Publications


  • Tildesley MJ, Vassall A, Riley S, Jit M, Sandmann FS, Hill EM, Thompson RN, Atkins BD, Edmunds WJ, Dyson L, Keeling MJ. Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study (2022) R. Soc. Open Sci., 9:211746. (Available here)
  • Ezanno P, Picault S, Bareille S, Beaunée B, Boender GJ, Dankwa EA, Deslandes F, Donnelly CA, Hagenaars TJ, Hayes S, Jori F, Lambert S, Mancini M, Munoz F, Pleydell D, Thompson RN, Vergu E, Vignes M, Vergne T. The African swine fever modelling challenge: model comparison and lessons learnt (2022) Epidemics, 100615. (Available here)
  • Akhmetzhanov AR, Ponce L, Thompson RN. Emergence potential of monkeypox in the Western Pacific Region, July 2022 (2022) Int. J. Inf. Dis. (Available here)
  • Kaye AR, Hart WS, Bromiley J, Iwami S, Thompson RN. A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments (2022) J. Theor. Biol. 548:111195. (Available here)
  • Leng T, Hill EM, Keeling MJ, Tildesley MJ, Thompson RN. The effect of notification window length on the epidemiological impact of COVID-19 contact tracing mobile applications (2022) Comms. Med. 2:74. (Available here)
  • Leng T, Hill EM, Thompson RN, Tildesley MJ, Keeling MJ, Dyson L. Assessing the impact of lateral flow testing strategies on within-school SARS-CoV-2 transmission and absences: A modelling study (2022) PLoS Comp. Biol. 18:e1010158. (Available here)
  • Parag KV, Thompson RN, Donnelly CA. Are epidemic growth rates more informative than reproduction numbers? (2022) J. Roy. Stat. Soc. A, 1:1-11. (Available here)
  • Linton NM, Lovell-Read FA, Southall E, Lee H, Akhmetzhanov A, Thompson RN, Nishiura H. When do epidemics end? Scientific insights from mathematical modelling studies (2022) Centaurus, 64:31-16. (Available here)
  • Hart WS, Miller E, Andrews NJ, Waight P, Maini PK, Funk S, Thompson RN. Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis (2022) Lancet Inf. Dis. 22:603-610. (Available here)
  • Leng T, Hill EM, Holmes A, Southall E, Thompson RN, Tildesley MJ, Keeling MJ, Dyson L. Quantifying pupil-to-pupil SARS-CoV-2 transmission and the impact of lateral flow testing in English secondary schools (2022) Nat. Commun., 13:1106. (Available here)
  • Singer BJ, Thompson RN, Bonsall MB. Evaluating strategies for spatial allocation of vaccines based on risk and centrality (2022) J. R. Soc. Interface, 19: 20210709. (Available here)
  • Hart WS, Abbott S, Endo A, Hellewell J, Miller E, Andrews N, Maini PK, Funk S, Thompson RN. Inference of the SARS-CoV-2 generation time using UK household data (2022) eLife 11:e70767. (Available here)
  • Kretzschmar ME, Ashby B, Fearon E, Overton CE, Panovska-Griffiths J, Pellis L, Quaife M, Rozhnova G, Scarabel F, Stage HB, Swallow B, Thompson RN, Tildesley MJ, Villela D. Challenges for modelling interventions for future pandemics (2022) Epidemics, 38:100546. (Available here)
  • Karr J, Malik-Sherriff RS, Osborne J, Gonzalez-Parra G, Forgoston E, Bowness R, Liu Y, Thompson RN, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, Glazier JA, Kulesza A. Model integration in computational biology : the role of reproducibility, credibility and utility (2022) Front. Sys. Bio. 2:822606. (Available here)
  • Griette Q, Liu Z, Magal P, Thompson RN. Real-time prediction of the end of an epidemic wave: COVID-19 in China as a case-study (2022) Fields Inst. Commun. 85:173-196. (Available here)
  • Lovell-Read FA, Shen S, Thompson RN. Estimating local outbreak risks and the effects of non-pharmaceutical interventions in age-structured populations: SARS-CoV-2 as a case study (2022) J. Theor. Biol. 535:110983. (Available here)
