PUBLICATIONS

The following are some representative publications to illustrate the 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. (Link)

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. (Link)

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

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. (Link)

Lui, Pengyu. (2019) A tree distinguishing polynomial. arXiv preprint. (Link)

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. (Link)

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 (Link)

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. (Link)