The following are some representative publications to illustrating research being conducted by the MAGPIE team (click to expand).

Mathematics for Evolutionary Trees

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

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

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

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

Modelling Diverse Pathogens

Chongguang Yang, Benjamin Sobkowiak, Vijay Naidu, Alexandru Codreanu, Nelly Ciobanu, Kenneth S. Gunasekera, Melanie H. Chitwood, Sofia Alexandru, Stela Bivol, Marcus Russi, Joshua Havumaki, Patrick Cudahy, Heather Fosburgh, Christopher J. Allender, Heather Centner, David M. Engelthaler, Nicolas A. Menzies, Joshua L. Warren, Valeriu Crudu, Caroline Colijn, Ted Cohen. (2021). Phylogeography and transmission of M. tuberculosis in Moldova. medRxiv 2021.06.30.21259748. doi: (Link)

Tyler S. Brown, Vegard Eldholm, Ola Brynildsrud, Magnus Osnes, Natalie Stennis, James Stimson, Caroline Colijn, Sofia Alexandru, Ecaterina Noroc, Nelly Ciobanu, Valeriu Crudu, Ted Cohen, Barun Mathema. (2021). Evolution and emergence of multidrug-resistant Mycobacterium tuberculosis in Chisinau, MoldovaMedRxiv. (Link)

Caroline Colijn, Jukka Corander, and Nicholas J. Croucher. (2020). Designing ecologically optimized pneumococcal vaccines using population genomicsNature microbiology. (Link)

Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene Bowers, David M. Engelthaler, Apurva Narechania, Julio Croda, Jason R. Andrews. (2019). Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference. biorxiv. (Link)

Hall, Matthew and Colijn, Caroline (2018). Transmission trees on a known pathogen phylogeny: enumeration and samplingbioRxiv 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 studyWellcome Open Research 3. The Wellcome Trust (Link)

Naidu, V. , Whalley, J. and Narayanan, A. (2017). Exploring the Effects of Gap-Penalties in Sequence-Alignment Approach to Polymorphic Virus Detection. Journal of Information Security, 8, 296-327. doi: 10.4236/jis.2017.84020. (Link

Genomic Epidemiology

Katharine S. Walter, Paulo César Pereira dos Santos, Thais Oliveira Gonçalves, Brunna Oliveira da Silva, Andrea da Silva Santos, Alessandra de Cássia Leite, Alessandra Moura da Silva, Flora Martinez Figueira Moreira, Roberto Dias de Oliveira, Everton Ferreira Lemos, Eunice Cunha, Yiran E. Liu, Albert Ko, Caroline Colijn, Ted Cohen, Barun Mathema, Julio Croda, Jason R. Andrews. (2021). The role of prisons in disseminating tuberculosis in Brazil: a genomic epidemiology study. medRxiv 2021.06.22.21259360. doi: (Link)

James Stimson, Jennifer Gardy, Barun Mathema, Valeriu Crudu, Ted Cohen, Caroline Colijn. (2019). Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular Biology and Evolution, 36, 3: 587–603. (Link)

Yuanwei Xu, Hollie Topliffe, James Stimson, Helen R. Stagg, Ibrahim Abubakar, Caroline Colijn (2019). Transmission analysis of a large TB outbreak in London: mathematical modelling study using genomic data. bioRxiv 761411; Microbial Genomics. (Link)

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)


Vaidyanathan, Venkatesh, et al. Effect of Ageing and Single Nucleotide Polymorphisms Associated with the Risk of Aggressive Prostate Cancer in a New Zealand Population. Molecular BioSystems, vol. 13, no. 10, 2017, pp. 1967–1980. (Link)

Vaidyanathan V, Naidu V, Karunasinghe N et al. SNP-SNP interactions as risk factors for aggressive prostate cancer [version 1; peer review: 2 approved]. F1000Research 2017, 6:621 (Link)

Vaidyanathan, Venkatesh, et al. Environmental Factors and Risk of Aggressive Prostate Cancer among a Population of New Zealand Men a Genotypic Approach. Molecular BioSystems, vol. 13, no. 4, 2017, pp. 681–698. (Link)

Naidu, V. , Whalley, J. and Narayanan, A. (2018). Generating Rule-Based Signatures for Detecting Polymorphic Variants Using Data Mining and Sequence Alignment Approaches. Journal of Information Security, 9, 265-298. doi: 10.4236/jis.2018.94019. (Link)