  • Glennon EE, Bruijnig M, Lessler J, Miller IF, Rice BL, Thompson RN, Wells K, Metcalf CJE. Challenges in modeling the emergence of novel pathogens (2021) Epidemics, 37:100516. (Available here)
  • Sachak-Patwa R, Byrne HM, Dyson L, Thompson RN. The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions (2021) Comms. Med., 1:39. (Available here)
  • Vegvari C, Abbott S, Ball F, Brooks-Pollock E, Challen R, Collyer BS, Dangerfield C, Gog JR, Gostic KM, Heffernan JM, Hollingsworth TD, Isham V, Kenah E, Mollison D, Panovska-Griffiths J, Pellis L, Roberts MG, Scalia Tomba G, Thompson RN, Trapman P. Commentary on the use of the reproduction number R during the COVID-19 pandemic (2021) Stat. Meth. Med. Res., 1:1-11. (Available here)
  • Gog JR, Hill EM, Danon L, Thompson RN. Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model (2021) Roy. Soc. Open Sci., 8:210530. (Available here)
  • Akhmetzhanov AR, Jung S-M, Cheng H-Y, Thompson RN. A hospital-related outbreak of SARS-CoV-2 associated with variant Epsilon (B.1.429) in Taiwan: transmission potential and outbreak containment under intensified contact tracing, January-February 2021 (2021) Int. J. Inf. Dis., 110:15-20. (Available here)
  • Iwanami S, Ejima K, Kim KS, Noshita K, Fujita Y, Miyazaki T, Kohno S, Miyazaki Y, Morimoto S, Nakaoka S, Koizumi Y, Asai Y, Aihara K, Watashi K, Thompson RN, Shibuya K, Fujiu K, Perelson AS, Iwami S, Wakita T. Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study (2021) PLoS Med., 18:e1003660. (Available here)
  • Hale T, Angrist N, Hale AJ, Kira B, Majumdar S, Petherick A, Phillips T, Sridhar D, Thompson RN, Webster S, Zhang Y. Government responses and COVID-19 deaths: Global evidence across multiple pandemic waves (2021) PLoS One, 16:e0253116. (Available here)
  • Southall E, Holmes A, Hill EM, Atkins BD, Leng T, Thompson RN, Dyson L, Keeling MJ, Tildesley MJ. An analysis of school absences in England during the COVID-19 pandemic (2021) BMC Med., 19:137. (Available here)
  • Lovell-Read FA, Funk S, Obolski U, Donnelly CA, Thompson RN. Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study (2021) J. R. Soc. Interface, 18:20201014. (Available here)
  • Hart WS, Maini PK, Thompson RN. High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing (2021) eLife, 10:e65534. (Available here)
  • Thompson RN, Hill EM, Gog JR. SARS-CoV-2 incidence and vaccine escape (2021) Lancet Inf. Dis., S1473-3099:00202-4. (Available here)
  • Kim KS, Ejima K, Iwanami S, Fujita Y, Ohashi H, Koizumi Y, Asai Y, Nakaoka S, Watashi K, Aihara K, Thompson RN, Ke R, Perelson AS, Iwami S. A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2 (2021) PLoS Biol., 19:e3001128. (Available here)
  • Singer BJ, Thompson RN, Bonsall MB. The effect of the definition of ‘pandemic’ on quantitative assessments of infectious disease outbreak risk (2021) Sci. Rep., 11:2547. (Available here)
  • Sachak-Patwa R, Byrne HM, Thompson RN. Accounting for cross-immunity can improve forecast accuracy during influenza epidemics (2020) Epidemics, 34:100432. (Available here)
  • Thompson RN, Thompson MJ, Hurrell JW, Sun L, Obolski U. Assessing the threat of major outbreaks of vector-borne diseases under a changing climate (2020) Astrophys. Space Sci. Proc., 57:25-35. (Available here)
  • Thompson RN, Gilligan CA, Cunniffe NJ. Will an outbreak exceed available resources for control? Estimating the risk from invading pathogens using practical definitions of a severe epidemic (2020) J. R. Soc. Interface, 17:20200690. (Available here)
  • Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherratt K, Thompson RN, White LF, et al. Practical considerations for measuring the effective reproductive number, R_t (2020) PLoS Comp. Biol., 16:e1008409. (Available here)
