Estimating contact-adjusted immunity levels against measles in South Korea and prospects for maintaining elimination status.
    J. Y. Chun, W. B. Park, N. J. Kim, E. H. Choi, S. Funk, M. Oh.
    Vaccine in press.

    Factors associated with measles transmission in the United States during the postelimination era.
    P. A. Gastañaduy, S. Funk, B. A. Lopman, P. A. Rota, M. Gambhir, B. Grenfell, P. Paul.
    JAMA Pediatrics in press.

    Combining serological and contact data to derive target immunity levels for achieving and maintaining measles elimination.
    S. Funk, J. K. Knapp, E. Lebo, S. E. Reef, A. J. Dabbagh, K. Kretsinger, M. Jit, W. J. Edmunds, P. M. Strebel.
    BMC Medicine 17(1).

    The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo.
    S. Funk, S. Takahashi, J. Hellewell, K. Gadroen, I. Carrion-Martin, M. van Lenthe, K. Rivette, S. Dietrich, W. J. Edmunds, M. R. Siddiqui, V. B. Rao.
    medRxiv https://doi.org/10.1101/19003434.

    Outbreak analytics: a developing data science for informing the response to emerging pathogens.
    J. A. Polonsky, A. Baidjoe, Z. N. Kamvar, A. Cori, K. Durski, W. J. Edmunds, R. M. Eggo, S. Funk, L. Kaiser, P. Keating, O. le Polain de Waroux, M. Marks, P. Moraga, O. Morgan, P. Nouvellet, R. Ratnayake, C. H. Roberts, J. Whitworth, T. Jombart.
    Philosophical Transactions of the Royal Society B 374(1776):20180276.

    Bias correction methods for test-negative designs in the presence of misclassification.
    A. Endo, S. Funk, A. J. Kucharski.
    medRxiv https://doi.org/10.1101/19002691.

    The measles crisis in Europe — the need for a joined-up approach.
    A. Robert, S. Funk, A. J. Kucharski.
    The Lancet 393(10185):2033.

    Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh.
    F. Finger, S. Funk, K. White, M. R. Siddiqui, W. J. Edmunds, A. J. Kucharski.
    BMC Medicine 17(1):58.

    Assessing the performance of real-time epidemic forecasts.
    S. Funk, A. Camacho, A. J. Kucharski, R. Lowe, R. M. Eggo, W. J. Edmunds.
    PLoS Comput Biol 15(2):e1006785.

    Fine-scale family structure shapes influenza transmission risk in households: insights from a study of primary school students in Matsumoto city, 2014/15.
    A. Endo, M. Uchida, A. J. Kucharski, S. Funk.
    bioRxiv https://doi.org/10.1101/527507.

    Reconstruction and prediction of viral disease epidemics.
    M. U. G. Kraemer, D. A. T. Cummings, S. Funk, R. C. Reiner, N. R. Faria, O. G. Pybus, S. Cauchemez.
    Epidemiology and Infection 147:e34.


    Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis.
    K. M. O’Reilly, R. Lowe, W. J. Edmunds, P. Mayaud, A. Kucharski, R. M. Eggo, S. Funk, D. Bhatia, K. Khan, M. U. G. Kraemer, A. Wilder-Smith, L. C. Rodrigues, P. Brasil, E. Massad, T. Jaenisch, S. Cauchemez, O. J. Brady, L. Yakob.
    BMC Medicine 16(1).

    Impact of public health responses during a measles outbreak in an Amish community in Ohio: modelling the dynamics of transmission.
    P. Gastañaduy, S. Funk, P. Paul, L. Tatham, N. Fisher, J. Budd, B. Fowler, S. de Fijter, M. DiOrio, G. S. Wallace, B. Grenfell.
    Am J Epidemiol 187(9):2002–2010.

