Bracher, J; Wolffram, D; Deuschel, J; Görgen, K; Ketterer, JL; Ullrich, A; Abbott, S; Barbarossa, MV; Bertsimas, D; Bhatia, S; +29 more... 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; List of Contributors by Team; List of Contributors by Team; (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: https://doi.org/10.1038/s41467-021-25207-0

Davies, Nicholas G; Abbott, Sam; Barnard, Rosanna C; Jarvis, Christopher I; Kucharski, Adam J; Munday, James D; Pearson, Carl AB; Russell, Timothy W; Tully, Damien C; Washburne, Alex D; +15 more... Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D; CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M; Funk, Sebastian; Jit, Mark; Atkins, Katherine E; Edmunds, W John; (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, N.Y.), 372 (6538). eabg3055-eabg3055. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abg3055

Leclerc, Quentin J; Nightingale, Emily S; Abbott, Sam; CMMID COVID-19 Working Group; Jombart, Thibaut; CMMID COVID-19 Working Group; (2021) Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England. Scientific reports, 11 (1). 7106-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-86266-3

Munday, James D; Sherratt, Katharine; Meakin, Sophie; Endo, Akira; Pearson, Carl AB; Hellewell, Joel; Abbott, Sam; Bosse, Nikos I; CMMID COVID-19 Working Group; Atkins, Katherine E; +4 more... Wallinga, Jacco; Edmunds, W John; van Hoek, Albert Jan; Funk, Sebastian; (2021) Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England. Nature communications, 12 (1). 1942-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-22213-0

Palmer, Joseph; Sherratt, Katharine; Martin-Nielsen, Richard; Bevan, Jonnie; Gibbs, Hamish; Group, Cmmid; Funk, Sebastian; Abbott, Sam; (2021) covidregionaldata: Subnational data for COVID-19 epidemiology. Journal of Open Source Software, 6 (63). p. 3290. DOI: https://doi.org/10.21105/joss.03290

Pavelka, Martin; Van-Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; Jarčuška, Pavol; Krajčí, Marek; Flasche, Stefan; Funk, Sebastian; CMMID COVID-19 working group, Inštitút Zdravotných Analýz; (2021) The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. Science (New York, N.Y.), 372 (6542). pp. 635-641. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abf9648

Sherratt, Katharine; Abbott, Sam; Meakin, Sophie R; Hellewell, Joel; Munday, James D; Bosse, Nikos; CMMID COVID-19 Working Group; Jit, Mark; Funk, Sebastian; (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 of London. Series B, Biological sciences, 376 (1829). 20200283-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2020.0283

Sherratt, Katharine; Abbott, Sam; Meakin, Sophie R; Hellewell, Joel; Munday, James D; Bosse, Nikos; Jit, Mark; Funk, Sebastian; (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 of London Series B, Biological sciences, 376 (1829). ISSN 0962-8436 DOI: https://doi.org/10.1101/2020.10.18.20214585

Abbott, Sam; Hellewell, Joel; Munday, James; CMMID nCoV working group; Funk, Sebastian; (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-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15718.1

Abbott, Sam; Hellewell, Joel; Thompson, Robin N; Sherratt, Katharine; Gibbs, Hamish P; Bosse, Nikos I; Munday, James D; Meakin, Sophie; Doughty, Emma L; Chun, June Young; +11 more... Chan, Yung-Wai Desmond; Finger, Flavio; Campbell, Paul; Endo, Akira; Pearson, Carl AB; Gimma, Amy; Russell, Tim; Flasche, Stefan; Kucharski, Adam J; Eggo, Rosalind M; Funk, Sebastian; (2020) Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Research, 5. p. 112. DOI: https://doi.org/10.12688/wellcomeopenres.16006.1

Abbott, Sam; Hellewell, Joel; Thompson, Robin N; Sherratt, Katharine; Gibbs, Hamish P; Bosse, Nikos I; Munday, James D; Meakin, Sophie; Doughty, Emma L; Chun, June Young; +11 more... Chan, Yung-Wai Desmond; Finger, Flavio; Campbell, Paul; Endo, Akira; Pearson, Carl AB; Gimma, Amy; Russell, Tim; Flasche, Stefan; Kucharski, Adam J; Eggo, Rosalind M; Funk, Sebastian; (2020) Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Research, 5. p. 112. DOI: https://doi.org/10.12688/wellcomeopenres.16006.2

Davis, Emma L; Lucas, Tim CD; Borlase, Anna; Pollington, Timothy M; Abbott, Sam; Ayabina, Diepreye; Crellen, Thomas; Hellewell, Joel; Pi, Li; Medley, Graham F; +2 more... Hollingsworth, T Déirdre; Klepac, Petra; (2020) An imperfect tool: contact tracing could provide valuable reductions in COVID-19 transmission if good adherence can be achieved and maintained. medRxiv preprint. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.06.09.20124008

