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Moriarty, Meadhbh and Murphy, Joanne M. and Brooker, Adam J. and Waites, William and Revie, Crawford W. and Adams, Thomas P. and Lewis, Matt and Reinardy, Helena C. and Phelan, John P. and Coyle, Johnny P. and Rabe, Berit and Ives, Stephen C. and Armstrong, John D. and Sandvik, Anne D. and Asplin, Lars and Karlsen, Ørjan and Garnier, Soizic and á Norði, Gunnvør and Gillibrand, Philip A. and Last, Kim S. and Murray, Alexander G. (2024) A gap analysis on modelling of sea lice infection pressure from salmonid farms. I. A structured knowledge review. Aquaculture Environment Interactions, 16. pp. 1-25. ISSN 1869-7534

Murphy, Joanne M. and Moriarty, Meadhbh and Brooker, Adam J. and Waites, William and Revie, Crawford W. and Adams, Thomas P. and Lewis, Matt and Reinardy, Helena C. and Phelan, John P. and Coyle, Johnny P. and Rabe, Berit and Ives, Stephen C. and Armstrong, John D. and Sandvik, Anne D. and Asplin, Lars and Karlsen, Ørjan and Garnier, Soizic and á Norði, Gunnvør and Gillibrand, Philip A. and Last, Kim S. and Murray, Alexander G. (2024) A gap analysis on modelling of sea lice infection pressure from salmonid farms. II. Identifying and ranking knowledge gaps: output of an international workshop. Aquaculture Environment Interactions, 16. pp. 27-42. ISSN 1869-7534

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

Knight, Gwenan M. and Pham, Thi Mui and Stimson, James and Funk, Sebastian and Jafari, Yalda and Pople, Diane and Evans, Stephanie and Yin, Mo and Brown, Colin S. and Bhattacharya, Alex and Hope, Russell and Semple, Malcolm G. and Abbott, Sam and Gimma, Amy and Gibbs, Hamish P. and Abbas, Kaja and Barnard, Rosanna C. and Sandmann, Frank G. and Bosse, Nikos I. and Mee, Paul and McCarthy, Ciara V. and Quaife, Matthew and Kucharski, Adam J. and Jarvis, Christopher I. and Hellewell, Joel and Finch, Emilie and Rosello, Alicia and Jit, Mark and Pung, Rachael and Eggo, Rosalind M. and Endo, Akira and Medley, Graham and Tully, Damien C. and Wong, Kerry L.M. and Liu, Yang and Sherratt, Katharine and Munday, James D. and Chapman, Lloyd A.C. and Hué, Stéphane and O’Reilly, Kathleen and Davies, Nicholas G. and Meakin, Sophie R. and Sun, Fiona Yueqian and Brady, Oliver and Villabona-Arenas, C. Julian and Atkins, Katherine E. and Prem, Kiesha and Hodgson, David and Koltai, Mihaly and Waites, William, ISARIC4C Investigators, CMMID COVID-19 Working Group (2022) The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020. BMC Infectious Diseases, 22 (1). 556. ISSN 1471-2334

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

Panovska-Griffiths, J. and Stuart, R.M. and Kerr, C.C. and Rosenfield, K. and Mistry, D. and Waites, W. and Klein, D.J. and Bonell, C. and Viner, R.M. (2022) Modelling the impact of reopening schools in the UK in early 2021 in the presence of the alpha variant and with roll-out of vaccination against SARS-CoV-2. Journal of Mathematical Analysis and Applications, 514 (2). 126050. ISSN 0022-247X

Waites, W. and Cavaliere, M. and Danos, V. and Datta, R. and Eggo, R. M. and Hallett, T. B. and Manheim, D. and Panovska-Griffiths, J. and Russell, T. W. and Zarnitsyna, V. I. (2022) Compositional modelling of immune response and virus transmission dynamics. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 380 (2233). pp. 1-24. 20210307. ISSN 1471-2962

Ackland, G. J. and Panovska-Griffiths, J. and Waites, W. and Cates, M. E. (2022) The Royal Society RAMP modelling initiative. Proceedings A: Mathematical, Physical and Engineering Sciences, 380 (2233). pp. 1-4. 20210316. ISSN 1471-2962

