The goals of this proposal are to improve our understanding of both the evolution and management of influenza by developing a unified modeling framework. In particular, the questions we will address are (1) How do given strain and subtype structures, and the associated patterns of cross-reactivity, affect disease dynamics? (2) How does cross-reactivity affect pathogen evolution? (3) How do strain structure and patterns of cross-reactivity self-organize over evolutionary time, for example into quasi-species, and how does this organization feed back to affect dynamics? (4) What are the implications of these issues for vaccination strategies, and what are the reciprocal effects of vaccination programs upon the organization of the viral population?
| Forsberg, Roald; Drummond, Alexei J; Hein, Jotun (2005) Tree measures and the number of segregating sites in time-structured population samples. BMC Genet 6:35 |
| Levin, Simon A; Dushoff, Jonathan; Plotkin, Joshua B (2004) Evolution and persistence of influenza A and other diseases. Math Biosci 188:17-28 |
| Feng, Zhilan; Smith, David L; McKenzie, F Ellis et al. (2004) Coupling ecology and evolution: malaria and the S-gene across time scales. Math Biosci 189:1-19 |
| Dushoff, Jonathan; Plotkin, Joshua B; Levin, Simon A et al. (2004) Dynamical resonance can account for seasonality of influenza epidemics. Proc Natl Acad Sci U S A 101:16915-6 |
| Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret et al. (2004) An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol 21:1913-22 |
| Einer-Jensen, Katja; Ahrens, Peter; Forsberg, Roald et al. (2004) Evolution of the fish rhabdovirus viral haemorrhagic septicaemia virus. J Gen Virol 85:1167-79 |
| Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald et al. (2004) A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 32:4925-36 |
| Forsberg, Roald; Christiansen, Freddy Bugge (2003) A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol Biol Evol 20:1252-9 |
| Plotkin, Joshua B; Dushoff, Jonathan (2003) Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proc Natl Acad Sci U S A 100:7152-7 |
| Rodrigo, Allen G; Goode, Matthew; Forsberg, Roald et al. (2003) Inferring evolutionary rates using serially sampled sequences from several populations. Mol Biol Evol 20:2010-8 |
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