Publications

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

• 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.

• 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.

• 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.

• 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.