    Genomic and epidemiological monitoring of yellow fever virus transmission potential.
    N. R. Faria, M. U. G. Kraemer, S. C. Hill, J. G. de Jesus, R. S. Aguiar, F. C. M. Iani, J. Xavier, J. Quick, L. du Plessis, S. Dellicour, J. Thézé, R. D. O. Carvalho, G. Baele, C. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. Obolski, L. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R. W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca, T. E. R. Adelino, M. A. A. Oliveira, M. V. F. Silva, L. Sacchetto, P. O. Figueiredo, I. M. Rezende, E. M. Mello, R. F. C. Said, D. A. Santos, M. L. Ferraz, M. G. Brito, L. F. Santana, M. T. Menezes, R. M. Brindeiro, A. Tanuri, F. C. P. dos Santos, M. S. Cunha, J. S. Nogueira, I. M. Rocco, A. C. da Costa, S. C. V. Komninakis, V. Azevedo, A. O. Chieppe, E. S. M. Araujo, M. C. L. Mendonça, C. C. dos Santos, C. D. dos Santos, A. M. Mares-Guia, R. M. R. Nogueira, P. C. Sequeira, R. G. Abreu, M. H. O. Garcia, A. L. Abreu, O. Okumoto, E. G. Kroon, C. F. C. de Albuquerque, K. Lewandowski, S. T. Pullan, M. Carroll, T. de Oliveira, E. C. Sabino, R. P. Souza, M. A. Suchard, P. Lemey, G. S. Trindade, B. P. Drumond, A. M. B. Filippis, N. J. Loman, S. Cauchemez, L. C. J. Alcantara, O. G. Pybus.
    Science doi:10.1126/science.aat7115:eaat7115.

    “Pathogen eradication” and “Emerging pathogens”: Difficult definitions in cystic fibrosis.
    P. H. Gilligan, D. G. Downey, J. S. Elborn, P. A. Flume, S. Funk, D. Gilpin, T. J. Kidd, J. McCaughan, B. C. Millar, P. G. Murphy, J. C. Rendall, J. C. Tunney, J. E. Moore.
    J Clin Microbiol 56(9):e00193–18.

    Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji.
    A. J. Kucharski, M. Kama, C. H. Watson, M. Aubry, S. Funk, A. D. Henderson, O. J. Brady, J. Vanhomwegen, J. Manuguerra, C. L. Lau, W. J. Edmunds, J. Aaskov, E. J. Nilles, V. Cao-Lormeau, S. Hué, M. L. Hibberd.
    eLife 7:e34848.

    The relative fitness of drug-resistant Mycobacterium tuberculosis : a modelling study of household transmission in Peru.
    G. M. Knight, M. Zimic, S. Funk, R. H. Gilman, J. S. Friedland, L. Grandjean.
    Journal of The Royal Society Interface 15(143):20180025.

    The impact of passive case detection on the transmission dynamics of gambiense Human African Trypanosomiasis.
    F. Checchi*, S. Funk*, D. Chandramohan, F. Chappuis, D. T. Haydon.
    PLoS Negl Trop Dis 12(4):e0006276.
    *: equal contribution

    The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt.
    C. Viboud, K. Sun, R. Gaffey, M. Ajelli, L. Fumanelli, S. Merler, Q. Zhang, G. Chowell, L. Simonsen, A. Vespignani, the RAPIDD Ebola Forecasting Challenge group.
    Epidemics 22:13–21.

    Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model.
    S. Funk, A. Camacho, A. J. Kucharski, R. M. Eggo, W. J. Edmunds.
    Epidemics 22:56–61.


    High Zika Virus Seroprevalence in Salvador, Northeastern Brazil Limits the Potential for Further Outbreaks.
    E. M. Netto, A. Moreira-Soto, C. Pedroso, C. Höser, S. Funk, A. J. Kucharski, A. Rockstroh, B. M. Kümmerer, G. S. Sampaio, E. Luz, S. N. Vaz, J. P. Dias, F. A. Bastos, R. Cabral, T. Kistemann, S. Ulbert, X. de Lamballerie, T. Jaenisch, O. J. Brady, C. Drosten, M. Sarno, C. Brites, J. F. Drexler.
    mBio 8(6):e01390–17.

    A mechanistic spatio-temporal framework for modelling individual-to-individual transmission — with an application to the 2014-2015 West Africa Ebola outbreak.
    M. S. Y. Lau, G. J. Gibson, H. Adrakey, A. McClelland, S. Riley, J. Zelner, G. Streftaris, S. Funk, J. Metcalf, B. D. Dalziel, B. T. Grenfell.
    PLoS Comput Biol 13(10):1-18.

