Katharine Sherratt†, Sam Abbott†, Sophie R. Meakin, Joel Hellewell, James D. Munday, Nikos Bosse, CMMID COVID-19 Working Group, Mark Jit and 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 , 376. doi: doi.org/10.1098/rstb.2020.0283

James D Munday, Katharine Sherratt, Sophie Meakin, Akira Endo, Carl AB Pearson, Joel Hellewell, Sam Abbott, Nikos I Bosse, Katherine E Atkins, Jacco Wallinga, 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 , 12 (1). doi: doi.org/10.1038/s41467-021-22213-0

Martin Pavelka, Kevin Van-Zandvoort, Sam Abbott, Katharine Sherratt, Marek Majdan, CMMID COVID, Inštitút Zdravotných Analýz, Pavol Jarčuška, Marek Krajčí, Stefan Flasche, Sebastian Funk (2021).
The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. Science , 372(6542). doi: doi.org/10.1126/science.abf9648

Johannes Bracher, Daniel Wolffram, Jannik Deuschel, Konstantin Goergen, Jakob L Ketterer, Alexander Ullrich, Sam Abbott, Maria Vittoria Barbarossa, Dimitris Bertsimas, Sangeeta Bhatia, Marcin Bodych, Nikos I Bosse, Jan Pablo Burgard, J Fuhrmann, S Funk, K Gogolewski, Q Gu, S Heyder, T Hotz, Y Kheifetz, H Kirsten, T Krueger, E Krymova, ML Li, JH Meinke, K Niedzielewski, T Ożański, F Rakowski, M Scholz, S Soni, A Srivastava, J Zieliński, D Zou, T Gneiting, M Schienle (2021).
Short-term forecasting of COVID-19 in Germany and Poland during the second wave–a preregistered study. medRxiv , . doi: doi.org/10.1101/2020.12.24.20248826

Akira Endo, Quentin J Leclerc, Gwenan M Knight, Graham F Medley, Katherine E Atkins, Sebastian Funk, Adam J Kucharski (2020).
Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome Open Research , 5(239). doi: doi.org/10.12688/wellcomeopenres.16344.3

Sam Abbott, Joel Hellewell, Robin N Thompson, Katharine Sherratt, Hamish P Gibbs, Nikos I Bosse, James D Munday, Sophie Meakin, Emma L Doughty, June Young Chun, Yung-Wai Desmond Chan, Flavio Finger, Paul Campbell, Akira Endo, Carl AB Pearson, Amy Gimma, Tim Russell, Stefan Flasche, 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 , 5 (112). doi: doi.org/10.12688/wellcomeopenres.16006.2

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 , 5(67). doi: doi.org/10.12688/wellcomeopenres.15842.3

Joel Hellewell, Sam Abbott, Amy Gimma, Nikos I Bosse, Christopher I Jarvis, Timothy W Russell, James D Munday, Adam J Kucharski, W John Edmunds, Fiona Sun, Stefan Flasche, Billy J Quilty, Nicholas Davies, Yang Liu, Samuel Clifford, Petra Klepac, Mark Jit, Charlie Diamond, Hamish Gibbs, Kevin van Zandvoort, Sebastian Funk, Rosalind M Eggo (2020).
Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. The Lancet Global Health , 8 (4). doi: doi.org/10.1016/S2214-109X(20)30074-7

Sam Abbott, Joel Hellewell, James Munday, Sebastian Funk, CMMID nCoV working group (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: doi.org/10.12688/wellcomeopenres.15718.1

Finger F, Funk S, White K, M. Siddiqui R, Edmunds WJ and Kucharski AJ (2019).
Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. BMC Medicine , 58 (2019). doi: doi.org/10.1186/s12916-019-1288-7

Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM and 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: doi.org/10.1371/journal.pcbi.1006785

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 Outbreaks , Edition 1. doi: doi.org/10.1371/currents.outbreaks.406ae55e83ec0b5193e30856b9235ed2