Publications

Below is a list of selected publications (sorted by year) illustrating the type of work conducted by our team.

ignoring entry 'munday24_forecastingebola' (line 537) because :
    A bibentry of bibtype 'Article' has to specify the field: journal

• Sherratt K, Grah R, Prasse B, Becker F, McLean J, Abbott S, Funk S (2025). “The influence of model structure and geographic specificity on predictive accuracy among European COVID-19 forecasts.” medRxiv. doi:10.1101/2025.04.10.25325611.

• Rao D, Tanveer A, Iftekhar E, Müller S, Sherratt K, Röbl K, Carrillo-Bustamante P, Heldt K, Fitzner J, Hanefeld J, Funk S (2025). “The utility of infectious disease modelling in informing policy for outbreak response: a scoping review.” medRxiv. doi:10.1101/2025.03.04.25323088.

• Hadley L, Rich C, Tasker A, Restif O, Funk S (2025). “How does policy modelling work in practice? A global analysis on the use of epidemiological modelling in health crises.” PLOS Global Public Health. doi:10.1371/journal.pgph.0004675.

• Hadley L, Rich C, Tasker A, Restif O, Funk S (2025). “Visual preferences for communicating modelling: a global analysis of COVID-19 policy and decision makers.” Infectious Disease Modelling. doi:10.1016/j.idm.2025.04.005.

• Stapper M, Funk S (2025). “Fine-Grid Spatial Interaction Matrices for Surveillance Models, with Application to Influenza in Germany.” medRxiv. doi:10.1101/2025.04.03.25325159.

• Bosse NI, Abbott S, Bracher J, van Leeuwen E, Cori A, Funk S (2024). “Human judgement forecasting of COVID-19 in the UK.” Wellcome Open Research. doi:10.12688/wellcomeopenres.19380.2.

• Sherratt K, Carnegie AC, Kucharski A, Cori A, Pearson CAB, Jarvis CI, Overton C, Weston D, Hill EM, Knock E, Fearon E, Nightingale E, Hellewell J, Edmunds WJ, Arenas JV, Prem K, Pi L, Baguelin M, Kendall M, Ferguson N, Davies N, Eggo RM, 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.” Wellcome Open Research. doi:10.12688/wellcomeopenres.19601.1.

• Sherratt K, Srivastava A, Ainslie K, Singh DE, Cublier A, Marinescu MC, Carretero J, Garcia AC, Franco N, Willem L, Abrams S, Faes C, Beutels P, Hens N, Müller S, Charlton B, Ewert R, Paltra S, Rakow C, Rehmann J, Conrad T, Schütte C, Nagel K, Abbott S, Grah R, Niehus R, Prasse B, Sandmann F, Funk S (2024). “Characterising information gains and losses when collecting multiple epidemic model outputs.” Epidemics, 47, 100765. ISSN 1755-4365, doi:10.1016/j.epidem.2024.100765, http://dx.doi.org/10.1016/j.epidem.2024.100765.

