Selected recent publications
Data-driven models for regional coral-reef dynamics. Zychaluk, K., Bruno, J.F., Clancy, D., McClanahan, T.R. and Spencer, M. Ecology Letters (accepted). Also has code and supporting information.
Empirical models of transitions between coral reef states: effects of regions, marine protected areas, and environmental change scenarios. Lowe, P.K., Bruno, J.F., Selig, E.R. and Spencer, M. PLoS ONE 6(11):e26339.
Quantifying parameter uncertainty in a coral reef model using Metropolis-Coupled Markov Chain Monte Carlo. D. Clancy, J. E. Tanner, S. McWilliam and M. Spencer (2010). Ecological Modelling 221:1337-1347 (the authoritative version is here). Also has an appendix.
A phylogenetic mixture model for gene family loss in parasitic bacteria. M. Spencer and A. Sangaralingam (2009). Molecular Biology and Evolution 26:1901-1908 (the authoritative version is here). Also has an appendix and an erratum.
Lotka-Volterra competition models for sessile organisms, Matthew Spencer and Jason Tanner (2008). Ecology 89: 1134-1143 (the authoritative version is here). Also has an appendix.
Past states of continuous-time Markov models for ecological communities, M. Spencer (2008). Mathematical Biosciences 211: 299-313 (the authoritative version is here).
Conditioned genome reconstruction: how to avoid choosing the conditioning genome M. Spencer, D. Bryant, E. Susko (2007). Systematic Biology 56: 25-43 (the authoritative version is here).
Testing for covarion-like evolution in protein sequences Wang, H.-C., Spencer, M., Susko, E. and Roger, A.J. (2007). Molecular Biology and Evolution 24: 294-305 (the authoritative version is here).
Sensitivity analysis of Markov models for communities of competing sessile organisms M. Spencer (2006), Journal of Animal Ecology 75: 1024-1033 (the authoritative version is here).
Modelling prokaryote gene content M. Spencer, E. Susko, A. J. Roger (2006). Evolutionary Bioinformatics Online 2:165-186 (the authoritative version is here).
Continuous-time Markov models for species interactions M. Spencer and E. Susko (2005). Ecology 86: 3272-3278 (the authoritative version is here).
Authenticity of ancient DNA results: a statistical approach. M. Spencer and C.J. Howe (2004). American Journal of Human Genetics 75: 240-250 (the authoritative version is here).
For a full list of publications, see my cv.
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