Overview
Availability
- Dr Sam Clifford is:
- Available for supervision
Fields of research
Qualifications
- Bachelor of Applied Mathematics, Queensland University of Technology
- Bachelor (Honours) of Applied Mathematics, Queensland University of Technology
- Doctor of Philosophy of Atmospheric Science, Queensland University of Technology
Works
Search Professor Sam Clifford’s works on UQ eSpace
2024
Journal Article
Could prophylactic antivirals reduce dengue incidence in a high-prevalence endemic area?
Jafari, Yalda, Brady, Oliver J., Briggs, Joseph R., Lien, Le Thuy, Mai, Huynh Kim, Nguyen, Hien Anh Thi, Van Loock, Marnix, Herrera-Taracena, Guillermo, Menten, Joris, Iwasaki, Chihiro, Takegata, Mizuki, Kitamura, Noriko, Do Thai, Hung, Minh, Bui Xuan, Morita, Kouichi, Anh, Dang Duc, Clifford, Sam, Prem, Kiesha, Hafalla, Julius, Edmunds, W. John, Yoshida, Lay Myint, Hibberd, Martin L. and Hue, Stephane (2024). Could prophylactic antivirals reduce dengue incidence in a high-prevalence endemic area?. PLoS Neglected Tropical Diseases, 18 (7) e0012334, e0012334. doi: 10.1371/journal.pntd.0012334
2023
Journal Article
Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission: a prospective cohort study in England
Clifford, Samuel, Waight, Pauline, Hackman, Jada, Hué, Stephane, Gower, Charlotte M., Kirsebom, Freja C. M., Skarnes, Catriona, Letley, Louise, Lopez Bernal, Jamie, Andrews, Nick, Flasche, Stefan and Miller, Elizabeth (2023). Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission: a prospective cohort study in England. Wellcome Open Research, 8 96, 96. doi: 10.12688/wellcomeopenres.17995.2
2023
Journal Article
Optimal age targeting for pneumococcal vaccination in older adults; a modelling study
Thindwa, Deus, Clifford, Samuel, Kleynhans, Jackie, von Gottberg, Anne, Walaza, Sibongile, Meiring, Susan, Swarthout, Todd D., Miller, Elizabeth, McIntyre, Peter, Andrews, Nick, Amin-Chowdhury, Zahin, Fry, Norman, Jambo, Kondwani C., French, Neil, Almeida, Samanta Cristine Grassi, Ladhani, Shamez N., Heyderman, Robert S., Cohen, Cheryl, de Cunto Brandileone, Maria Cristina and Flasche, Stefan (2023). Optimal age targeting for pneumococcal vaccination in older adults; a modelling study. Nature Communications, 14 (1) 888. doi: 10.1038/s41467-023-36624-8
2022
Journal Article
Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events
Pung, Rachael, Firth, Josh A., Spurgin, Lewis G., Chang, Annie, Kong, Jade, Wong, Jazzy, Jin, Ooi Jo, Selvaraj, Deepa, Yong, Dominique, Lang, Jocelyn, Sivalingam, Abilash, Procter, Simon R., Flasche, Stefan, Waites, William, Prem, Kiesha, Pearson, Carl A. B., Gibbs, Hamish P., Sherratt, Katharine, Villabona-Arenas, C. Julian, Wong, Kerry L. M., Liu, Yang, Mee, Paul, Chapman, Lloyd A. C., Atkins, Katherine E., Quaife, Matthew, Munday, James D., Funk, Sebastian, Eggo, Rosalind M., Huè, Stèphane ... Kucharski, Adam J. (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, 1. doi: 10.1038/s41467-022-29522-y
2022
Journal Article
Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level
Meakin, Sophie, Abbott, Sam, Bosse, Nikos, Munday, James, Gruson, Hugo, Hellewell, Joel, Sherratt, Katharine, Chapman, Lloyd A. C., Prem, Kiesha, Klepac, Petra, Jombart, Thibaut, Knight, Gwenan M., Jafari, Yalda, Flasche, Stefan, Waites, William, Jit, Mark, Eggo, Rosalind M., Villabona-Arenas, C. Julian, Russell, Timothy W., Medley, Graham, Edmunds, W. John, Davies, Nicholas G., Liu, Yang, Hué, Stéphane, Brady, Oliver, Pung, Rachael, Abbas, Kaja, Gimma, Amy, Mee, Paul ... Funk, Sebastian (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, 1. doi: 10.1186/s12916-022-02271-x
2022
Journal Article
Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era
