PUBLICATIONS

The following are some representative publications to illustrate the sort of research being conducted by the MAGPIE team.

MATHEMATICS FOR EVOLUTIONARY TREES

Colijn, Caroline and Plazzotta, Giacomo (2017). A metric on phylogenetic tree shapes. Systematic Biology 67, 1: 113-126. Oxford University Press.

Kendall, Michelle, Ayabina, Diepreye, Xu, Yuanwei, Stimson, James and Colijn, Caroline (2018). Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees. Statistical Science 33, 1: 70-85. Institute of Mathematical Statistics.

Metzig, Cornelia and Colijn, Caroline (2018). Preferential Attachment in Systems and Networks of Constant Size. arXiv preprint arXiv:1811.04972.

Colijn, Caroline, Jones, Nick, Johnston, Iain G., Yaliraki, Sophia and Barahona, Mauricio (2017). Toward precision healthcare: context and mathematical challenges, Frontiers in Physiology 8, 136. Frontiers.

MODELLING DIVERSE PATHOGENS

Hall, Matthew and Colijn, Caroline (2018). Transmission trees on a known pathogen phylogeny: enumeration and sampling. bioRxiv 160812. Cold Spring Harbor Laboratory.

Kendall, Michelle, Ayabina, Diepreye, Xu, Yuanwei, Stimson, James and Colijn, Caroline (2018). Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees. Statistical Science 33, 1: 70-85. Institute of Mathematical Statistics.

Lees, John A., Kendall, Michelle, Parkhill, Julian, Colijn, Caroline, Bentley, Stephen D. and Harris, Simon R. (2018). Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study. Wellcome Open Research 3. The Wellcome Trust.

Colijn, Caroline and Plazzotta, Giacomo (2017). A metric on phylogenetic tree shapes. Systematic Biology 67, 1: 113-126. Oxford University Press.

GENOMIC EPIDEMIOLOGY

Didelot, Xavier, Fraser, Christophe, Gardy, Jennifer and Colijn, Caroline (2017). Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Molecular Biology and Evolution 34, 4: 997-1007. Oxford University Press.