• Sherratt K, Gruson H, Grah R, Johnson H, Niehus R, Prasse B, Sandmann F, Deuschel J, Wolffram D, Abbott S, Ullrich A, Gibson G, Ray EL, Reich NG, Sheldon D, Wang Y, Wattanachit N, Wang L, Trnka J, Obozinski G, Sun T, Thanou D, Pottier L, Krymova E, Meinke JH, Barbarossa MV, Leithauser N, Mohring J, Schneider J, Wlazlo J, Fuhrmann J, Lange B, Rodiah I, Baccam P, Gurung H, Stage S, Suchoski B, Budzinski J, Walraven R, Villanueva I, Tucek V, Smid M, Zajicek M, Alvarez CP, Reina B, Bosse NI, Meakin SR, Castro L, Fairchild G, Michaud I, Osthus D, Loro PAD, Maruotti A, Eclerova V, Kraus A, Kraus D, Pribylova L, Dimitris B, Li ML, Saksham S, Dehning J, Mohr S, Priesemann V, Redlarski G, Bejar B, Ardenghi G, Parolini N, Ziarelli G, Bock W, Heyder S, Hotz T, Singh DE, Guzman-Merino M, Aznarte JL, Morina D, Alonso S, Alvarez E, Lopez D, Prats C, Burgard JP, Rodloff A, Zimmermann T, Kuhlmann A, Zibert J, Pennoni F, Divino F, Catala M, Lovison G, Giudici P, Tarantino B, Bartolucci F, Lasinio GJ, Mingione M, Farcomeni A, Srivastava A, Montero-Manso P, Adiga A, Hurt B, Lewis B, Marathe M, Porebski P, Venkatramanan S, Bartczuk RP, Dreger F, Gambin A, Gogolewski K, Gruziel-Slomka M, Krupa B, Moszyński A, Niedzielewski K, Nowosielski J, Radwan M, Rakowski F, Semeniuk M, Szczurek E, Zielinski J, Kisielewski J, Pabjan B, Holger K, Kheifetz Y, Scholz M, Przemyslaw B, Bodych M, Filinski M, Idzikowski R, Krueger T, Ozanski T, Bracher J, Funk S (2023). “Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations.” eLife. doi:10.7554/elife.81916.

• Bosse NI, Abbott S, Cori A, van Leeuwen E, Bracher J, Funk S (2023). “Scoring epidemiological forecasts on transformed scales.” PLOS Computational Biology. doi:10.1371/journal.pcbi.1011393.

• Munday JD, Abbott S, Meakin S, Funk S (2023). “Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England.” PLOS Computational Biology. doi:10.1371/journal.pcbi.1011453.

• Sherratt K, Srivastava A, Ainslie K, Singh DE, Cublier A, Marinescu MC, Carretero J, Garcia AC, Franco N, Willem L, Abrams S, Faes C, Beutels P, Hens N, Müller S, Charlton B, Ewert R, Paltra S, Rakow C, Rehmann J, Conrad T, Schütte C, Nagel K, Abbott S, Grah R, Niehus R, Prasse B, Sandmann F, Funk S (2023). “Characterising information gains and losses when collecting multiple epidemic model outputs.” medRxiv. doi:10.1101/2023.07.05.23292245.

• Hart WS, Abbott S, Endo A, Hellewell J, Miller E, Andrews N, Maini PK, Funk S, Thompson RN (2022). “Inference of the SARS-CoV-2 generation time using UK household data.” eLife. doi:10.7554/elife.70767.

• Meakin S, Abbott S, Bosse N, Munday J, Gruson H, Hellewell J, Sherratt K, Chapman LAC, Prem K, Klepac P, Jombart T, Knight GM, Jafari Y, Flasche S, Waites W, Jit M, Eggo RM, Villabona-Arenas CJ, Russell TW, Medley G, Edmunds WJ, Davies NG, Liu Y, Hué S, Brady O, Pung R, Abbas K, Gimma A, Mee P, Endo A, Clifford S, Sun FY, McCarthy CV, Quilty BJ, Rosello A, Sandmann FG, Barnard RC, Kucharski AJ, Procter SR, Jarvis CI, Gibbs HP, Hodgson D, Lowe R, Atkins KE, Koltai M, Pearson CAB, Finch E, Wong KLM, Quaife M, O’Reilly K, Tully DC, Funk S (2022). “Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level.” BMC Medicine. doi:10.1186/s12916-022-02271-x.

• Endo A, Murayama H, Abbott S, Ratnayake R, Pearson CAB, Edmunds WJ, Fearon E, Funk S (2022). “Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022.” Science. doi:10.1126/science.add4507.