Barnard, Rosanna C., Davies, Nicholas G., Munday, James D., Lowe, Rachel, Knight, Gwenan M., Leclerc, Quentin J., Tully, Damien C., Hodgson, David, Pung, Rachael, Hellewell, Joel, Koltai, Mihaly, Simons, David, Abbas, Kaja, Kucharski, Adam J., Procter, Simon R., Sandmann, Frank G., Pearson, Carl A. B., Prem, Kiesha, Showering, Alicia, Meakin, Sophie R., O’Reilly, Kathleen, McCarthy, Ciara V., Quaife, Matthew, Wong, Kerry L. M., Jafari, Yalda, Deol, Arminder K., Houben, Rein M. G. J., Diamond, Charlie, Jombart, Thibaut ... Edmunds, W. John (2022). Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era. Nature Communications, 13 (1) 4879. doi: 10.1038/s41467-022-32404-y
2022
Journal Article
Correction: The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices (BMC Public Health, (2022), 22, 1, (716), 10.1186/s12889-022-13069-0)
Nightingale, Emily S., Abbott, Sam, Russell, Timothy W., Rees, Eleanor M., Eggo, Rosalind M., Quaife, Matthew, Sun, Fiona Yueqian, Pearson, Carl A. B., Prem, Kiesha, Munday, James D., Meakin, Sophie R., van Zandvoort, Kevin, Edmunds, W. John, Rosello, Alicia, Funk, Sebastian, O’Reilly, Kathleen, Quilty, Billy J., Procter, Simon R., Gimma, Amy, Kucharski, Adam J., Deol, Arminder K., Emery, Jon C., Bosse, Nikos I., Gibbs, Hamish P., Simons, David, Hué, Stéphane, Jarvis, Christopher I., Klepac, Petra, Liu, Yang ... Brady, Oliver J. (2022). Correction: The local burden of disease during the first wave of the COVID-19 epidemic in England: estimation using different data sources from changing surveillance practices (BMC Public Health, (2022), 22, 1, (716), 10.1186/s12889-022-13069-0). BMC Public Health, 22 (1) 1140. doi: 10.1186/s12889-022-13320-8
2022
Journal Article
Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK
Waites, William, Pearson, Carl A. B., Gaskell, Katherine M., House, Thomas, Pellis, Lorenzo, Johnson, Marina, Gould, Victoria, Hunt, Adam, Stone, Neil R. H., Kasstan, Ben, Chantler, Tracey, Lal, Sham, Roberts, Chrissy H., Goldblatt, David, Abbas, Kaja, Abbott, Sam, Atkins, Katherine E., Barnard, Rosanna C., Bosse, Nikos I., Brady, Oliver, Chan, Yung-Wai Desmond, Chapman, Lloyd A. C., Clifford, Samuel, Davies, Nicholas G., Edmunds, W. John, Eggo, Rosalind M., Endo, Akira, Finch, Emilie, Flasche, Stefan ... Eggo, Rosalind M. (2022). Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK. Scientific Reports, 12 (1) 8550, 1. doi: 10.1038/s41598-022-12517-6
2022
Journal Article
Ultrafine particle exposure and biomarkers of effect on small airways in children
Robinson, Paul D., Salimi, Farhad, Cowie, Christine T., Clifford, Samuel, King, Gregory G., Thamrin, Cindy, Hardaker, Kate, Mazaheri, Mandana, Morawska, Lidia, Toelle, Brett G. and Marks, Guy B. (2022). Ultrafine particle exposure and biomarkers of effect on small airways in children. Environmental Research, 214 (Part 1) 113860, 113860. doi: 10.1016/j.envres.2022.113860
2022
Journal Article
Association of pneumococcal carriage in infants with the risk of carriage among their contacts in Nha Trang, Vietnam: A nested cross-sectional survey
Qian, George, Toizumi, Michiko, Clifford, Sam, Le, Lien Thuy, Papastylianou, Tasos, Satzke, Catherine, Quilty, Billy, Iwasaki, Chihiro, Kitamura, Noriko, Takegata, Mizuki, Bui, Minh Xuan, Nguyen, Hien Anh Thi, Dang, Duc Anh, van Hoek, Albert Jan, Yoshida, Lay Myint and Flasche, Stefan (2022). Association of pneumococcal carriage in infants with the risk of carriage among their contacts in Nha Trang, Vietnam: A nested cross-sectional survey. PLOS Medicine, 19 (5) e1004016, e1004016-5. doi: 10.1371/journal.pmed.1004016
2022
Journal Article
Using trained dogs and organic semi-conducting sensors to identify asymptomatic and mild SARS-CoV-2 infections: an observational study
