, Rusert P, Regoes RR, Trkola A.

PLoS Pathog. 2015 Jan 8;11(1):e1004595. doi: 10.1371/journal.ppat.1004595. eCollection 2015 Jan.


Protective efficacy of individual CD8+ T cell specificities in chronic viral infection.

Johnson S, Bergthaler A, Graw F, Flatz L, Bonilla WV, Siegrist CA, Lambert PH, Regoes RR, Pinschewer DD.

J Immunol. 2015 Feb 15;194(4):1755-62. doi: 10.4049/jimmunol.1401771. Epub 2015 Jan 7.


Granulocytes impose a tight bottleneck upon the gut luminal pathogen population during Salmonella typhimurium colitis.

Maier L, Diard M, Sellin ME, Chouffane ES, Trautwein-Weidner K, Periaswamy B, Slack E, Dolowschiak T, Stecher B, Loverdo C, Regoes RR, Hardt WD.

PLoS Pathog. 2014 Dec 18;10(12):e1004557. doi: 10.1371/journal.ppat.1004557. eCollection 2014 Dec. Erratum in: PLoS Pathog. 2015 Jul;11(7):e1005047.


Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain's exceptional capacity for sequence variation.

Brandenberg OF, Rusert P, Magnus C, Weber J, Böni J, Günthard HF, Regoes RR, Trkola A.

Retrovirology. 2014 Sep 25;11:75. doi: 10.1186/s12977-014-0075-y.


Disentangling human tolerance and resistance against HIV.

Regoes RR, McLaren PJ, Battegay M, Bernasconi E, Calmy A, Günthard HF, Hoffmann M, Rauch A, Telenti A, Fellay J; Swiss HIV Cohort Study.

PLoS Biol. 2014 Sep 16;12(9):e1001951. doi: 10.1371/journal.pbio.1001951. eCollection 2014 Sep.


Predicting the impact of CD8+ T cell polyfunctionality on HIV disease progression.

Graw F, Regoes RR.

J Virol. 2014 Sep 1;88(17):10134-45. doi: 10.1128/JVI.00647-14. Epub 2014 Jun 25.


Cecum lymph node dendritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment.

Kaiser P, Regoes RR, Dolowschiak T, Wotzka SY, Lengefeld J, Slack E, Grant AJ, Ackermann M, Hardt WD.

PLoS Biol. 2014 Feb 18;12(2):e1001793. doi: 10.1371/journal.pbio.1001793. eCollection 2014 Feb.


Can non-lytic CD8+ T cells drive HIV-1 escape?

Seich Al Basatena NK, Chatzimichalis K, Graw F, Frost SD, Regoes RR, Asquith B.

PLoS Pathog. 2013;9(11):e1003656. doi: 10.1371/journal.ppat.1003656. Epub 2013 Nov 14.


Lymph node colonization dynamics after oral Salmonella Typhimurium infection in mice.

Kaiser P, Slack E, Grant AJ, Hardt WD, Regoes RR.

PLoS Pathog. 2013 Sep;9(9):e1003532. doi: 10.1371/journal.ppat.1003532. Epub 2013 Sep 19.


Mathematical models: a key to understanding HIV envelope interactions?

Magnus C, Brandenberg OF, Rusert P, Trkola A, Regoes RR.

J Immunol Methods. 2013 Dec 15;398-399:1-18. doi: 10.1016/j.jim.2013.09.002. Epub 2013 Sep 13.


Stabilization of cooperative virulence by the expression of an avirulent phenotype.

Diard M, Garcia V, Maier L, Remus-Emsermann MN, Regoes RR, Ackermann M, Hardt WD.

Nature. 2013 Feb 21;494(7437):353-6. doi: 10.1038/nature11913.


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

Regoes RR.

PLoS Comput Biol. 2012;8(11):e1002767. doi: 10.1371/journal.pcbi.1002767. Epub 2012 Nov 8.


Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed.

Regoes RR, Hamblin S, Tanaka MM.

Proc Biol Sci. 2013 Jan 7;280(1750):20122047. doi: 10.1098/rspb.2012.2047. Epub 2012 Nov 7.


Analysis of the subunit stoichiometries in viral entry.

Magnus C, Regoes RR.

PLoS One. 2012;7(3):e33441. doi: 10.1371/journal.pone.0033441. Epub 2012 Mar 30.