    The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia.
    S. Funk, I. Ciglenecki, A. Tiffany, E. Gignoux, A. Camacho, R. M. Eggo, A. J. Kucharski, W. J. Edmunds, J. Bolongei, P. Azuma, P. Clement, T. S. Alpha, E. Sterk, B. Telfer, G. Engel, L. A. Parker, M. Suzuki, N. Heijenberg, B. Reeder.
    Philos T R Soc B 372(1721).

    Disease severity determines health-seeking behaviour amongst individuals with influenza-like illness in an internet-based cohort.
    M. Peppa, W. J. Edmunds, S. Funk.
    BMC Infect Dis 17:238.

    Spatial and temporal dynamics of superspreading events in the 2014–2015 West Africa Ebola epidemic.
    M. S. Y. Lau, B. D. Dalziel, S. Funk, A. McClelland, A. Tiffany, S. Riley, C. J. E. Metcalf, B. T. Grenfell.
    Proc Natl Acad Sci U S A 114(9):2337–2342.

    Mathematical Modeling of Programmatic Requirements for Yaws Eradication.
    M. Marks, O. Mitjà, C. Fitzpatrick, K. Asiedu, A. W. Solomon, D. C. Mabey, S. Funk.
    Emerg Infect Dis 23(1):22.

    Aedes aegypti Control Through Modernized, Integrated Vector Management.
    L. Yakob, S. Funk, A. Camacho, O. Brady, W. J. Edmunds.
    PLoS Curr 2017 Jan 30. Edition 1.

    Real-time dynamic modelling for the design of a cluster-randomized phase 3 Ebola vaccine trial in Sierra Leone.
    A. Camacho, R. Eggo, N. Goeyvaerts, A. Vandebosch, R. Mogg, S. Funk, A. Kucharski, C. Watson, T. Vangeneugden, W. Edmunds.
    Vaccine 35(4):544–551.


    Comparative Analysis of Dengue and Zika Outbreaks Reveals Differences by Setting and Virus.
    S. Funk, A. J. Kucharski, A. Camacho, R. M. Eggo, L. Yakob, L. M. Murray, W. J. Edmunds.
    PLoS Negl Trop Dis 10(12):1-16.

    Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013-14 French Polynesia Outbreak.
    A. J. Kucharski, S. Funk, R. M. Eggo, H. Mallet, W. J. Edmunds, E. J. Nilles.
    PLoS Negl Trop Dis 10(5):e0004726.

    Effectiveness of Ring Vaccination as Control Strategy for Ebola Virus Disease.
    A. J. Kucharski, R. M. Eggo, C. H. Watson, A. Camacho, S. Funk, W. J. Edmunds.
    Emerg Infect Dis 22(1):105–108.


    Estimating the probability of demonstrating vaccine efficacy in the declining Ebola epidemic: a Bayesian modelling approach.
    A. Camacho, R. M. Eggo, S. Funk, C. H. Watson, A. J. Kucharski, W. J. Edmunds.
    BMJ Open 5(12):e009346.

    Duration of Ebola virus RNA persistence in semen of survivors: population-level estimates and projections.
    R. M. Eggo, C. H. Watson, A. Camacho, A. J. Kucharski, S. Funk, W. J. Edmunds.
    Euro Surveill 20(48):30083.

    Measuring the impact of Ebola control measures in Sierra Leone.
    A. J. Kucharski, A. Camacho, S. Flasche, R. E. Glover, W. J. Edmunds, S. Funk.
    Proc Natl Acad Sci U S A 112(46):14366–14371.

    Updated estimate of the duration of the meningo-encephalitic stage in gambiense human African trypanosomiasis.
    F. Checchi, S. Funk, D. Chandramohan, D. T. Haydon, F. Chappuis.
    BMC Res Notes 8:292.

    Seven challenges in modeling vaccine preventable diseases.
    C. J. E. Metcalf, V. Andreasen, O. N. Bjørnstad, K. Eames, W. J. Edmunds, S. Funk, T. D. Hollingsworth, J. Lessler, C. Viboud, B. T. Grenfell.
    Epidemics 10:11–15.