• Endo A, Uchida M, Liu Y, Atkins KE, Kucharski AJ, Funk S, Abbas K, van Zandvoort K, Bosse NI, Waterlow NR, Tully DC, Meakin SR, Quaife M, Russell TW, Jit M, Foss AM, Rosello A, Quilty BJ, Prem K, Knight GM, Abbott S, Klepac P, Brady O, Pearson CAB, Medley G, Clifford S, Jarvis CI, Munday JD, Sandmann FG, Sun FY, Jombart T, Hellewell J, Gibbs HP, Barnard RC, Eggo RM, Gimma A, Williams J, Davies NG, Nightingale ES, Procter SR, Edmunds WJ, Showering A, Lowe R, Sherratt K, Villabona-Arenas CJ, Simons D, Chan YD, Flasche S (2022). “Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools.” Proceedings of the National Academy of Sciences. doi:10.1073/pnas.2203019119.

• Bosse NI, Abbott S, Bracher J, Hain H, Quilty BJ, Jit M, van Leeuwen E, Cori A, Funk S (2022). “Comparing human and model-based forecasts of COVID-19 in Germany and Poland.” PLOS Computational Biology. doi:10.1371/journal.pcbi.1010405.

• Funk S, Abbott S, Bracher J (2022). “Sebastian Funk, Sam Abbott and Johannes Bracher’s discussion contribution to the papers in Session 2 of the Royal Statistical Society’s Special Topic Meeting on Covid‐19 Transmission: 11 June 2021.” Journal of the Royal Statistical Society: Series A (Statistics in Society). doi:10.1111/rssa.12974.

• Abbott S, Sherratt K, Bosse N, Gruson H, Bracher J, Funk S (2022). “Evaluating an epidemiologically motivated surrogate model of a multi-model ensemble.” medRxiv. doi:10.1101/2022.10.12.22280917.

• Abbott S, Sherratt K, Gerstung M, Funk S (2022). “Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England.” medRxiv. doi:10.1101/2022.01.08.22268920.

• Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S (2021). “Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England.” Nature Communications, 12(1). doi:10.1038/s41467-021-22213-0.

• Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, Jit M, Funk S (2021). “Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England.” Philosophical Transactions of the Royal Society B: Biological Sciences, 376(1829). doi:10.1098/rstb.2020.0283.

• Endo A, Leclerc QJ, Knight GM, Medley GF, Atkins KE, Funk S, Kucharski AJ (2021). “Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks.” Wellcome Open Research, 5, 239. doi:10.12688/wellcomeopenres.16344.3.

• Bracher J, Wolffram D, Deuschel J, Görgen K, Ketterer JL, Ullrich A, Abbott S, Barbarossa MV, Bertsimas D, Bhatia S, Bodych M, Bosse NI, Burgard JP, Castro L, Fairchild G, Fuhrmann J, Funk S, Gogolewski K, Gu Q, Heyder S, Hotz T, Kheifetz Y, Kirsten H, Krueger T, Krymova E, Li ML, Meinke JH, Michaud IJ, Niedzielewski K, Ożański T, Rakowski F, Scholz M, Soni S, Srivastava A, Zieliński J, Zou D, Gneiting T, Schienle M, Li ML, Bertsimas D, Bouardi HT, Lami OS, Soni S, Abbott S, Bosse NI, Funk S, Barbarossa MV, Fuhrmann J, Meinke JH, Bracher J, Deuschel J, Gneiting T, Görgen K, Ketterer J, Schienle M, Ullrich A, Wolffram D, Górski Ł, Gruziel-Słomka M, Kaczorek A, Moszyński A, Niedzielewski K, Nowosielski J, Radwan M, Rakowski F, Semeniuk M, Zieliński J, Bartczuk R, Kisielewski J, Bhatia S, Biecek P, Bezborodov V, Bodych M, Krueger T, Burgard JP, Heyder S, Hotz T, Osthus DA, Michaud IJ, Castro L, Fairchild G, Kheifetz Y, Kirsten H, Scholz M, Gambin A, Gogolewski K, Miasojedow B, Szczurek E, Rabczenko D, Rosińska M, Bawiec M, Bodych M, Ożański T, Pabjan B, Rafajłlowicz E, Skubalska-Rafajłowicz E, Rafajłowicz W, Migalska A, Szczurek E, Flahault A, Manetti E, Choirat C, Haro BB, Krymova E, Lee G, Obozinski G, Sun T, Thanou D, Gu Q, Xu P, Chen J, Wang L, Zou D, Zhang W, Srivastava A, Prasanna VK, Xu FT, List of Contributors by Team, CovidAnalytics-DELPHI, epiforecasts-EpiExpert, piforecasts-EpiNow2, FIAS FZJ-Epi1Ger, German, olish Forecast Hub Coordination Team, ICM-agentModel, Imperial-ensemble2, ITWW-county repro, LANL-GrowthRate, LeipzigIMISE-SECIR, MIMUW-StochSEIR, MOCOS-agent1, SDSC ISG-TrendModel, UCLA-SuEIR, USC-SIkJalpha (2021). “A Pre-Registered Short-Term Forecasting Study of COVID-19 in Germany and Poland during the Second Wave.” Nature Communications, 12(1), 5173. ISSN 2041-1723, doi:10.1038/s41467-021-25207-0.