Influence of the fibroblastic reticular network on cell-cell interactions in lymphoid organs.

Graw F, Regoes RR.

PLoS Comput Biol. 2012;8(3):e1002436. doi: 10.1371/journal.pcbi.1002436. Epub 2012 Mar 22.


Restricted occupancy models for neutralization of HIV virions and populations.

Magnus C, Regoes RR.

J Theor Biol. 2011 Aug 21;283(1):192-202. doi: 10.1016/j.jtbi.2011.06.004. Epub 2011 Jun 12.


Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies.

Rusert P, Krarup A, Magnus C, Brandenberg OF, Weber J, Ehlert AK, Regoes RR, Günthard HF, Trkola A.

J Exp Med. 2011 Jul 4;208(7):1419-33. doi: 10.1084/jem.20110196. Epub 2011 Jun 6.


Comparison of cytotoxic T lymphocyte efficacy in acute and persistent lymphocytic choriomeningitis virus infection.

Graw F, Richter K, Oxenius A, Regoes RR.

Proc Biol Sci. 2011 Nov 22;278(1723):3395-402. doi: 10.1098/rspb.2011.0453. Epub 2011 Mar 30.


Vaccination alters the balance between protective immunity, exhaustion, escape, and death in chronic infections.

Johnson PL, Kochin BF, McAfee MS, Stromnes IM, Regoes RR, Ahmed R, Blattman JN, Antia R.

J Virol. 2011 Jun;85(11):5565-70. doi: 10.1128/JVI.00166-11. Epub 2011 Mar 16.


Population biological principles of drug-resistance evolution in infectious diseases.

zur Wiesch PA, Kouyos R, Engelstädter J, Regoes RR, Bonhoeffer S.

Lancet Infect Dis. 2011 Mar;11(3):236-47. doi: 10.1016/S1473-3099(10)70264-4. Review.


MPER-specific antibodies induce gp120 shedding and irreversibly neutralize HIV-1.

Ruprecht CR, Krarup A, Reynell L, Mann AM, Brandenberg OF, Berlinger L, Abela IA, Regoes RR, Günthard HF, Rusert P, Trkola A.

J Exp Med. 2011 Mar 14;208(3):439-54. doi: 10.1084/jem.20101907. Epub 2011 Feb 28.


Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation.

Takizawa H, Regoes RR, Boddupalli CS, Bonhoeffer S, Manz MG.

J Exp Med. 2011 Feb 14;208(2):273-84. doi: 10.1084/jem.20101643. Epub 2011 Feb 7.


Theoretical analysis of the evolution of immune memory.

Graw F, Magnus C, Regoes RR.

BMC Evol Biol. 2010 Dec 8;10:380. doi: 10.1186/1471-2148-10-380. Erratum in: BMC Evol Biol. 2011;11:54.


Epidemiological and clinical consequences of within-host evolution.

Alizon S, Luciani F, Regoes RR.

Trends Microbiol. 2011 Jan;19(1):24-32. doi: 10.1016/j.tim.2010.09.005. Epub 2010 Nov 4. Review.


Population genetics meets cancer genomics.

Regoes RR.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18241-2. doi: 10.1073/pnas.1013177107. Epub 2010 Oct 8. No abstract available.


Similar impact of CD8+ T cell responses on early virus dynamics during SIV infections of rhesus macaques and sooty mangabeys.

Kouyos RD, Gordon SN, Staprans SI, Silvestri G, Regoes RR.

PLoS Comput Biol. 2010 Aug 26;6(8). pii: e1000901. doi: 10.1371/journal.pcbi.1000901.


Estimating the stoichiometry of HIV neutralization.

Magnus C, Regoes RR.

PLoS Comput Biol. 2010 Mar 19;6(3):e1000713. doi: 10.1371/journal.pcbi.1000713.


Investigating CTL mediated killing with a 3D cellular automaton.

Graw F, Regoes RR.

PLoS Comput Biol. 2009 Aug;5(8):e1000466. doi: 10.1371/journal.pcbi.1000466. Epub 2009 Aug 21.


Estimating the stoichiometry of human immunodeficiency virus entry.

Magnus C, Rusert P, Bonhoeffer S, Trkola A, Regoes RR.

J Virol. 2009 Feb;83(3):1523-31. doi: 10.1128/JVI.01764-08. Epub 2008 Nov 19.

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