Applied mathematics and data science to tackle infectious diseases
Here you can find lists of selected publications and grants relevant to infectious diseases. Visit the webpage of members of the group to see complete lists relevant to infectious diseases and other topics.
Francisco J. Perez-Reche, Nick Taylor, Chris McGuigan, Philip Conaglen, Ken J. Forbes, Norval J. Strachan and Naomi Honhold. Estimated Dissemination Ratio -a practical alternative to the Reproduction Number for infectious diseases. Front. Public Health (Accepted, 14 Jun 2021). Link
FJ Perez-Reche, O Rotariu, BS Lopes, KJ Forbes, and NJC Strachan. Mining whole genome sequence data to efficiently attribute individuals to source populations. Sci. Rep. 10, 1214 (2020). Link
F Perez-Reche, KJ Forbes, NJC Strachan. Importance of untested infectious individuals for the suppression of COVID-19 epidemics. (2020) medRxiv
FJ Perez-Reche, NJC Strachan. Estimating the number of COVID-19 cases being introduced into UK Higher Education Institutions during Autumn 2020. (2020) medRxiv
E. Mourkas, A. J. Taylor, G. Méric, S. C. Bayliss, B. Pascoe, L. Mageiros, J. K. Calland, M. D. Hitchings, A. Ridley, A. Vidal, K. J. Forbes, N. J. C. Strachan, C. T. Parker, J. Parkhill, K. A. Jolley, A. J. Cody, M. C. J. Maiden, D. J. Kelly, S. K. Sheppard, Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. PNAS. 117, 11018–11028 (2020). Link
E. Franz, O. Rotariu, B. S. Lopes, J. L. Bono, C. Laing, V. Gannon, A. H. A. M. Van Hoek, I. Friesema, N. P. French, T. George, P. J. Biggs, P. Jaros, M. Rivas, I. Chinen, J. Campos, G. E. Mellor, P. S. Chandry, F. Perez-Reche, K. J. Forbes, N. J. Strachan, Reply to Baba and Kanamori. Clinical Infectious Diseases. 71, 1353–1355 (2020). Link
S. N. Taraskin, F. J. Pérez-Reche, Bifurcations in synergistic epidemics on random regular graphs. J. Phys. A: Math. Theor. 52, 195101 (2019). Link
A. Painset, J. T. Björkman, K. Kiil, L. Guillier, J.-F. Mariet, B. Félix, C. Amar, O. Rotariu, S. Roussel, F. Perez-Reche, S. Brisse, A. Moura, M. Lecuit, K. Forbes, N. Strachan, K. Grant, E. Møller-Nielsen, T. J. Dallman, LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe. Microbial Genomics. 5 (2019). Link
P. A. Dzianach, G. A. Dykes, N. J. C. Strachan, K. J. Forbes, F. J. Pérez-Reche, Challenges of biofilm control and utilization: lessons from mathematical modelling. Journal of The Royal Society Interface. 16, 20190042 (2019). Link
S. P. Rushton, R. A. Sanderson, P. J. Diggle, M. D. F. Shirley, A. P. Blain, I. Lake, J. A. Maas, W. D. K. Reid, J. Hardstaff, N. Williams, N. R. Jones, D. Rigby, N. J. C. Strachan, K. J. Forbes, P. R. Hunter, T. J. Humphrey, S. J. O’Brien, Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden. Journal of Translational Medicine. 17, 34 (2019). Link
E. Franz, O. Rotariu, B. S. Lopes, M. MacRae, J. L. Bono, C. Laing, V. Gannon, R. Söderlund, A. H. A. M. van Hoek, I. Friesema, N. P. French, T. George, P. J. Biggs, P. Jaros, M. Rivas, I. Chinen, J. Campos, C. Jernberg, K. Gobius, G. E. Mellor, P. S. Chandry, F. Perez-Reche, K. J. Forbes, N. J. C. Strachan, Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7. Clinical Infectious Diseases (2018). Link
K.J. Forbes, B.L. Lopes and N. Strachan. iCaMPS-4. Employing Source Attribution and Molecular Epidemiology to measure the impact of interventions on human campylobacteriosis in Scotland. An extension focused on the role of Scottish broiler production on human campylobacteriosis cases. (2018) Link
M. Bao, G. J. Pierce, S. Pascual, M. González-Muñoz, S. Mattiucci, I. Mladineo, P. Cipriani, I. Bušelić, N. J. C. Strachan, Assessing the risk of an emerging zoonosis of worldwide concern: anisakiasis. Scientific Reports. 7, 43699 (2017). Link
