Bonhoeffer Group

Evolution of drug resistance

We use mathematical/computational models to investigate the evolution of drug resistance in viruses and bacteria. The models are used in part for parameter inference and in part for simulation.  Most of this work is carried out in close collaboration with experimentalists and clinicians. 

Key publications:

• Regoes, RR, Bonhoeffer, S
  Emergence of drug-resistant influenza virus: Population dynamical
  considerations
  SCIENCE (2006) 312:389-391
  Abstract
  
• Bonhoeffer, S, Chappey, C, Parkin, NT, Whitcomb, JM,
  Petropoulos, CJ
  Evidence for positive epistasis in HIV-1
  SCIENCE (2004) 306:1547-1550
  Abstract
• Levin, BR, Lipsitch, M, Bonhoeffer, S
  Evolution and disease - Population biology, evolution, and infectious disease: Convergence and synthesis
  SCIENCE (1999)
  283:806-809
  Abstract

Evolution of sex and recombination

The evolutionary benefit of sexual reproduction/recombination remains one of the major unsolved problems in evolution. Our interest in the evolution of recombination started with our attempts to obtain a better understanding of the role of recombination in HIV for the evolution of drug resistance. It turned out that HIV is an interesting model system to study the evolution of recombination in a more general context. Currently we study the evolution of recombination modifiers and the maintenance of sex in to test various leading hypotheses for the evolutionary origin and maintenance of sex.

Key publications:

• Salathe, M, Kouyos, RD, Bonhoeffer, S
  The state of affairs in the kingdom of the Red Queen
  TRENDS IN ECOLOGY & EVOLUTION (2008) 23:439-445
  Abstract
• Kouyos, RD, Silander, OK, Bonhoeffer, S
  Epistasis between deleterious mutations and the evolution of recombination
  TRENDS IN ECOLOGY & EVOLUTION (2007) 22:308-315
  Abstract
  

Evolution on complex fitness landscapes

Populations evolve on complex fitness landscapes. Currently little is known about the generic properties of realistic fitness landscapes. We have recently investigated the evolution of sexual reproduction/recombination on complex fitness landscapes. Ongoing work focuses on reconstructing good approximations for realistic fitness landscapes from experimental data.

Key publications:

Misevic, D, Kouyos, RD, Bonhoeffer, S
Predicting the Evolution of Sex on Complex Fitness Landscapes
PLOS COMPUTATIONAL BIOLOGY (2009) 5:-
Abstract

Molecular epidemiology and phylogenetics

As more and more genetic data on pathogens are becoming available, we are developing and applying phylogenetic approaches to infer critical parameters of infectious disease epidemiology.

Key publications:

Kouyos, RD et al
Predicting the Evolution of Sex on Complex Fitness Landscapes
JOURNAL OF INFECTIOUS DISEASE, in press