Endo, Akira; Centre for the Mathematical Modelling of Infectious Diseases COV; Abbott, Sam; Kucharski, Adam J; Funk, Sebastian; (2020) Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Research, 5. 67-. DOI: https://doi.org/10.12688/wellcomeopenres.15842.3

Funk, S; Abbott, S; Atkins, BD; Baguelin, M; Baillie, JK; Birrell, P; Blake, J; Bosse, NI; Burton, J; Carruthers, J; +37 more... Davies, NG; De Angelis, D; Dyson, L; Edmunds, WJ; Eggo, RM; Ferguson, NM; Gaythorpe, K; Gorsich, E; Guyver-Fletcher, G; Hellewell, J; Hill, EM; Holmes, A; House, TA; Jewell, C; Jit, M; Jombart, T; Joshi, I; Keeling, MJ; Kendall, E; Knock, ES; Kucharski, AJ; Lythgoe, KA; Meakin, SR; Munday, JD; Openshaw, PJM; Overton, CE; Pagani, F; Pearson, J; Perez-Guzman, PN; Pellis, L; Scarabel, F; Semple, MG; Sherratt, K; Tang, M; Tildesley, MJ; Van Leeuwen, E; Whittles, LK; (2020) Short-term forecasts to inform the response to the Covid-19 epidemic in the UK. medRxiv preprint - BMJ Yale. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.11.11.20220962

Gostic, Katelyn M; McGough, Lauren; Baskerville, Edward B; Abbott, Sam; Joshi, Keya; Tedijanto, Christine; Kahn, Rebecca; Niehus, Rene; Hay, James A; De Salazar, Pablo M; +15 more... Hellewell, Joel; Meakin, Sophie; Munday, James D; Bosse, Nikos I; Sherrat, Katharine; Thompson, Robin N; White, Laura F; Huisman, Jana S; Scire, Jérémie; Bonhoeffer, Sebastian; Stadler, Tanja; Wallinga, Jacco; Funk, Sebastian; Lipsitch, Marc; Cobey, Sarah; (2020) Practical considerations for measuring the effective reproductive number, Rt. PLOS COMPUTATIONAL BIOLOGY, 16 (12). e1008409-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008409

Gostic, Katelyn M; McGough, Lauren; Baskerville, Edward B; Abbott, Sam; Joshi, Keya; Tedijanto, Christine; Kahn, Rebecca; Niehus, Rene; Hay, James; De Salazar, Pablo M; +15 more... Hellewell, Joel; Meakin, Sophie; Munday, James; Bosse, Nikos I; Sherrat, Katharine; Thompson, Robin N; White, Laura F; Huisman, Jana S; Scire, Jérémie; Bonhoeffer, Sebastian; Stadler, Tanja; Wallinga, Jacco; Funk, Sebastian; Lipsitch, Marc; Cobey, Sarah; (2020) Practical considerations for measuring the effective reproductive number, R t. medRxiv preprint. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.06.18.20134858

Hellewell, Joel; Abbott, Sam; Gimma, Amy; Bosse, Nikos I; Jarvis, Christopher I; Russell, Timothy W; Munday, James D; Kucharski, Adam J; Edmunds, W John; Centre for the Mathematical Modelling of Infectious Diseases COV; +2 more... Funk, Sebastian; Eggo, Rosalind M; (2020) Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. The Lancet. Global health, 8 (4). e488-e496. ISSN 2214-109X DOI: https://doi.org/10.1016/S2214-109X(20)30074-7

Imai, Natsuko; Gaythorpe, Katy AM; Abbott, Sam; Bhatia, Sangeeta; van Elsland, Sabine; Prem, Kiesha; Liu, Yang; Ferguson, Neil M; (2020) Adoption and impact of non-pharmaceutical interventions for COVID-19. Wellcome open research, 5. 59-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15808.1

Imai, Natsuko; Gaythorpe, Katy AM; Abbott, Sam; Bhatia, Sangeeta; van Elsland, Sabine; Prem, Kiesha; Liu, Yang; Ferguson, Neil M; (2020) Adoption and impact of non-pharmaceutical interventions for COVID-19. Wellcome Open Res, 5. 59-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15808.1