    Nine challenges in incorporating the dynamics of behaviour in infectious diseases models.
    S. Funk, S. Bansal, C. T. Bauch, K. T. D. Eames, W. J. Edmunds, A. P. Galvani, P. Klepac.
    Epidemics 10:21–25.

    Modeling infectious disease dynamics in the complex landscape of global health.
    H. Heesterbeek, R. M. Anderson, V. Andreasen, S. Bansal, D. De Angelis, C. Dye, K. T. D. Eames, W. J. Edmunds, S. D. W. Frost, S. Funk, T. D. Hollingsworth, T. House, V. Isham, P. Klepac, J. Lessler, J. O. Lloyd-Smith, C. J. E. Metcalf, D. Mollison, L. Pellis, J. R. C. Pulliam, M. G. Roberts, C. Viboud, I. N. I. I. D. D. Collaboration.
    Science 347(6227):aaa4339.

    Seven challenges for modelling indirect transmission: vector-borne diseases, macroparasites and neglected tropical diseases.
    T. D. Hollingsworth, J. R. C. Pulliam, S. Funk, J. E. Truscott, V. Isham, A. L. Lloyd.
    Epidemics 10:16–20.

    Six challenges in the eradication of infectious diseases.
    P. Klepac, S. Funk, T. D. Hollingsworth, C. J. E. Metcalf, K. Hampson.
    Epidemics 10:97–101.

    Evaluation of the benefits and risks of introducing Ebola community care centers, Sierra Leone.
    A. J. Kucharski, A. Camacho, F. Checchi, R. Waldman, R. F. Grais, J. Cabrol, S. Briand, M. Baguelin, S. Flasche, S. Funk, W. J. Edmunds.
    Emerg Infect Dis 21(3):393–399.

    Nine challenges in modelling the emergence of novel pathogens.
    J. O. Lloyd-Smith, S. Funk, A. R. McLean, S. Riley, J. L. N. Wood.
    Epidemics 10:35–39.

    Five challenges in evolution and infectious diseases.
    C. J. E. Metcalf, R. B. Birger, S. Funk, R. D. Kouyos, J. O. Lloyd-Smith, V. A. A. Jansen.
    Epidemics 10:40–44.

    Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study.
    A. Camacho, A. Kucharski, Y. Aki-Sawyerr, M. A. White, S. Flasche, M. Baguelin, T. Pollington, J. R. Carney, R. Glover, E. Smout, A. Tiffany, W. J. Edmunds, S. Funk.
    PLoS Curr 2015 Feb 10. Edition 1.

    Ebola virus disease in the Democratic Republic of the Congo, 1976-2014.
    A. Rosello, M. Mossoko, S. Flasche, A. J. Van Hoek, P. Mbala, A. Camacho, S. Funk, A. Kucharski, B. K. Ilunga, W. J. Edmunds, P. Piot, M. Baguelin, J. M. Tamfum.
    eLife 4:e09015.


    Potential for large outbreaks of Ebola virus disease.
    A. Camacho, A. J. Kucharski, S. Funk, J. Breman, P. Piot, W. J. Edmunds.
    Epidemics 9e:70–78.

    Association between recruitment methods and attrition in Internet-based studies.
    P. Bajardi, D. Paolotti, A. Vespignani, K. Eames, S. Funk, W. J. Edmunds, C. Turbelin, M. Debin, V. Colizza, R. Smallenburg, C. Koppeschaar, A. O. Franco, V. Faustino, A. Carnahan, M. Rehn, F. Merletti, J. Douwes, R. Firestone, L. Richiardi.
    PLoS One 9(12):e114925.

    Ebola: the power of behaviour change.
    S. Funk, G. M. Knight, V. A. A. Jansen.
    Nature 515(7528):492.

    Detecting differential transmissibilities that affect the size of self-limited outbreaks.
    S. Blumberg, S. Funk, J. R. C. Pulliam.
    PLoS Pathog 10(10):e1004452.

    Mapping Ebola in wild animals for better disease control.
    S. Funk, P. Piot.
    eLife 3:e04565.

    Incidence and risk factors for influenza-like-illness in the UK: online surveillance using Flusurvey.
    A. J. Adler, K. T. D. Eames, S. Funk, W. J. Edmunds.
    BMC Infect Dis 14:232.

