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Meakin, Sophie and Abbott, Sam and Bosse, Nikos and Munday, James and Gruson, Hugo and Hellewell, Joel and Sherratt, Katharine and Chapman, Lloyd A.C. and Prem, Kiesha and Klepac, Petra and Jombart, Thibaut and Knight, Gwenan M. and Jafari, Yalda and Flasche, Stefan and Waites, William and Jit, Mark and Eggo, Rosalind M. and Villabona-Arenas, C. Julian and Russell, Timothy W. and Medley, Graham and Edmunds, W. John and Davies, Nicholas G. and Liu, Yang and Hué, Stéphane and Brady, Oliver and Pung, Rachael and Abbas, Kaja and Gimma, Amy and Mee, Paul and Endo, Akira and Clifford, Samuel and Sun, Fiona Yueqian and McCarthy, Ciara V. and Quilty, Billy J. and Rosello, Alicia and Sandmann, Frank G. and Barnard, Rosanna C. and Kucharski, Adam J. and Procter, Simon R. and Jarvis, Christopher I. and Gibbs, Hamish P. and Hodgson, David and Lowe, Rachel and Atkins, Katherine E. and Koltai, Mihaly and Pearson, Carl A.B. and Finch, Emilie and Wong, Kerry L.M. and Quaife, Matthew and O’Reilly, Kathleen, CMMID COVID-19 Working Group (2022) Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level. BMC Medicine, 20 (1). 86. ISSN 1741-7015

Barnard, Rosanna C. and Davies, Nicholas G. and Munday, James D. and Lowe, Rachel and Knight, Gwenan M. and Leclerc, Quentin J. and Tully, Damien C. and Hodgson, David and Pung, Rachael and Hellewell, Joel and Koltai, Mihaly and Simons, David and Abbas, Kaja and Kucharski, Adam J. and Procter, Simon R. and Sandmann, Frank G. and Pearson, Carl A.B. and Prem, Kiesha and Showering, Alicia and Meakin, Sophie R. and O’Reilly, Kathleen and McCarthy, Ciara V. and Quaife, Matthew and Wong, Kerry L.M. and Jafari, Yalda and Deol, Arminder K. and Houben, Rein M.G.J. and Diamond, Charlie and Jombart, Thibaut and Villabona-Arenas, C. Julian and Waites, William and Eggo, Rosalind M. and Endo, Akira and Gibbs, Hamish P. and Klepac, Petra and Williams, Jack and Quilty, Billy J. and Brady, Oliver and Emery, Jon C. and Atkins, Katherine E. and Chapman, Lloyd A.C. and Sherratt, Katharine and Abbott, Sam and Bosse, Nikos I. and Mee, Paul and Funk, Sebastian and Lei, Jiayao and Liu, Yang and Flasche, Stefan and Rudge, James W., Centre for Mathematical Modelling of Infectious Diseases COVID-19 working group (2022) Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era. Nature Communications, 13 (1). 4879. ISSN 2041-1723

Pung, Rachael and Firth, Josh A. and Spurgin, Lewis G. and Chang, Annie and Kong, Jade and Wong, Jazzy and Jin, Ooi Jo and Selvaraj, Deepa and Yong, Dominique and Lang, Jocelyn and Sivalingam, Abilash and Procter, Simon R. and Flasche, Stefan and Waites, William and Prem, Kiesha and Pearson, Carl A.B. and Gibbs, Hamish P. and Sherratt, Katharine and Villabona-Arenas, C. Julian and Wong, Kerry L.M. and Liu, Yang and Mee, Paul and Chapman, Lloyd A.C. and Atkins, Katherine E. and Quaife, Matthew and Munday, James D. and Funk, Sebastian and Eggo, Rosalind M. and Huè, Stèphane and Davies, Nicholas G. and Hodgson, David and Abbas, Kaja and McCarthy, Ciara V. and Hellewell, Joel and Abbott, Sam and Bosse, Nikos I. and Brady, Oliver and Barnard, Rosanna C. and Jit, Mark and Tully, Damien C. and Medley, Graham and Sun, Fiona Yueqian and Jarvis, Christopher I. and Lowev, Rachel and O’Reilly, Kathleen and Meakin, Sophie R. and Endo, Akira and Sandmann, Frank G. and Edmunds, W. John and Koltai, Mihaly, Singapore CruiseSafe working group, CMMID COVID-19 Working Group (2022) Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events. Nature Communications, 13 (1). 1956. ISSN 2041-1723

