Kendall, M.*, Ferretti, L.*, Wymant, C., Tsallis, D., Petrie, J., Di Francia, A., Di Lauro, F., Abeler-Dörner, L., Manley, H., Panovska-Griffiths, J., Ledda, A., Didelot, X., Fraser, C. (2024) Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements, Science, 385 (6710) eadm8103. [pdf]
My publications are listed here, each with a link to the full text pdf where possible. They are organised into three broad categories: COVID-19, Phylogenetic trees and transmission trees, and Key predistribution.
COVID-19
Sherratt K., Carnegie, A. C., Kucharski, A., Cori, A., Pearson, C. A. B., Jarvis, C. I., Overton, C., Weston, D., Hill, E. M., Knock, E., Fearon, E., Nightingale, E., Hellewell, J., Edmunds, W. J., Villabona Arenas, J., Prem, K., Pi, L., Baguelin, M., Kendall, M., Ferguson, N., Davies, N., Eggo, R. M., van Elsland, S., Russell, T., Funk, S., Liu, Y., Abbott, S. (2024) Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic [version 1; peer review: 2 approved], Wellcome Open Research, 9:12. [pdf]
Ferretti, L., Wymant, C., Petrie, J., Tsallis, D., Kendall, M., Ledda, A., Di Lauro, F., Fowler, A., Di Francia, A., Panovska-Griffiths, J., Abeler-Dörner, L., Charalambides, M., Briers, M., Fraser, C. (2023) Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts, Nature, 626, 145–-150. [pdf]
Kendall, M., Tsallis, D., Wymant, C., Di Francia, A., Balogun, Y., Didelot, X., Ferretti, L., Fraser, C. (2023) Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year, Nature Communications, 14 858. [pdf]
Ferretti, L., Wymant, C., Nurtay, A., Zhao, L., Hinch, R., Bonsall, D., Kendall, M., Masel, J., Bell, J., Hopkins, S., Kilpatrick, A. M., Peto, T., Abeler-Dörner, L., Fraser, C. (2021) Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts, medRxiv preprint. [pdf]
Hinch, R., Probert, W. J. M., Nurtay, A., Kendall, M., Wymant, C., Hall, M., Lythgoe, K., Bulas Cruz, A., Zhao, L., Stewart, A., Ferretti, L., Montero, D., Warren, J., Mather, N., Abueg, M., Wu, N., Legat, O., Bentley, K., Mead, T., Van-Vuuren, K., Feldner-Busztin, D., Ristori, T., Finkelstein, A., Bonsall, D. G., Abeler-Dörner, L., Fraser, C. (2021) OpenABM-Covid19 - An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing, PLOS Computational Biology, 17(7): e1009146. [pdf]
Wymant, C.*, Ferretti, L.*, Tsallis, D., Charalambides, M., Abeler-Dörner, L., Bonsall, D., Hinch, R., Kendall, M., Milsom, L., Ayres, M., Holmes, C., Briers, M., Fraser, C. (2021) The epidemiological impact of the NHS COVID-19 App, Nature, 594, 408–412. [pdf]
Colizza, V., Grill, E., Mikolajczyk, R., Cattuto C., Kucharski, A., Riley, S., Kendall, M., Lythgoe, K., Bonsall, D., Wymant, C., Abeler-Dörner, L., Ferretti, L., Fraser, C. (2021) Time to evaluate COVID-19 contact-tracing apps, Nature Medicine, 27, 361-362. [pdf]
Kendall, M., Milsom, L., Abeler-Dörner, L., Wymant, C., Ferretti, L., Briers, M., Holmes, C., Bonsall, D., Abeler, J., Fraser, C. (2020) Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis, The Lancet Digital Health, 2(12):E658-E666. [pdf]
Ferretti, L., Ledda, A., Wymant, C., Zhao, L., Ledda, V., Abeler-Dörner, L., Kendall, M., Nurtay, A., Cheng, H., Ng, T., Lin, H., Hinch, R., Masel, J., Kilpatrick, A. M., Fraser, C. (2020) The timing of COVID-19 transmission, medRxiv preprint. [pdf]
Ferretti, L.*, Wymant, C.*, Kendall, M., Zhao, L., Nurtay, A., Abeler-Dörner, L., Parker, M., Bonsall, D., Fraser, C. (2020) Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing Science 368(6491). [pdf]
Phylogenetic trees and transmission trees
Torres Ortiz, A., Kendall, M., Storey, N., Hatcher, J., Dunn, H., Roy, S., Williams, R., Williams, C., Goldstein, R. A., Didelot, X., Harris, K., Breuer, J., Grandjean, L. (2023) Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks, eLife 12:e84384. [pdf]
Didelot, X., Helekal, D., Kendall, M., Ribeca, P. (2023) Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease, Bioinformatics, 39(1). [pdf]
Didelot, X., Kendall, M., Xu, Y., White, P. J., McCarthy, N. (2021) Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo Current Protocols, 1, e60. [pdf]
Lees, J. A., Kendall, M., Parkhill, J., Colijn, C., Bentley, S. D. and Harris, S. R. (2018) Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 2; referees: 3 approved], Wellcome Open Research, 3(33). [pdf]
Kendall, M., Ayabina, D., Xu, Y., Stimson, J. and Colijn, C. (2018) Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees, Statistical Science, 33(1):70-85 [pdf]
Kendall, M., Eldholm, V. and Colijn, C. (2018) Comparing phylogenetic trees according to tip label categories, bioRxiv preprint [pdf]
Grandjean, L. et al (2017) Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru, PLoS ONE, 12(12):e0189838 [pdf]
Ratmann, O. et al (2017) HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences, AIDS Research and Human Retroviruses, 33(11):1083-1098 [pdf]
Jombart, T.*, Kendall, M.*, Almagro-Garcia, J. and Colijn, C. (2017) treespace: statistical exploration of landscapes of phylogenetic trees, Molecular Ecology Resources, 17(6):1385-1392 [pdf]
Ratmann, O. et al (2017) Phylogenetic tools for generalized HIV-1 epidemics: findings from the PANGEA-HIV methods comparison, Molecular Biology and Evolution, 34(1):185-203 [pdf]
Kendall, M. and Colijn, C. (2016) Mapping phylogenetic trees to reveal distinct patterns of evolution, Molecular Biology and Evolution, 33(10):2735-2743 [pdf]
Key predistribution
Kendall, M. and Martin, K. M. (2016) Graph-theoretic design and analysis of key predistribution schemes, Designs, Codes and Cryptography, 81(1): 11-34
Kendall, M., Martin, K. M., Ng, S.-L., Paterson, M. B., & Stinson, D. R. (2014) Broadcast-enhanced key predistribution schemes, ACM Transactions on Sensor Networks, 11(1): 1–33
Kendall, M. (2013) Combinatorial Aspects of Key Predistribution for Resource-Constrained Networks, Doctoral Thesis, Royal Holloway, University of London. [pdf]
Kendall, E., Kendall, M. & Kendall, W.S. (2012) A generalised formula for calculating the resilience of random key predistribution schemes, eprint archive [pdf]
Kendall, M. and Martin, K. M. (2012) On the role of expander graphs in key predistribution schemes for wireless sensor networks, In Research in Cryptology, volume 7242 of Lecture Notes in Computer Science, 62-82