List of publications by Viktor Müller
Research Papers
1. Müller, V., Marée, A. F. M. & De Boer, R. J. (2001) Release of virus from lymphoid tissue
affects human immunodeficiency virus type 1 and hepatitis C virus kinetics in the blood. J
Virol 75, 2597-2603.
2. Müller, V., Marée, A. F. & De Boer, R. J. (2001) Small variations in multiple parameters
account for wide variations in HIV-1 set-points: a novel modelling approach. Proc Roy Soc
Lond B 268, 235-242.
3. Müller, V., Vigueras-Gomez, J. F. & Bonhoeffer, S. (2002) Decelerating decay of latently
infected cells during prolonged therapy for human immunodeficiency virus type 1 infection. J
Virol 76, 8963-8965.
4. Müller, V. & Bonhoeffer, S. (2003) Quantitative constraints on the scope of negative
selection. Trends Immunol 24, 132-135.
Response to comment: Müller, V. & Bonhoeffer, S. (2003) Response to Bandeira and
Faro: Closing the circle of constraints. Trends Immunol 24, 173-5.
5. Bonhoeffer, S., Funk, G. A., Günthard, H. F., Fischer, M. & Müller, V. (2003) Glancing
behind virus load variation in HIV-1 infection. Trends Microbiol 11, 499-504.
6. Bretscher, M. T., Althaus, C. L., Müller, V. & Bonhoeffer, S. (2004) Recombination in
HIV and the evolution of drug resistance: for better or for worse? Bioessays 26, 180-188.
7. Müller, V. & Bonhoeffer, S. (2005) Guanine–adenine bias: a general property of retroid
viruses that is unrelated to host-induced hypermutation. Trends Genet, 21, 264-268.
8. Müller, V., Ledergerber, B., Perrin, L., Klimkait, T., Furrer, H., Telenti, A., Bernasconi, E.,
Vernazza, P., Günthard, H. F., Bonhoeffer, S., and the Swiss HIV Cohort Study. (2006)
Stable virulence levels in the HIV epidemic of Switzerland over two decades. AIDS, 20, 889894.
9. Müller, V. & De Boer, R. J. (2006) The integration hypothesis: an evolutionary pathway to
benign SIV infection. PLoS Pathog 2(3), e15.
10. Huigen, M. C., de Graaf, L., Eggink, D., Schuurman, R., Müller, V., Stamp, A.,
Stammers, D. K., Boucher, C. A. & Nijhuis, M. (2007) Evolution of a novel 5-amino-acid
insertion in the beta3-beta4 loop of HIV-1 reverse transcriptase. Virology, 364, 395-406.
11. Bartha, I., Simon, P. & Müller, V. (2008) Has HIV evolved to induce immune
pathogenesis? Trends Immunol 29, 322-328.
12. Sloot, P. M., Coveney, P. V., Ertaylan, G., Müller, V., Boucher, C. A. & Bubak, M.
(2009) HIV decision support: from molecule to man. Phil Trans R Soc A 367, 2691-2703.
13. Müller, V., Maggiolo, F., Suter, F., Ladisa, N., De Luca, A., Antinori, A., Sighinolfi, L.,
Quiros-Roldan, E., Carosi, G. & Torti, G. (2009) Increasing Clinical Virulence in Two
Decades of the Italian HIV Epidemic. PLoS Pathog 5(5), e1000454.
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14. Müller, V., von Wyl, V., Yerly, S., Böni, J., Klimkait, T., Bürgisser, P., Ledergerber, B.,
Günthard, H. F., Bonhoeffer, S. and the Swiss HIV Cohort Study (2009) African descent is
associated with slower CD4 decline in treatment-naïve patients of the Swiss HIV Cohort
Study. AIDS 23, 1269–1276.
15. Sousa, J. D. de, Müller, V., Lemey, P. & Vandamme, A-M. (2010). High GUD incidence
in the early 20th century created a particularly permissive time window for the origin and
initial spread of epidemic HIV strains. PLoS ONE 5(4): e9936.