McCarthy, Ciara V. and O’Mara, Oscar and van Leeuwen, Edwin and Sherratt, Katharine and Abbas, Kaja and Wong, Kerry Lm and Atkins, Katherine E. and Lowe, Rachel and Meakin, Sophie R. and Davies, Nicholas G. and Russell, Timothy W. and O’Reilly, Kathleen and Hué, Stéphane and Finch, Emilie and Villabona-Arenas, C. Julian and Edmunds, W. John and Jafari, Yalda and Tully, Damien C. and Bosse, Nikos I. and Pearson, Carl A.B. and Hodgson, David and Kucharski, Adam J. and Medley, Graham and Liu, Yang and Procter, Simon R. and Waites, William and Abbott, Sam and Barnard, Rosanna C. and Sun, Fiona Yueqian and Gibbs, Hamish P. and Eggo, Rosalind M. and Chapman, Lloyd A.C. and Flasche, Stefan and Endo, Akira and Mee, Paul and Munday, James D. and Koltai, Mihaly and Gimma, Amy and Jarvis, Christopher I. and Quaife, Matthew and Clifford, Samuel and Funk, Sebastian and Prem, Kiesha and Knight, Gwenan M. and Pung, Rachael and Brady, Oliver and Quilty, Billy J. and Jit, Mark and Sandmann, Frank, CMMID COVID-19 Working Group (2022) The impact of COVID-19 vaccination in prisons in England and Wales : a metapopulation model. BMC Public Health, 22 (1). 1003. ISSN 1471-2458

Gimma, Amy and Munday, James D. and Wong, Kerry L.M. and Coletti, Pietro and van Zandvoort, Kevin and Prem, Kiesha and Klepac, Petra and Rubin, G. James and Funk, Sebastian and Edmunds, W. John and Jarvis, Christopher I. and Chapman, Lloyd A.C. and Clifford, Samuel and Jombart, Thibaut and O’Reilly, Kathleen and Lei, Jiayao and Abbas, Kaja and Krauer, Fabienne and Flasche, Stefan and Rosello, Alicia and Knight, Gwenan M. and Tully, Damien C. and Atkins, Katherine E. and Pung, Rachael and Eggo, Rosalind M. and Hodgson, David and Koltai, Mihaly and Jafari, Yalda and Russell, Timothy W. and Sandmann, Frank G. and Brady, Oliver and Waterlow, Naomi R. and Jit, Mark and Sun, Fiona Yueqian and Pearson, Carl A.B. and Waites, William and Finch, Emilie and Endo, Akira and Medley, Graham and McCarthy, Ciara V. and Kucharski, Adam J. and Mee, Paul and Gibbs, Hamish P. and Davies, Nicholas G. and Quilty, Billy J. and Meakin, Sophie R. and Villabona-Arenas, C. Julian and Bosse, Nikos I. and Hellewell, Joel and Procter, Simon R., CMMID COVID-19 Working Group (2022) Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey : a repeated cross-sectional study. PLOS Medicine, 19 (3). e1003907. ISSN 1549-1277

Finch, Emilie and Lowe, Rachel and Fischinger, Stephanie and de St Aubin, Michael and Siddiqui, Sameed M. and Dayal, Diana and Loesche, Michael A. and Rhee, Justin and Beger, Samuel and Hu, Yiyuan and Gluck, Matthew J. and Mormann, Benjamin and Hasdianda, Mohammad A. and Musk, Elon R. and Alter, Galit and Menon, Anil S. and Nilles, Eric J. and Kucharski, Adam J. and Lei, Jiayao and Funk, Sebastian and Sun, Fiona Yueqian and Gimma, Amy and Nightingale, Emily S. and Medley, Graham and Abbott, Sam and Krauer, Fabienne and Davies, Nicholas G. and Jit, Mark and Endo, Akira and Brady, Oliver and Foss, Anna M. and Chan, Yung Wai Desmond and Jombart, Thibaut and van Zandvoort, Kevin and Eggo, Rosalind M. and Liu, Yang and Knight, Gwenan M. and Pearson, Carl A.B. and Abbas, Kaja and Atkins, Katherine E. and Clifford, Samuel and Koltai, Mihaly and Jafari, Yalda and Tully, Damien C. and Jarvis, Christopher I. and O'Reilly, Kathleen and Bosse, Nikos I. and Prem, Kiesha and Waites, William and Flasche, Stefan, the CMMID COVID-19 working group, the SpaceX COVID-19 Cohort Collaborative (2022) SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort. PLOS Biology, 20 (2). e3001531. ISSN 1544-9173

Munday, James D. and Jarvis, Christopher I. and Gimma, Amy and Wong, Kerry L.M. and van Zandvoort, Kevin and Liu, Yang and Hellewell, Joel and Davies, Nicholas G. and Villabona-Arenas, C. Julian and Eggo, Rosalind M. and Endo, Akira and Bosse, Nikos I. and Gibbs, Hamish P. and Pearson, Carl A.B. and Sun, Fiona Yueqian and Jit, Mark and O’Reilly, Kathleen and Jafari, Yalda and Atkins, Katherine E. and Waterlow, Naomi R. and Rosello, Alicia and Chan, Yung Wai Desmond and Foss, Anna M. and Quilty, Billy J. and Russell, Timothy W. and Flasche, Stefan and Procter, Simon R. and Waites, William and Barnard, Rosanna C. and Kucharski, Adam J. and Jombart, Thibaut and Medley, Graham and Lowe, Rachel and Krauer, Fabienne and Tully, Damien C. and Prem, Kiesha and Lei, Jiayao and Brady, Oliver and Sandmann, Frank G. and Meakin, Sophie R. and Abbas, Kaja and Knight, Gwenan M. and Quaife, Matthew and Koltai, Mihaly and Abbott, Sam and Clifford, Samuel and Funk, Sebastian and Edmunds, W. John, CMMID COVID-19 Working Group (2021) Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data. BMC Medicine, 19 (1). 233. ISSN 1741-7015