Guest, Claire, Dewhirst, Sarah Y., Lindsay, Steve W., Allen, David J., Aziz, Sophie, Baerenbold, Oliver, Bradley, John, Chabildas, Unnati, Chen-Hussey, Vanessa, Clifford, Samuel, Cottis, Luke, Dennehy, Jessica, Foley, Erin, Gezan, Salvador A., Gibson, Tim, Greaves, Courtenay K., Kleinschmidt, Immo, Lambert, Sébastien, Last, Anna, Morant, Steve, Parker, Josephine E. A., Pickett, John, Quilty, Billy J., Rooney, Ann, Shah, Manil, Somerville, Mark, Squires, Chelci, Walker, Martin, Logan, James G. ... Davis, Jane (2022). Using trained dogs and organic semi-conducting sensors to identify asymptomatic and mild SARS-CoV-2 infections: an observational study. Journal of Travel Medicine, 29 (3) taac043, 1-10. doi: 10.1093/jtm/taac043
2022
Journal Article
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
Gimma, Amy, Munday, James D., Wong, Kerry L.M., Coletti, Pietro, van Zandvoort, Kevin, Prem, Kiesha, Klepac, Petra, Rubin, G. James, Funk, Sebastian, Edmunds, W. John, Jarvis, Christopher I., Chapman, Lloyd A.C., Clifford, Samuel, Jombart, Thibaut, O’Reilly, Kathleen, Lei, Jiayao, Abbas, Kaja, Krauer, Fabienne, Flasche, Stefan, Rosello, Alicia, Knight, Gwenan M., Tully, Damien C., Atkins, Katherine E., Pung, Rachael, Eggo, Rosalind M., Hodgson, David, Koltai, Mihaly, Jafari, Yalda, Russell, Timothy W. ... Nightingale, Emily S. (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, e1003907-3. doi: 10.1371/journal.pmed.1003907
2022
Journal Article
SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort
Finch, Emilie, Lowe, Rachel, Fischinger, Stephanie, de St Aubin, Michael, Siddiqui, Sameed M., Dayal, Diana, Loesche, Michael A., Rhee, Justin, Beger, Samuel, Hu, Yiyuan, Gluck, Matthew J., Mormann, Benjamin, Hasdianda, Mohammad A., Musk, Elon R., Alter, Galit, Menon, Anil S., Nilles, Eric J., Kucharski, Adam J., Lei, Jiayao, Funk, Sebastian, Sun, Fiona Yueqian, Gimma, Amy, Nightingale, Emily S., Medley, Graham, Abbott, Sam, Krauer, Fabienne, Davies, Nicholas G., Jit, Mark, Endo, Akira ... Sandmann, Frank G. (2022). SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort. PLoS Biology, 20 (2) e3001531, e3001531-2. doi: 10.1371/journal.pbio.3001531
2021
Journal Article
The importance of saturating density dependence for population-level predictions of SARS-CoV-2 resurgence compared with density-independent or linearly density-dependent models, England, 23 March to 31 July 2020
Nightingale, Emily S., Brady, Oliver J., Yakob, Laith, Gimma, Amy, Jit, Mark, Jarvis, Christopher I., Waterlow, Naomi R., Procter, Simon R., Auzenbergs, Megan, Tully, Damien C., Simons, David, Endo, Akira, Hellewell, Joel, Lowe, Rachel, Foss, Anna M., van Zandvoort, Kevin, Pearson, Carl A.B., Showering, Alicia, Klepac, Petra, Medley, Graham, Quilty, Billy J., Diamond, Charlie, Edmunds, W. John, Rosello, Alicia, Barnard, Rosanna C., Abbas, Kaja, Sherratt, Katharine, Williams, Jack, Meakin, Sophie R. ... Munday, James D. (2021). The importance of saturating density dependence for population-level predictions of SARS-CoV-2 resurgence compared with density-independent or linearly density-dependent models, England, 23 March to 31 July 2020. Eurosurveillance, 26 (49) 2001809, 49. doi: 10.2807/1560-7917.ES.2021.26.49.2001809
2021
Journal Article
Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data
Munday, James D., Jarvis, Christopher I., Gimma, Amy, Wong, Kerry L. M., van Zandvoort, Kevin, Liu, Yang, Hellewell, Joel, Davies, Nicholas G., Villabona-Arenas, C. Julian, Eggo, Rosalind M., Endo, Akira, Bosse, Nikos I., Gibbs, Hamish P., Pearson, Carl A. B., Sun, Fiona Yueqian, Jit, Mark, O’Reilly, Kathleen, Jafari, Yalda, Atkins, Katherine E., Waterlow, Naomi R., Rosello, Alicia, Chan, Yung-Wai Desmond, Foss, Anna M., Quilty, Billy J., Russell, Timothy W., Flasche, Stefan, Procter, Simon R., Waites, William, Barnard, Rosanna C. ... Edmunds, W. John (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, 1. doi: 10.1186/s12916-021-02107-0
2021
Journal Article
The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories
Liu, Yang, Morgenstern, Christian, Kelly, James, Lowe, Rachel, Munday, James, Villabona-Arenas, C. Julian, Gibbs, Hamish, Pearson, Carl A. B., Prem, Kiesha, Leclerc, Quentin J., Meakin, Sophie R., Edmunds, W. John, Jarvis, Christopher I., Gimma, Amy, Funk, Sebastian, Quaife, Matthew, Russell, Timothy W., Emory, Jon C., Abbott, Sam, Hellewell, Joel, Tully, Damien C., Houben, Rein M. G. J., O’Reilly, Kathleen, Gore-Langton, Georgia R., Kucharski, Adam J., Auzenbergs, Megan, Quilty, Billy J., Jombart, Thibaut, Rosello, Alicia ... Jit, Mark (2021). The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories. BMC Medicine, 19 (1) 40, 1. doi: 10.1186/s12916-020-01872-8
2021
Journal Article
The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment
Jarvis, Christopher I., Gimma, Amy, van Zandvoort, Kevin, Wong, Kerry L. M., Abbas, Kaja, Villabona-Arenas, C. Julian, O’Reilly, Kathleen, Quaife, Matthew, Rosello, Alicia, Kucharski, Adam J., Gibbs, Hamish P., Atkins, Katherine E., Barnard, Rosanna C., Bosse, Nikos I., Procter, Simon R., Meakin, Sophie R., Sun, Fiona Yueqian, Abbott, Sam, Munday, James D., Russell, Timothy W., Flasche, Stefan, Sherratt, Katharine, Eggo, Rosalind M., Davies, Nicholas G., Quilty, Billy J., Auzenbergs, Megan, Hellewell, Joel, Jombart, Thibaut, Jafari, Yalda ... Edmunds, W. John (2021). The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment. BMC Medicine, 19 (1) 52, 1. doi: 10.1186/s12916-021-01924-7
2021
Journal Article
Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England
Munday, James D., Sherratt, Katharine, Meakin, Sophie, Endo, Akira, Pearson, Carl A. B., Hellewell, Joel, Abbott, Sam, Bosse, Nikos I., Eggo, Rosalind M., Simons, David, O’Reilly, Kathleen, Russell, Timothy W., Lowe, Rachel, Leclerc, Quentin J., Emery, Jon C., Klepac, Petra, Nightingale, Emily S., Quaife, Matthew, van Zandvoort, Kevin, Knight, Gwenan M., Jombart, Thibaut, Villabona-Arenas, C. Julian, Rees, Eleanor M., Diamond, Charlie, Auzenbergs, Megan, Medley, Graham, Foss, Anna M., Gore-Langton, Georgia R., Deol, Arminder K. ... 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, 1. doi: 10.1038/s41467-021-22213-0
2021
Journal Article
Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England
Leclerc, Quentin J., Fuller, Naomi M., Keogh, Ruth H., Diaz-Ordaz, Karla, Sekula, Richard, Semple, Malcolm G., Baillie, J. Kenneth, Openshaw, Peter J. M., Carson, Gail, Alex, Beatrice, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chand, Meera, Cooke, Graham S., Docherty, Annemarie B., Dunning, Jake, da Silva Filipe, Ana, Fletcher, Tom, Green, Christopher A., Harrison, Ewen M., Hiscox, Julian A., Ho, Antonia Ying Wai, Horby, Peter W., Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lim, Wei Shen ... Knight, Gwenan M. (2021). Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England. BMC Health Services Research, 21 (1) 566, 1. doi: 10.1186/s12913-021-06509-x
2021
Journal Article
Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England
Leclerc, Quentin J., Nightingale, Emily S., Abbott, Sam, Rees, Eleanor M., Eggo, Rosalind M., Quaife, Matthew, Sun, Fiona Yueqian, Pearson, Carl A. B., Prem, Kiesha, Munday, James D., Meakin, Sophie R., Medley, Graham, van Zandvoort, Kevin, Edmunds, W. John, Rosello, Alicia, Funk, Sebastian, O’Reilly, Kathleen, Quilty, Billy J., Procter, Simon R., Gimma, Amy, Kucharski, Adam J., Deol, Arminder K., Emery, Jon C., Bosse, Nikos I., Gibbs, Hamish P., Simons, David, Hué, Stéphane, Jarvis, Christopher I., Klepac, Petra ... Jombart, Thibaut (2021). Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England. Scientific Reports, 11 (1) 7106, 1. doi: 10.1038/s41598-021-86266-3
Supervision
Availability
- Dr Sam Clifford is:
- Available for supervision
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