Jit, Mark; Jombart, Thibaut; Nightingale, Emily S; Endo, Akira; Abbott, Sam; LSHTM Centre for Mathematical Modelling of Infectious Diseases C; Edmunds, W John; (2020) Estimating number of cases and spread of coronavirus disease (COVID-19) using critical care admissions, United Kingdom, February to March 2020. EUROSURVEILLANCE, 25 (18). pp. 6-10. ISSN 1560-7917 DOI: https://doi.org/10.2807/1560-7917.ES.2020.25.18.2000632

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. Wellcome open research, 5. 78-. DOI: https://doi.org/10.12688/wellcomeopenres.15786.1

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. medRxiv. DOI: https://doi.org/10.1101/2020.03.10.20033761

Pavelka, Martin; Van-Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; Analýz, Inštitút Zdravotných; Jarčuška, Pavol; Krajčí, Marek; Flasche, Stefan; Funk, Sebastian; (2020) The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. MedRxiv. DOI: https://doi.org/10.1101/2020.12.02.20240648

Price, David J; Shearer, Freya M; Meehan, Michael T; McBryde, Emma; Moss, Robert; Golding, Nick; Conway, Eamon J; Dawson, Peter; Cromer, Deborah; Wood, James; +3 more... Abbott, Sam; McVernon, Jodie; McCaw, James M; (2020) Early analysis of the Australian COVID-19 epidemic. ELIFE, 9. e58785-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.58785

Russell, Timothy W; Golding, Nick; Hellewell, Joel; Abbott, Sam; Wright, Lawrence; Pearson, Carl AB; Zandvoort, Kevin van; Jarvis, Christopher I; Gibbs, Hamish; Liu, Yang; +3 more... Eggo, Rosalind M; Edmunds, W John; Kucharski, Adam J; (2020) Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections. DOI: https://doi.org/10.1101/2020.07.07.20148460

Russell, Timothy W; Golding, Nick; Hellewell, Joel; Abbott, Sam; Wright, Lawrence; Pearson, Carl AB; van Zandvoort, Kevin; Jarvis, Christopher I; Gibbs, Hamish; Liu, Yang; +4 more... Eggo, Rosalind M; Edmunds, W John; Kucharski, Adam J; CMMID COVID-19 working group; (2020) Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections. BMC medicine, 18 (1). 332-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-020-01790-9

Russell, Timothy W; Hellewell, Joel; Jarvis, Christopher I; Van Zandvoort, Kevin; Abbott, Sam; Ratnayake, Ruwan; Flasche, Stefan; Eggo, Rosalind M; Edmunds, W John; Kucharski, Adam J; (2020) Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship. BMJ global health. ISSN 2059-7908 DOI: https://doi.org/10.1101/2020.03.05.20031773

Russell, Timothy W; Hellewell, Joel; Jarvis, Christopher I; van Zandvoort, Kevin; Abbott, Sam; Ratnayake, Ruwan; Cmmid Covid-Working Group; Flasche, Stefan; Eggo, Rosalind M; Edmunds, W John; +1 more... Kucharski, Adam J; (2020) Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020. Euro Surveill, 25 (12). ISSN 1560-7917 DOI: https://doi.org/10.2807/1560-7917.ES.2020.25.12.2000256

Abbott, Sam; Christensen, Hannah; Welton, Nicky J; Brooks-Pollock, Ellen; (2019) Estimating the effect of the 2005 change in BCG policy in England: a retrospective cohort study, 2000 to 2015. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 24 (49). ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2019.24.49.1900220

Stone, Jack; Fraser, Hannah; Lim, Aaron G; Walker, Josephine G; Ward, Zoe; MacGregor, Louis; Trickey, Adam; Abbott, Sam; Strathdee, Steffanie A; Abramovitz, Daniela; +33 more... Maher, Lisa; Iversen, Jenny; Bruneau, Julie; Zang, Geng; Garfein, Richard S; Yen, Yung-Fen; Azim, Tasnim; Mehta, Shruti H; Milloy, Michael-John; Hellard, Margaret E; Sacks-Davis, Rachel; Dietze, Paul M; Aitken, Campbell; Aladashvili, Malvina; Tsertsvadze, Tengiz; Mravčík, Viktor; Alary, Michel; Roy, Elise; Smyrnov, Pavlo; Sazonova, Yana; Young, April M; Havens, Jennifer R; Hope, Vivian D; Desai, Monica; Heinsbroek, Ellen; Hutchinson, Sharon J; Palmateer, Norah E; McAuley, Andrew; Platt, Lucy; Martin, Natasha K; Altice, Frederick L; Hickman, Matthew; Vickerman, Peter; (2018) Incarceration history and risk of HIV and hepatitis C virus acquisition among people who inject drugs: a systematic review and meta-analysis. The Lancet infectious diseases, 18 (12). pp. 1397-1409. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(18)30469-9