PUBLICATIONS

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

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 Size. arXiv 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 shapes. Systematic 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 challenges, Frontiers in Physiology 8, 136. Frontiers. (Link)

MODELLING DIVERSE PATHOGENS

Caroline Colijn, Jukka Corander, and Nicholas J. Croucher. (2020). Designing ecologically optimized pneumococcal vaccines using population genomics. Nature 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. https://doi.org/10.1101/733642 (Link)

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)

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

James Stimson, Jennifer Gardy, Barun Mathema, Valeriu Crudu, Ted Cohen, Caroline Colijn, Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions, Molecular Biology and Evolution, Volume 36, Issue 3, March 2019, Pages 587–603, https://doi.org/10.1093/molbev/msy242 (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; doi: https://doi.org/10.1101/761411 (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)

OTHER

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)