Please also visit Carsten’s google scholar page for metrics on our publications. We strongly support open access as well as transparency, and publish our research open access whenever possible. If you cannot find any of the papers, code, or data, please contact me.

Journal Articles and Reviews


  • Domingues P*, Eletto D*, Magnus C*, Turkington HL, Schmutz S, Zagordi O, Lenk M, Huber M, Beer M, Stertz S, Hale BG. Profiling host ANP32A splicing landscapes to predict influenza A virus polymerase adaptation. Nature Communications 10. 3396(2019). Paper. Twitter. Shiny App. Analyses.


  • Bošková V, Stadler T* and Magnus C* (2018). The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic. Virus Evolution. Paper. Media coverage.
  • Reh L, Magnus C, Kadelka C, Kühnert D, Uhr T, Weber J, Morris L, Moore PL, Trkola A (2018). Phenotypic deficits in the HIV-1 Envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage. PLoS Pathogens 14(1): e1006825. Paper.
  • Barido-Sottani J*, Bošková V*, du Plessis L*, Kühnert D*, Magnus C*, Mitov V*, Müller N, Pečerska J*, Rasmussen DA*, Zhang C, Drummond A, Heath T, Pybus O, Vaughan T, Stadler T (2018). Taming the BEAST – A community teaching material resource for BEAST 2 –. Systematic Biology 67(1). 170-174. Paper. Media coverage.


  • Brandenberg OF*, Magnus C*, Rusert P, Günthard HF, Regoes RR, Trkola A (2017). Predicting in vivo efficacy of HIV-1 antibody neutralization from stoichiometric parameters. PLoS Pathogens 13(5): e1006313. Paper. Media coverage.
  • Beauparlant D, Rusert P, Magnus C, Kadelka C, Weber J, Uhr T, Zagordi O, Oberle C, Duenas-Decamp MJ, Clapham P, Metzner KJ, Günthard HF, Trkola A (2017). Delineating CD4 dependency of HIV-1: Adaptation to infect low level CD4 expressing target cells widens cellular tropism but severely impacts on envelope functionality. PLoS Pathogens 13(3): e1006255. Paper.
  • Oberle CS, Magnus C, Joos B, Rusert P, Beauparlant D, Kouyos R, Trkola A, Metzner KJ, Günthard HF (2017). Reply to correspondence `Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a “stochastic” process' by Gonzalez et al. Retrovirology 14:14. Paper.


  • Oberle CS, Joos B, Rusert P, Campbell NK, Beauparlant D, Kuster H, Weber J, Schenkel CD, Scherrer AU, Magnus C, Kouyos R, Rieder P, Niederönst B, Braun DL, Pavlovic J, Böni J, Yerly S, Klimkait T, Aubert V, Trkola A, Metzner KJ, Günthard HF (2016). Tracing HIV-1 transmission: Envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology 13:62. Paper.
  • 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 and the Swiss HIV Cohort Study (2016). Determinants of HIV-1 broadly neutralising antibody induction. Nature Medicine.Vol 22. 1260-1267. Paper. Media coverage
  • Magnus C, Reh L, Trkola A (2016). HIV-1 resistance to neutralizing antibodies: Determination of antibody concentrations leading to escape mutant evolution. Virus Research. SI: Systems Biology. Vol 218. 57-70. Paper.


  • Regoes RR and Magnus C (2015). The Role of Chance in Primate Lentiviral Infectivity: From Protomer to Host Organism. Book chapter in: Progress in Molecular Biology and Translational Science: The Molecular Basis of Viral Infection. Vol 129: 327–351. Paper.
  • Brandenberg OF, Magnus C, Regoes RR, Trkola A (2015). The HIV-1 Entry Process: A Stoichiometric View. Trends in Mircrobiology 23(12). 763 - 774. Paper.
  • Reh L, Magnus C, Schanz M, Weber J, Uhr T, Rusert P, Trkola A (2015). Capacity of Broadly Neutralizing Antibodies to Inhibit HIV-1 Cell-Cell Transmission is Strain- and Epitope-Dependent. PLoS Pathogens 11(7): e1004966. Paper.
  • Abel zur Wiesch P, Abel S, Gkotzis S, Ocampo P, Engelstaedter J, Hinkley T, Magnus C, Waldor MK, Udekwu K, Cohen T (2015). Classic reaction kinetics can explain complex patterns of antibiotic action. Science Translational Medicine Vol 7(287). Paper.
  • Brandenberg OF, Magnus C, Rusert P, Regoes RR, Trkola A (2015). Different Infectivity of HIV-1 Strains Is Linked to Number of Envelope Trimers Required for Entry. PLoS Pathogens 11(1): e1004595. Paper.


  • Brandenberg OF, Rusert P, Magnus C, Weber J, Böni J, Günthard HF, Regoes RR, Trkola A (2014). Rescue of V1V2 Mutant Infectivity by 1 HIV-1 Cell-Cell Transmission Supports the Domain’s Exceptional Capacity for Sequence Variation. Retrovirology 11:75. Paper.


  • Magnus C, Brandenberg OF, Rusert P, Trkola A , Regoes RR (2013). Mathematical models: a key to understanding HIV envelope interactions? Journal of Immunological Methods. Journal of Immunological Methods 398-399: 1-18. Paper.
  • Magnus C (2013). Virus Neutralisation: New Insights from Kinetic Neutralisation Curves. PLOS Computational Biology 9(2):e1002900. Paper.


  • Alizon S* and Magnus C* (2012). Modelling the Course of an HIV Infection: Insights from Ecology and Evolution. Viruses 2012, 4, 1984-2013. Paper.
  • Magnus C and Regoes RR (2012). Analysis of the Subunit Stoichiometries in Viral Entry. PLoS ONE 7(3): e33441. Paper.


  • Rusert P, Krarup A*, Magnus C*, Brandenberg OF*, Weber J, Ehlert A-K, Regoes RR, GüŸnthard HF, Trkola A (2011). Interaction of the V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. The Journal of Experimental Medicine 208(7): 1419-1433. Paper. Media coverage.
  • Magnus C and Regoes RR (2011). Restricted Occupancy Models for Neutralization of HIV Virions and Populations. Journal of Theoretical Biology 283:192-202. Paper.


  • Graw F*, Magnus C* and Regoes RR (2010). Theoretical analysis of the evolution of immune memory. BMC Evolutionary Biology 2010 10:380. Paper.
  • Magnus C and Regoes RR (2010). Estimating the Stoichiometry of HIV Neutralization. PLoS Computational Biology 6(3):e1000713. Paper. Media coverage.


  • Magnus C, Rusert P, Bonhoeffer S, Trkola A and Regoes RR (2009). Estimating the Stoichiometry of Human Immunodeficiency Virus Entry. Journal of Virology 83(3):1523D1531. Paper. F1000 must read, Media coverage.

* equal contribution

Master theses

  • Francesco Bosia: The influence of viral within-host evolution on transmission chain reconstruction: a simulation study. ETH Zurich. 2017. Link
  • Ziliya Usmanova: Estimating the time of antibody-induced mutant evolution in HIV infection ETH Zurich. 2018. Link