Panovska-Griffiths, J. and Swallow, B. and Hinch, R. and Cohen, J. and Rosenfeld, K. and Stuart, R. M. and Ferretti, L. and Di Lauro, F. and Wymant, C. and Izzo, A. and Waites, W. and Viner, R. and Bonell, C. and Fraser, C. and Klein, D. and Kerr, C. C., The COVID-19 Genomics UK (COG-UK) Consortium (2022) Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Proceedings A: Mathematical, Physical and Engineering Sciences, 380 (2233). 2021.0315. ISSN 1471-2962

Panovska-Griffiths, J. and Waites, W. and Ackland, G. J. (2022) Technical challenges of modelling real-life epidemics and examples of overcoming these. Proceedings A: Mathematical, Physical and Engineering Sciences, 380 (2233). 20220179. ISSN 1471-2962

Fritz, Hagen and Bastami, Sepehr and Lin, Calvin and Nweye, Kingsley and To, Tung and Chen, Lauren and Le, Dung and Ibarra, Angelina and Zhang, Wendy and Park, June Young and Waites, William and Tang, Mengjia and Misztal, Pawel and Novoselac, Atila and Thomaz, Edison and Kinney, Kerry and Nagy, Zoltan (2022) Design, fabrication, and calibration of the Building EnVironment and Occupancy (BEVO) Beacon : a rapidly-deployable and affordable indoor environmental quality monitor. Building and Environment, 222. 109432. ISSN 0360-1323

Chen, Yuyang and Waites, William, CMMID COVID-19 Working Group (2022) Measuring the effects of COVID-19-related disruption on dengue transmission in southeast Asia and Latin America : a statistical modelling study. The Lancet Infectious Diseases, 22 (5). pp. 657-667. ISSN 1474-4457

Waites, William and Pearson, Carl A. B. and Gaskell, Katherine M. and House, Thomas and Pellis, Lorenzo and Johnson, Marina and Gould, Victoria and Hunt, Adam and Stone, Neil R. H. and Kasstan, Ben and Chantler, Tracey and Lal, Sham and Roberts, Chrissy H. and Goldblatt, David and Marks, Michael and Eggo, Rosalind M., CMMID COVID-19 Working Group (2022) Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK. Scientific Reports, 12. 8550. ISSN 2045-2322

Karr, Jonathan and Malik-Sheriff, Rahuman S. and Osborne, James and Gonzalez-Parra, Gilberto and Forgoston, Eric and Bowness, Ruth and Liu, Yaling and Thompson, Robin and Garira, Winston and Barhak, Jacob and Rice, John and Torres, Marcella and Dobrovolny, Hana M. and Tang, Tingting and Waites, William and Glazier, James A. and Faeder, James R. and Kulesza, Alexander (2022) Model integration in computational biology : the role of reproducibility, credibility and utility. Frontiers in Systems Biology, 2. 822606. ISSN 2674-0702

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

Cheetham, Nathan and Waites, William and Ebyarimpa, Irene and Leber, Werner and Brennan, Katie and Panovska-Griffiths, Jasmina (2021) Determining the level of social distancing necessary to avoid future COVID-19 epidemic waves : a modelling study for North East London. Scientific Reports, 11 (1). 5806. ISSN 2045-2322

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

Panovska-Griffiths, J. and Kerr, C. C. and Waites, W. and Stuart, R. M. and Mistry, D. and Foster, D. and Klein, D. J. and Viner, R. M. and Bonell, C. (2021) Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK. Scientific Reports, 11 (1). 8747. ISSN 2045-2322

Sera, Francesco and Armstrong, Ben and Abbott, Sam and Meakin, Sophie and O’Reilly, Kathleen and von Borries, Rosa and Schneider, Rochelle and Royé, Dominic and Hashizume, Masahiro and Pascal, Mathilde and Tobias, Aurelio and Vicedo-Cabrera, Ana Maria and Gasparrini, Antonio and Lowe, Rachel and Waites, William, MCC Collaborative Research Network, CMMID COVID-19 Working Group (2021) A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries. Nature Communications, 12. 5968. ISSN 2041-1723

Waites, W. and Cavaliere, M. and Manheim, D. and Panovska-Griffiths, J. and Danos, V. (2021) Rule-based epidemic models. Journal of Theoretical Biology, 530. 110851. ISSN 0022-5193

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

Gaskell, Katherine M. and Johnson, Marina and Gould, Victoria and Hunt, Adam and Stone, Neil RH and Waites, William and Kasstan, Ben and Chantler, Tracey and Lal, Sham and Roberts, Chrissy H. and Goldblatt, David and Eggo, Rosalind M. and Marks, Michael (2021) SARS-CoV-2 seroprevalence in a strictly-Orthodox Jewish community in the UK : a retrospective cohort study. The Lancet Regional Health - Europe, 6. 100127.