E. M. Nielsen, J. T. Björkman, K. Kiil, K. Grant, T. Dallman, A. Painset, C. Amar, S. Roussel, L. Guillier, B. Félix, O. Rotariu, F. Perez‐Reche, K. Forbes, N. Strachan, Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis. EFSA Supporting Publications. 14, 1151E (2017). Link
J. Gómez-Gardeñes, L. Lotero, S. N. Taraskin, F. J. Pérez-Reche, Explosive Contagion in Networks. Scientific reports. 6, 19767 (2016). Link
P Clusella, P Grassberger, FJ Perez-Reche, A Politi. Immunization and Targeted Destruction of Networks using Explosive Percolation Phys. Rev. Lett. 117(20), 208301 (2016). Link
V. Gupta, S. Haider, U. Sood, J. A. Gilbert, M. Ramjee, K. Forbes, Y. Singh, B. S. Lopes, R. Lal, Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach. Scientific Reports. 6, 29043 (2016). Link
D. Broder-Rodgers, F. J. Pérez-Reche, S. N. Taraskin, Effects of local and global network connectivity on synergistic epidemics. Physical Review E. 92, 062814 (2015). Link
S. N. Taraskin, F. J. Pérez-Reche, Effects of variable-state neighborhoods for spreading synergystic processes on lattices. Physical Review E. 88, 062815 (2013). Link
F. J. Pérez-Reche, S. N. Taraskin, W. Otten, M. P. Viana, L. D. F. Costa, C. a. Gilligan, Prominent Effect of Soil Network Heterogeneity on Microbial Invasion. Physical Review Letters. 109, 098102 (2012). Link
F. J. Pérez-Reche, F. M. Neri, S. N. Taraskin, C. A. Gilligan, Prediction of invasion from the early stage of an epidemic. Journal of the Royal Society Interface. 9 (2012). Link
F. J. Pérez-Reche, J. J. Ludlam, S. N. Taraskin, C. A. Gilligan, Synergy in Spreading Processes: From Exploitative to Explorative Foraging Strategies. Physical Review Letters. 106, 218701 (2011). Link
M. C. James, A. S. Bowman, K. J. Forbes, F. Lewis, J. E. Mcleod, L. Gilbert, Environmental determinants of Ixodes ricinus ticks and the incidence of Borrelia burgdorferi sensu lato, the agent of Lyme borreliosis, in Scotland. Parasitology. 140, 237–246 (2013). Link
T. P. Handford, F. J. Pérez-Reche, S. N. Taraskin, L. Da. F. Costa, M. Miazaki, F. M. Neri, C. A. Gilligan, Epidemics in networks of spatially correlated three-dimensional root-branching structures. Journal of the Royal Society Interface. 8 (2011). Link
F. M. Neri, A. Bates, W. S. Füchtbauer, F. J. Pérez-Reche, S. N. Taraskin, W. Otten, D. J. Bailey, C. A. Gilligan, The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System. PLoS Computational Biology. 7, e1002174 (2011). Link
F. M. Neri, F. J. Pérez-Reche, S. N. Taraskin, C. A. Gilligan, Heterogeneity in susceptible-infected-removed (SIR) epidemics on lattices. Journal of the Royal Society Interface. 8 (2011). Link
F. J. Pérez-Reche, S. N. Taraskin, L. da F. Costa, F. M. Neri, C. A. Gilligan, Complexity and anisotropy in host morphology make populations less susceptible to epidemic outbreaks. Journal of The Royal Society Interface. 7, 1083–1092 (2010). Link
SK Sheppard, JF Dallas, NJC Strachan, M Macrae, ND McCarthy, D Falush, ID Ogden, MCJ Maiden, KJ Forbes. Campylobacter Genotyping to Determine the Source of Human Infection. Clinical Infectious Diseases, 48, 1072-1078 (2009). Link
PFM Teunis, ID Ogden, NJC Strachan. Hierarchical dose response of E. coli O157:H7 from human outbreaks incorporating heterogeneity in exposure. Epidemiology & Infection 136(6) 761 (2008). Link
K Forbes, N Strachan and M Maiden. Employing source attribution and molecular epidemiology to measure the impact of interventions on human campylobacteriosis in Scotland. Food Standards Scotland, i-CaMPS-4. (2015-2017) £230,000.