16. Frentz, D., Boucher, C. A., Assel, M., De Luca, A., Fabbiani, M., Incardona, F., Libin, P.,
Manca, N., Müller, V., Nualláin, B. Ó., Paredes, R., Prosperi, M., Quiros-Roldan, E., Ruiz,
L., Sloot, P. M., Torti, C., Vandamme, A-M., Van Laethem, K., Zazzi, M. & van de Vijver,
D. A. (2010). Comparison of HIV-1 genotypic resistance test interpretation systems in
predicting virological outcomes over time. PLoS ONE 5(7): e11505.
17. Sadiq, S. K., Könnyü, B., Müller, V. & Coveney, P. V. (2011). Reaction kinetics of
catalyzed competitive heteropolymer cleavage. J Phys Chem B 115(37): 11017-27.
18. Herbeck, J. T., Müller, V., Maust, B. S., Ledergerber, B., Torti, C., Di Giambenedetto, S.,
Gras, L., Günthard, H. F., Jacobson, L. P., Mullins, J. I. & Gottlieb, G. S. (2012). Is the
virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease
progression and transmission. AIDS 26(2):193-205.
19. Kožíšek, M., Henke, S., Šašková, K. G., Jacobs, G. B., Schuch, A., Buchholz, B., Müller,
V., Kräusslich, H-G., Řezáčová P., Konvalinka, J. & Bodem, J. (2012). Mutations in HIV-1
gag and pol Compensate for the Loss of Viral Fitness Caused by a Highly Mutated Protease.
Antimicrob Agents Chemother 56(8): 4320-4330.
20. Sousa, J. D. de, Alvarez, C., Vandamme, A-M. & Müller, V. (2012). Enhanced
Heterosexual Transmission Hypothesis for the origin of pandemic HIV-1. Viruses 4(10):
1950-1983.
21. Könnyű B, Sadiq SK, Turányi T, Hírmondó R, Müller B, Kräusslich H-G, Coveney PV &
Müller V. (2013). Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology
Approach. PLoS Comput Biol 9(6): e1003103. doi:10.1371/journal.pcbi.1003103
22. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW,
Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF,
Bernasconi E, Vernazza P, Klimkait T, Yerly S, O’Brien SJ, Listgarten J, Pfeifer N, Lippert
C, Fusi N, Kutalik Y, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J
(2013). A genome-to-genome analysis of associations between human genetic variation, HIV1 sequence diversity, and viral control. eLife 2: e01123.
23. Bartha I, Assel M, Sloot PMA, Zazzi M, Torti C, Schülter E, De Luca A, Sönnerborg A,
Abecasis AB, Van Laethem K, Rosi A, Svärd J, Paredes R, van de Vijver DAMC, Vandamme
A-M & Müller V (2013). Superinfection with drug-resistant HIV is rare and does not
contribute substantially to therapy failure in a large European cohort. BMC Inf Dis 13:537.
24. Apari P, Sousa, J. D. de & Müller V (2014). Why Sexually Transmitted Infections Tend
to Cause Infertility: an Evolutionary Hypothesis. PLoS Pathog. 10(8): e1004111.
25. Rózsa L, Apari P & Müller V (2015). From bad to worse: can our microbiome turn
against us when we are old or seriously ill? Biology Direct 10: 3.
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26. Ferdinandy B, Mones E, Vicsek T & Müller V (2015). HIV competition dynamics over
sexual networks: first comer advantage conserves founder effects. PLoS Comput Biol 11(2):
e1004093.
Review
Müller, V. & Bonhoeffer, S. (2003) Mathematical approaches in the study of viral kinetics
and drug resistance in HIV-1 infection. Curr Drug Targets – Infect Disord 3, 329-344.
Book Chapter
Müller, V. & Bonhoeffer, S. (2008) Intra-host dynamics and evolution of HIV infection. In:
Origin and Evolution of Viruses, (Domingo, E., Holland, J., Parrish, C., eds) Second Edition,
Elsevier pp 279-301.
Commentaries and Editorials
Abecasis, A. B. & Müller, V. (2010) Dynamics of Transmitted HIV-1 Drug Resistance - The
San Francisco Model. AIDS Rev 12, 122-123.
Müller, V., Fraser, C. & Herbeck, J. T. (2011) A strong case for viral genetic factors in HIV
virulence. Viruses 3, 204-216.
Müller, V. (2012). A plea for caution: huge risks associated with lab-bred flu. Viruses 4, 276279.