    Determinants of follow-up participation in the Internet-based European influenza surveillance platform Influenzanet.
    P. Bajardi, A. Vespignani, S. Funk, K. T. Eames, W. J. Edmunds, C. Turbelin, M. Debin, V. Colizza, R. Smallenburg, C. E. Koppeschaar, A. O. Franco, V. Faustino, A. Carnahan, M. Rehn, D. Paolotti.
    J Med Internet Res 16(3):e78.


    Estimation of the quality of life effect of seasonal influenza infection in the UK with the internet-based Flusurvey cohort: an observational cohort study.
    A. Camacho, K. Eames, A. Adler, S. Funk, J. Edmunds.
    Lancet 382:S8.

    Quantifying trends in disease impact to produce a consistent and reproducible definition of an emerging infectious disease.
    S. Funk, T. L. Bogich, K. E. Jones, A. M. Kilpatrick, P. Daszak.
    PLoS One 8(8):e69951.

    Using network theory to identify the causes of disease outbreaks of unknown origin.
    T. L. Bogich*, S. Funk*, T. R. Malcolm, N. Chhun, J. H. Epstein, A. A. Chmura, A. M. Kilpatrick, J. S. Brownstein, O. C. Hutchison, C. Doyle-Capitman, R. Deaville, S. S. Morse, A. A. Cunningham, P. Daszak.
    J R Soc Interface 10(81):20120904.
    [PDF] [Corrected Fig. 2]
    *: equal contribution

    Word usage mirrors community structure in the online social network Twitter.
    J. Bryden, S. Funk, V. A. Jansen.
    EPJ Data Sci. 2(1).

    Identifying transmission cycles at the human-animal interface: the role of animal reservoirs in maintaining gambiense human african trypanosomiasis.
    S. Funk, H. Nishiura, H. Heesterbeek, W. J. Edmunds, F. Checchi.
    PLoS Comput Biol 9(1):e1002855.


    The Talk of the Town: Modelling the Spread of Information and Changes in Behaviour.
    S. Funk, V. A. A. Jansen.
    In: P. Manfredi, A. d’Onofrio: Modeling the Interplay Between Human Behavior and the Spread of Infectious Diseases, Springer, Berlin / Heidelberg, pp. 93–102.

    Using the internet to estimate influenza vaccine effectiveness.
    W. J. Edmunds, S. Funk.
    Expert Rev Vaccines 11(9):1027–1029.

    Using mathematical models in a unified approach to predict the next emerging infectious disease.
    T. L. Bogich, K. J. Olival, P. R. Hosseini, C. Zambrana-Torrelio, E. Loh, S. Funk, I. L. Brito, J. H. Epstein, J. S. Brownstein, D. O. Joly, M. A. Levy, K. E. Jones, S. S. Morse, A. A. Aguirre, W. B. Karesh, J. A. Mazet, P. Daszak.
    In: A. Aguirre, R. Ostfeld, P. Daszak: New Directions in Conservation Medicine, Oxford University Press, Oxford, pp. 607–617.


    Stability in flux: community structure in dynamic networks.
    J. Bryden*, S. Funk*, N. Geard*, S. Bullock, V. A. A. Jansen.
    J R Soc Interface 8(60):1031–1040.
    *: equal contribution


    Modelling the influence of human behaviour on the spread of infectious diseases: a review.
    S. Funk, M. Salathé, V. A. A. Jansen.
    J R Soc Interface 7(50):1247–1256.

    Interacting epidemics on overlay networks.
    S. Funk, V. A. A. Jansen.
    Phys Rev E Stat Nonlin Soft Matter Phys 81(3 Pt 2):036118.

    Endemic disease, awareness, and local behavioural response.
    S. Funk, E. Gilad, V. A. A. Jansen.
    J Theor Biol 264(2):501–509.


    The spread of awareness and its impact on epidemic outbreaks.
    S. Funk, E. Gilad, C. Watkins, V. A. A. Jansen.
    Proc Natl Acad Sci U S A 106(16):6872–6877.
    [PDF] [Corrected Fig. 2] [Simulation movies]