N Strachan, K Forbes and F Perez-Reche. Listeria whole genome sequencing. EFSA. (2014-2016) €70,000 (part of a €420,000 project with the Danish Statens Serum Institut (SSI), French Agency for Food, Environmental and Occupational Health and Safety (ANSES) and Public Health England (PHE)).
K Forbes and N Strachan. Next Generation Sequencing of E. coli O157 isolates from humans, food and the environment. FSAS & the University of Aberdeen. (2012-2013) £30,500.
K Forbes and F Perez-Reche. A Microbiological Survey of Minced Beef on Retail Sale in Scotland. SAC Commercial. (2018-2020) £4188.
F Perez-Reche, P Grassberger, A Politi and F Ginelli. Complex percolation for epidemics on networks and applications of mutual information. Leverhulme Trust (2015-2016) £18,300.
F Perez-Reche, A Politi and R Levi. Networks: From structure to function. EPSRC NetworkPlus “Emergence and Physics Far From Equilibrium” (2019) £10,550.
K Killham, N Strachan, et al. Reducing E. coli O157 risk in rural communities. ESRC (2007-2010) £1.48M FEC.
N Strachan. Expert opinion on preparation of rare beef burgers. Aberdeen City Council. (2016) £2323.
N Strachan. Providing lectures for a risk assessment course. EU BTSF (2015-2018) €6000.
N Strachan, G Pierce and I Theodossiou. EU parasite risk assessment with integrated tools in EU fish production value chains –PARASITE (2012-2015), EU, €4.0M, €210,000 to Aberdeen.
F Perez-Reche, N Strachan, G Dykes, K Forbes. Campylobacter jejuni biofilm structure and cell dispersal £70,000 from Curtin University and University of Aberdeen Collaborative Scholarship (2017-21).
K Forbes, N Strachan, M Stevens, A Psifidi, L Vervelde. A systems-wide approach to the control of Campylobacter in the food chain: exploiting genetic variation. £806,000 from Scottish Government RESAS (2016-19).
N Strachan, K Forbes, O Rotariu O, C McGuigan. Factors affecting variations in Campylobacter disease rates in Scotland. £399,849 from Food Standards Scotland (2014-18).
S O'Brien, M Bennett, P Diggle, K Forbes, R Griffith, T Humphrey, P Hunter, I Lake, D Rigby, S Rushton, N Strachan, R Wadsworth, C Winstanley, B Wren. Sources, Seasonality, Transmission and Control: Campylobacter and human behaviour in a changing environment. £3,419,121 from MRC (2012 -2017).
K Forbes, I Ogden, N Strachan, M Maiden. i-CaMPS-3. Employing Source Attribution and Molecular Epidemiology to measure the impact of interventions on human campylobacteriosis in Scotland. £754,875 from Food Standards Agency (2012-16).
K Forbes, N Strachan and D Smith. Foodborne pathogen adaptation and survival through the food chain. £212,722 from RERAD (2011-16).