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

Hodgson, David and Waites, William, CMMID COVID-19 Working Group (2021) The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant. Eurosurveillance, 26 (20). 2100428. ISSN 1025-496X

Waites, William, CMMID COVID-19 Working Group, COVID-19 Genomics UK (COG-UK) Consortium (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372 (6538). eabg3055. ISSN 0036-8075

Sturniolo, Simone and Waites, William and Colbourn, Tim and Manheim, David and Panovska-Griffiths, Jasmina (2021) Testing, tracing and isolation in compartmental models. PLoS Computational Biology, 17 (3). e1008633. ISSN 1553-734X

Yang, Guoli and Csikász-Nagy, Attila and Waites, William and Xiao, Gaoxi and Cavaliere, Matteo (2020) Information cascades and the collapse of cooperation. Scientific Reports, 10 (1). 8004. ISSN 2045-2322

Waites, William and Davies, Jamie A. (2019) Emergence of structure in mouse embryos : structural entropy morphometry applied to digital models of embryonic anatomy. Journal of Anatomy, 235 (4). pp. 706-715. ISSN 1469-7580

Waites, William and Misirli, Göksel and Cavaliere, Matteo and Danos, Vincent and Wipat, Anil (2018) A genetic circuit compiler : generating combinatorial genetic circuits with web semantics and inference. ACS Synthetic Biology, 7 (12). pp. 2812-2823. ISSN 2161-5063

Waites, William and Cavaliere, Matteo and Cachat, Elise and Danos, Vincent and Dvies, Jamie A. (2018) An information-theoretic measure for patterning in epithelial tissues. IEEE Access, 6. pp. 40302-40312. 8405520. ISSN 2169-3536

Misirli, Goksel and Cavaliere, Matteo and Waites, William and Pocock, Matthew and Madsen, Curtis and Gilfellon, Owen and Honorato-Zimmer, Ricardo and Zuliani, Paolo and Danos, Vincent and Wipat, Anil (2016) Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics, 32 (6). pp. 908-917. ISSN 1367-4811

Jones, Richard and MacGillivray, Mark and Murray-Rust, Peter and Pitman, Jim and Sefton, Peter and O'Steen, Ben and Waites, William (2011) Open bibliography for science, technology, and medicine. Journal of Cheminformatics, 3 (10). 47. ISSN 1758-2946

Book Section

Bañón, Marta and Chen, Pinzhen and Haddow, Barry and Heafield, Kenneth and Hoang, Hieu and Esplà-Gomis, Miquel and Forcada, Mikel and Kamran, Amir and Kirefu, Faheem and Koehn, Philipp and Ortiz-Rojas, Sergio and Pla, Leopoldo and Ramírez-Sánchez, Gema and Sarrías, Elsa and Strelec, Marek and Thompson, Brian and Waites, William and Wiggins, Dion and Zaragoza, Jaume; (2020) ParaCrawl : web-scale acquisition of parallel corpora. In: ACL 2020 - 58th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference. Proceedings of the Annual Meeting of the Association for Computational Linguistics . Association for Computational Linguistics (ACL), USA, pp. 4555-4567. ISBN 9781952148255

Report

Waites, William (2023) Report on Storm Babet in Granton Harbour. University of Strathclyde, Glasgow, UK.

Monograph

Waites, William and Cavaliere, Matteo and Danos, Vincent and Datta, Ruchira and Eggo, Rosalind M. and Hallett, Timothy B. and Manheim, David and Panovska-Griffiths, Jasmina and Russell, Timothy W. and Zarnitsyna, Veronika I. (2021) Compositional modelling of immune response and virus transmission dynamics. Other. arXiv.org, Ithaca, N.Y..