Here is a list of some publications I quite like, in no particular order.

• Etherington, G. J., Ring, S. M., Charleston, M. A., Dicks, J., Rayward-Smith, V. and Roberts, I. N., Journal of General Virology (accepted).
• Jermiin, L. S., Poladian, L. and Charleston, M. A. Is the "Big Bang" in Animal Evoluton Real? Science, 2005 310:1910-1911.
• Charleston, M. A. Jungles: A new solution to the host-parasite phylogeny problem. Mathematical Biology 149:191-223, 1998. (pdf) (ps)
• Charleston, M. A. Towards a characterization of landscapes of combinatorial optimisation problems, with special reference to the phylogeny problem. Journal of Computational Biology 2:439-450, 1995.
• Charleston, M. A. Hitch-hiking: A parallel heuristic search strategy, applied to the phylogeny problem. Journal of Computational Biology 8(1):79-91, 2001.
• Charleston, M. A. Principles of cophylogeny maps. In Biological Evolution and Statistical Physics, Springer-Verlag, edited by Michael Lässig and Angelo Valleriani, 2002.
• Charleston, M. A. Recent advances in cophylogeny mapping. In Advances in Parasitology, volume 54, edited by D. T. J. Littlewood, Elsevier Academic Press, Amsterdam, 2003. (pdf)
• Charleston, M. A. and Perkins, S. L. Lizards, Malaria, and Jungles in the Caribbean. In Tangled trees: phylogeny, cospeciation, and coevolution (University of Chicago Press, Chicago), edited by R. D. M. Page, pp65-92, 2002.
• Charleston, M. A. and Robertson, D. L. Host Switching in Lentiviruses Can Account for Phylogenetic Similarity with the Primate Phylogeny. Systematic Biology 51(3):528-535, 2002. (pdf)
• Jackson, A. P. and Charleston, M. A. A cophylogenetic perspective of RNA-virus evolution. Molecular Biology and Evolution 21(1):45-57, 2004. (pdf)
• Mu, J., Joy, D. A., Huang, Y., Carlton, J., Walker, J, Barnwell, J., Beerli, P., Charleston, M. A., Pybus, O. G. and Su, X. Z. Host switch leads to emergence of Plasmodium vivax malaria in humans. Molecular Biology and Evolution 22(8):1686-1693, 2005.
• Page, R. D. M. and Charleston, M. A. Trees within trees: phylogeny and historical associations. TREE 13(9):356-359}, 1998.
• Page, R. D. M. and Charleston, M. A. Comments on Allard and Carpenter (1996), or the "Aquatic Ape" Hypothesis Revisited. Cladistics 15(1):73-74, 1999. (pdf)
• Penny, D., McComish, B. J., Charleston, M. A. and Hendy, M. D. Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution. Journal of Molecular Evolution 53:711-723, 2001. (pdf)
• Pybus, O. G., Charleston, M. A., Gupta, S., Rambaut, A., Holmes, E. C., and Harvey, P. H. The Epidemic Behavior of the Hepatitis C Virus. Science 292(June):2323-2325, 2001.