• Pavelka M, Van-Zandvoort K, Abbott S, Sherratt K, Majdan M, Jarčuška P, 'MK, Flasche S, Funk S (2021). “The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia.” Science, 372(6542), 635–641. doi:10.1126/science.abf9648.

• Palmer J, Sherratt K, Martin-Nielsen R, Bevan J, Gibbs H, Group C, Funk S, Abbott S (2021). “covidregionaldata: Subnational data for COVID-19 epidemiology.” Journal of Open Source Software. doi:10.21105/joss.03290.

• Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Funk S, Eggo RM, Sun F, Flasche S, Quilty BJ, Davies N, Liu Y, Clifford S, Klepac P, Jit M, Diamond C, Gibbs H, van Zandvoort K (2020). “Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.” The Lancet Global Health, 8(4), e488–e496. doi:10.1016/s2214-109x(20)30074-7.

• Abbott S, Hellewell J, Thompson RN, Sherratt K, Gibbs HP, Bosse NI, Munday JD, Meakin S, Doughty EL, Chun JY, Chan YD, Finger F, Campbell P, Endo A, Pearson CAB, Gimma A, Russell T, Flasche S, Kucharski AJ, Eggo RM, Funk S (2020). “Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts.” Wellcome Open Research, 5, 112. doi:10.12688/wellcomeopenres.16006.2.

• Abbott S, Hellewell J, Munday J, Funk S (2020). “The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis.” Wellcome Open Research, 5, 17. doi:10.12688/wellcomeopenres.15718.1.

• Endo A, Abbott S, Kucharski AJ, Funk S (2020). “Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China.” Wellcome Open Research, 5, 67. doi:10.12688/wellcomeopenres.15842.3.

• Robert A, Kucharski AJ, Gastañaduy PA, Paul P, Funk S (2020). “Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.” Journal of The Royal Society Interface. doi:10.1098/rsif.2020.0084.

• Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ (2019). “Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15.” PLOS Computational Biology, 15(2), e1006785. doi:10.1371/journal.pcbi.1006785.

• Finger F, Funk S, White K, Siddiqui MR, Edmunds WJ, Kucharski AJ (2019). “Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh.” BMC Medicine, 17(1). doi:10.1186/s12916-019-1288-7.

• Camacho A, Kucharski A, Aki-Sawyerr Y, White MA, Flasche S, Baguelin M, Pollington T, Carney JR, Glover R, Smout E, Tiffany A, Edmunds WJ, Funk S (2015). “Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study.” PLoS Currents. doi:10.1371/currents.outbreaks.406ae55e83ec0b5193e30856b9235ed2.