Procter, Simon R. and Abbas, Kaja and Flasche, Stefan and Griffiths, Ulla and Hagedorn, Brittany and O’Reilly, Kathleen M. and Waites, William, CMMID COVID-19 Working Group (2021) SARS-CoV-2 infection risk during delivery of childhood vaccination campaigns : a modelling study. BMC Medicine, 19. 198. ISSN 1741-7015

McCarthy, C. V. and Flasche, S. and Waites, W. and Williams, J., CMMID COVID-19 Working Group (2021) Global and national estimates of the number of healthcare workers at high risk of SARS-CoV-2 infection. Journal of Hospital Infection, 111. pp. 205-207. ISSN 1532-2939

Baguelin, Marc and Flasche, Stefan and Camacho, Anton and Demiris, Nikolaos and Miller, Elizabeth and Edmunds, W. John (2013) Assessing optimal target populations for influenza vaccination programmes : an evidence synthesis and modelling study. PLOS Medicine, 10 (10). e1001527. ISSN 1549-1277

Flasche, Stefan and Edmunds, W. John and Miller, Elizabeth and Goldblatt, David and Robertson, Charles and Yoon Hong, Choi (2013) The impact of specific and non-specific immunity on the ecology of Streptococcus pneumoniae and the implications for vaccination. Proceedings of the Royal Society B: Biological Sciences, 280 (1771). 20131939.

Choi, Yoon H. and Jit, Mark and Flasche, Stefan and Gay, Nigel and Miller, Elizabeth (2012) Mathematical modelling long-term effects of replacing Prevnar7 with Prevnar13 on invasive pneumococcal diseases in England and Wales. PLoS One, 7 (7). pp. 1-11. ISSN 1932-6203

Flasche, Stefan and Slack, M. and Miller, Elizabeth (2011) Long term trends introduce a potential bias when evaluating the impact of the pneumococcal conjugate vaccination programme in England and Wales. Eurosurveillance, 16 (20). pp. 13-18. 19868. ISSN 1560-7917

Flasche, Stefan and Albert Jan, Van Hoek and Sheasby, Elizabeth and Waight, Pauline and Andrews, Nick and Sheppard, Carmen and George, Robert and Miller, Elizabeth (2011) Effect of pneumococcal conjugate vaccination on serotype-specific carriage and invasive disease in England: a cross-sectional study. PLOS Medicine, 8 (4). e1001017.

Weinberger, Daniel M. and Harboe, Zitta B. and Flasche, Stefan and Scott, J. Anthony and Lipsitch, Marc (2011) Prediction of serotypes causing invasive pseumococal disease in unvaccinated and vaccinated populations. Epidemiology, 22 (2). pp. 199-207. ISSN 1044-3983

Ghani, Azra C and Baquelin, Marc and Griffin, Jamie T. and Flasche, Stefan and Pebody, R.G. and Albert Jan, Van Hoek and Cauchemez, Simon and Hall, Ian M. and Donnelly, Christl A. and Robertson, Christopher and White, Michael T. and Barrass, Iain and Fraser, Christophe and Bermingham, Alison and Truscott, James and Ellis, Joanna and Jenkins, Helen E. and Kafatos, George and Garske, Tini and Harris, Ross and McMenamin, J. and Hawkins, Colin and Phin, Nick and Charlett, André and Zambon, Maria and Edmunds, W. John and Catchpole, Mike and Leach, Steve and White, Peter and Ferguson, Neil M. and Coooper, Ben S. (2010) The early transmission dynamics of H1N1 pandemic influenza in the United Kingdom. PLOS Currents: Influenza, RRN1130.

Ghani, Azra C and Baguelin, Marc and Griffin, Jamie T and Flasche, Stefan and Pebody, Richard and Van Hoek, Albert Jan and Cauchemez, Simon and Hall, Ian M and Donnelly, Christl A and Robertson, Chris and White, Michael T and Barrass, Iain and Fraser, Christophe and Bermingham, Alison and Truscott, James and Ellis, Joanna and Jenkins, Helen E and Kafatos, George and Garske, Tini and Harris, Ross and McMenamin, Jim and Hawkins, Colin and Phin, Nick and Charlett, André and Zambon, Maria and Edmunds, W. John and Catchpole, Mike and Leach, Steve and White, Peter J and Ferguson, Neil M and Cooper, Ben S (2010) The early transmission dynamics of H1N1pdm influenza in the United Kingdom. PLoS Currents. ISSN 2157-3999