Publications

Below is a list of selected publications (sorted by year) illustrating the type of work conducted by our team. See also our ongoing projects and software.

Katharine Sherratt, Rok Grah, Bastian Prasse, Friederike Becker, Jamie McLean, Sam Abbott, Sebastian Funk (2025). The influence of model structure and geographic specificity on predictive accuracy among European COVID-19 forecasts. medRxiv.

D Rao, A Tanveer, EN Iftekhar, …, J Fitzner, J Hanefeld, S Funk (2025). The utility of infectious disease modelling in informing policy for outbreak response: a scoping review. medRxiv.

Liza Hadley, Caylyn Rich, Alex Tasker, Olivier Restif, Sebastian Funk (2025). How does policy modelling work in practice? A global analysis on the use of epidemiological modelling in health crises. PLOS Global Public Health.

Liza Hadley, Caylyn Rich, Alex Tasker, Olivier Restif, Sebastian Funk (2025). Visual preferences for communicating modelling: a global analysis of COVID-19 policy and decision makers. Infectious Disease Modelling.

Manuel Stapper, Sebastian Funk (2025). Fine-Grid Spatial Interaction Matrices for Surveillance Models, with Application to Influenza in Germany. medRxiv.

Friederike Becker, Katharine Sherratt, Nikos I. Bosse, Sebastian Funk (2025). The influence of ensemble size and composition on the performance of combined real-time COVID-19 forecasts. medRxiv.

Duaa Rao, Aleena Tanveer, Emil Nafis Iftekhar, …, Julia Fitzner, Johanna Hanefeld, Sebastian Funk (2025). The utility of infectious disease modelling in informing decisions for outbreak response: A scoping review. PLOS Global Public Health.

Katharine Sherratt, Anna C. Carnegie, Adam Kucharski, …, Sebastian Funk, Yang Liu, Sam Abbott (2025). Improving modelling for epidemic response: a progress update from a community of UK infectious disease modellers. Interface Focus.

Manuel Stapper, Sebastian Funk (2025). Mind the Baseline: The Hidden Impact of Reference Model Selection on Forecast Assessment. medRxiv.

Kaitlyn E. Johnson, Maria L. Tang, Emily Tyszka, …, Jonathon Mellor, Johannes Bracher, Sam Abbott (2025). Baseline nowcasting methods for handling delays in epidemiological data. Wellcome Open Research.

Nikos I. Bosse, Sam Abbott, Johannes Bracher, Edwin van Leeuwen, Anne Cori, Sebastian Funk (2024). Human judgement forecasting of COVID-19 in the UK. Wellcome Open Research.

Katharine Sherratt, Anna C Carnegie, Adam Kucharski, …, Sebastian Funk, Yang Liu, Sam Abbott (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.

Katharine Sherratt, Ajitesh Srivastava, Kylie Ainslie, …, Bastian Prasse, Frank Sandmann, Sebastian Funk (2024). Characterising information gains and losses when collecting multiple epidemic model outputs. Epidemics.

Katharine Sherratt, Hugo Gruson, Rok Grah, …, Tomasz Ozanski, Johannes Bracher, Sebastian Funk (2023). Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations. eLife.

Nikos I. Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk (2023). Scoring epidemiological forecasts on transformed scales. PLOS Computational Biology.

James D. Munday, Sam Abbott, Sophie Meakin, Sebastian Funk (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.

William Stephen Hart, Sam Abbott, Akira Endo, …, Philip K Maini, Sebastian Funk, Robin N Thompson (2022). Inference of the SARS-CoV-2 generation time using UK household data. eLife.

Sophie Meakin, Sam Abbott, Nikos Bosse, …, Kathleen O’Reilly, Damien C. Tully, Sebastian Funk (2022). Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level. BMC Medicine.

Akira Endo, Hiroaki Murayama, Sam Abbott, …, W. John Edmunds, Elizabeth Fearon, Sebastian Funk (2022). Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022. Science.

Akira Endo, Mitsuo Uchida, Yang Liu, …, David Simons, Yung-Wai Desmond Chan, Stefan Flasche (2022). Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. Proceedings of the National Academy of Sciences.

Nikos I. Bosse, Sam Abbott, Johannes Bracher, …, Edwin van Leeuwen, Anne Cori, Sebastian Funk (2022). Comparing human and model-based forecasts of COVID-19 in Germany and Poland. PLOS Computational Biology.

Sebastian Funk, Sam Abbott, Johannes Bracher (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).

Sam Abbott, Katharine Sherratt, Nikos Bosse, Hugo Gruson, Johannes Bracher, Sebastian Funk (2022). Evaluating an epidemiologically motivated surrogate model of a multi-model ensemble. medRxiv.

Sam Abbott, Katharine Sherratt, Moritz Gerstung, Sebastian Funk (2022). Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England. medRxiv.

James D. Munday, Katharine Sherratt, Sophie Meakin, …, W. John Edmunds, Albert Jan van Hoek, Sebastian Funk (2021). Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England. Nature Communications.

Katharine Sherratt, Sam Abbott, Sophie R. Meakin, …, Nikos Bosse, Mark Jit, Sebastian Funk (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.

Akira Endo, Quentin J. Leclerc, Gwenan M. Knight, Graham F. Medley, Katherine E. Atkins, Sebastian Funk, Adam J. Kucharski (2021). Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome Open Research.

J. Bracher, D. Wolffram, J. Deuschel, …, 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.

Martin Pavelka, Kevin Van-Zandvoort, Sam Abbott, …, Marek Krajč '{}, Stefan Flasche, Sebastian Funk (2021). The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. Science.

Joseph Palmer, Katharine Sherratt, Richard Martin-Nielsen, …, Cmmid Group, Sebastian Funk, Sam Abbott (2021). covidregionaldata: Subnational data for COVID-19 epidemiology. Journal of Open Source Software.

Joel Hellewell, Sam Abbott, Amy Gimma, …, Charlie Diamond, Hamish Gibbs, Kevin van Zandvoort (2020). Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. The Lancet Global Health.

Sam Abbott, Joel Hellewell, Robin N. Thompson, …, Adam J. Kucharski, Rosalind M. Eggo, Sebastian Funk (2020). Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Research.

Sam Abbott, Joel Hellewell, James Munday, Sebastian Funk (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.

Akira Endo, Sam Abbott, Adam J. Kucharski, Sebastian Funk (2020). Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Research.

Alexis Robert, Adam J. Kucharski, Paul A. Gastañaduy, Prabasaj Paul, Sebastian Funk (2020). Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data. Journal of The Royal Society Interface.

Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds (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.

Flavio Finger, Sebastian Funk, Kate White, M. Ruby Siddiqui, W. John Edmunds, Adam J. Kucharski (2019). Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. BMC Medicine.

Anton Camacho, Adam Kucharski, Yvonne Aki-Sawyerr, …, Amanda Tiffany, W. John Edmunds, Sebastian Funk (2015). Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study. PLoS Currents.