  • Parag KV, Donnelly CA, Jha R, Thompson RN. An exact method for quantifying the reliability of end-of-epidemic declarations in real time (2020) PLoS Comp. Biol., 16:e1008478. (Available here)
  • Lourenço J, Thompson RN, Thézé J, Obolski U. Characterising West Nile virus epidemiology in Israel using a transmission suitability index (2020) Euro Surveill., 25:1900629. (Available here)
  • White LF, Moser CB, Thompson RN, Pagano M. Statistical estimation of the reproductive number from case notification data (2020) Am. J. Epidem., 140:kwaa211 (Available here)
  • Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Gog JR, Glendinning P, Hart WS, Heesterbeek H, House T, Keeling M, et al. Key questions for modelling COVID-19 exit strategies (2020) Proc. Roy. Soc. B, 287:20201405. (Available here)
  • Thompson, RN. Epidemiological models are important tools for guiding COVID-19 interventions (2020) BMC Med., 18:152 (Available here)
  • Hart WS, Maini PK, Yates CA, Thompson RN. A theoretical framework for transitioning from patient-level to population-scale epidemiological dynamics: influenza A as a case study (2020) J. Roy. Soc. Interface, 17:20200230 (Available here)
  • Daon Y, Thompson RN, Obolski U. Estimating COVID-19 outbreak risk through air travel (2020) J. Trav. Med., 1:taaa093 (Available here)
  • Abbott S, Hellewell J, Thompson RN, Sherratt K, Gibbs HP, Bosse NI, Munday JD, Meakin S, Doughty EL, Chun JY, Chan Y-WD, Finger F, Campbell P, Endo A, Pearson CAB, Gimma A, Russell T, CMMID COVID modelling group, Flasche S, Kucharski AJ, Eggo RM, Funk S. Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts (2020) Wellcome Open Research (Available here)
  • Thompson RN, Lovell-Read FL, Obolski U. Time from symptom onset to hospitalisation of coronavirus disease 2019 (COVID-19) cases: Implications for the proportion of transmissions from infectors with few symptoms (2020) J. Clin. Med., 9:1297 (Available here)
  • Thompson RN, Cunniffe NJ. The probability of detection of SARS-CoV-2 in saliva (2020) Stat. Meth. Med. Res., 29:1049-1050 (Available here)
  • Thompson RN. Pandemic potential of 2019-nCoV (2020) Lancet Inf. Dis., 3099:30068 (Available here)
  • Thompson RN. Novel coronavirus outbreak in Wuhan, China, 2020: Intense surveillance Is vital for preventing sustained transmission in new locations (2020) J. Clin. Med., 9:498 (Available here)
  • Jung S-M, Kinoshita R, Thompson RN, Linton NM, Yang Y, Akhmetzhanov AR, Nishiura H. Epidemiological identification of a novel pathogen in real time: Analysis of the atypical pneumonia outbreak in Wuhan, China, 2019-2020 (2020) J. Clin. Med., 9:637 (Available here)
  • Greischar MA, Alexander HK, Bashey F, Bento AI, Bhattacharya A, Bushman M, Childs LM, Daversa DR, Day T, Faust CL, Gallagher ME, Gandon S, Glidden CK, Halliday FW, Hanley KA, Kamiya T, Read AF, Schwabl P, Sweeny AR, Tate AT, Thompson RN, et al. Evolutionary consequences of feedbacks between within-host competition and disease control (2020) Evol. Med. Public Health, 1: 30-34 (Available here)
  • Thompson RN, Jalava K, Obolski U. Sustained transmission of Ebola in new locations: more likely than previously thought (2019) Lancet Inf. Dis., 19:1058-1059 (Available here)
  • Hart WS, Hochfilzer LFR, Cunniffe NJ, Lee H, Nishiura H, Thompson RN. Accurate forecasts of the effectiveness of interventions against Ebola may require models that account for variations in symptoms during infection (2019) Epidemics, 29:100371 (Available here)
  • Cullerne J, French A, Poon D, Baxter A, Thompson RN. The pedagogical power of context: extending the epidemiology of Eyam (2019) Phys Educ, 55:015021 (Available here)
  • Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, Kamvar ZN, Demarsh PA, Dahlqwist E, Li S, Miguel E, Jombart T, Lessler J, Cauchemez S, Cori A. Improved inference of time-varying reproduction numbers during infectious disease outbreaks (2019) Epidemics, 29:100356 (Available here)
  • Thompson RN, Thompson CP, Pelerman O, Gupta S, Obolski U. Increased frequency of travel in the presence of cross-immunity may act to decrease the chance of a global pandemic (2019) Phil. Trans. Roy. Soc. B, 374:20180274 (Available here)
  • Thompson RN, Brooks-Pollock E. Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants (2019) Phil. Trans. Roy. Soc. B, 374:20190038 (Available here)
  • Thompson RN, Wymant C, Spriggs RA, Raghwani J, Fraser C, Lythgoe KA. Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission (2019) Virus Evol., 5:vey038 (Available here)
  • Thompson RN, Morgan OW, Jalava K. Rigorous surveillance is necessary for high confidence in end-of-outbreak declarations for Ebola and other infectious diseases (2019) Phil. Trans. Roy. Soc. B (Available here)
  • Thompson RN, Brooks-Pollock E. Preface to theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’ (2019) Phil. Trans. Roy. Soc. B (Available here)
  • Obolski U, Gori A, Lourenço J, Thompson C, Thompson RN, French N, Heyderman R, Gupta S. Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data (2019) Sci. Rep. (Available here)
  • Abdullah N, Kelly JT, Graham SC, Birch J, Gonçalves-Carneiro D, Mitchell T, Thompson RN, Lythgoe KA, Logan N, Hosie MJ, Bavro VN, Willett BJ, Heaton MP, Bailey D. Structure-guided identification of a nonhuman morbillivirus with zoonotic potential (2018) J. Virol., 92:e01248 (Available here)
  • Somveille M, Firth JA, Aplin LM, Farine DR, Sheldon BC, Thompson RN. Movement and conformity interact to establish local behavioural traditions in animal populations (2018) PLoS Comp. Biol., 14:e1006647 (Available here)
  • Suffert F, Thompson RN. Some reasons why the latent period should not always be considered constant over the course of a plant disease epidemic (2018) Plant Pathol., 67:1831-1840 (Available here)
  • Thompson RN, Hart WS. Effect of confusing symptoms and infectiousness on forecasting and control of Ebola outbreaks (2018) Clin. Inf. Dis., 67:1472-1474 (Available here)
  • Obolski U, Lourenço J, Thompson C, Thompson RN, Gori A, Gupta S. Vaccination can drive an increase in frequencies of antibiotic resistance among non-vaccine serotypes of Streptococcus pneumoniae (2018) Proc. Natl. Acad. Sci., 201718712 (Available here)
  • Thompson RN, Gilligan CA, Cunniffe NJ. Control fast or control smart: when should invading pathogens be controlled? (2018) PLoS Comp. Biol., 14:e1006014 (Available here)
  • Raghwani J, Thompson RN, Koelle K. Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution (2017) Virus Evol., 3:vex034 (Available here)
  • Kraemer MUG, Faria NR, Reiner Jr. RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study (2017) Lancet Inf. Dis., 17:330-338 (Available here)
  • Thompson RN, Gilligan CA, Cunniffe NJ. Detecting presymptomatic infection is necessary to forecast major epidemics in the earliest stages of infectious disease outbreaks (2016) PLoS Comp. Biol., 12:e1004836 (Available here)
  • Thompson RN, Cobb RC, Gilligan CA, Cunniffe NJ. Management of invading pathogens should be informed by epidemiology rather than administrative boundaries (2016) Ecol. Model., 324:28-32 (Available here)
  • Thompson RN, Yates CA, Baker RE. Modelling cell migration and adhesion during development (2012) Bull. Math. Biol., 74:2793-2809 (Available here)
  • Tappin SJ, Howard TA, Hampson MM, Thompson RN, Burns CE. On the autonomous detection of coronal mass ejections in heliospheric imager data (2012) J. Geophys. Res., 117:A05103 (Available here)