Bosse, N I; (2024) Navigating Uncertainty - Evaluating Human and Model-Based Forecasting of COVID-19. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04673558

Sherratt, Katharine; Carnegie, Anna C; Kucharski, Adam; Cori, Anne; Pearson, Carl AB; Jarvis, Christopher I; Overton, Christopher; Weston, Dale; Hill, Edward M; Knock, Edward; +17 more... Fearon, Elizabeth; Nightingale, Emily; Hellewell, Joel; Edmunds, W John; Villabona Arenas, Julián; Prem, Kiesha; Pi, Li; Baguelin, Marc; Kendall, Michelle; Ferguson, Neil; Davies, Nicholas; Eggo, Rosalind M; van Elsland, Sabine; Russell, Timothy; Funk, Sebastian; Liu, Yang; Abbott, Sam; (2024) Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic. Wellcome open research, 9. 12-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.19601.1

Cooper, Ben S; Evans, Stephanie; Jafari, Yalda; Pham, Thi Mui; Mo, Yin; Lim, Cherry; Pritchard, Mark G; Pople, Diane; Hall, Victoria; Stimson, James; +8 more... Eyre, David W; Read, Jonathan M; Donnelly, Christl A; Horby, Peter; Watson, Conall; Funk, Sebastian; Robotham, Julie V; Knight, Gwenan M; (2023) The burden and dynamics of hospital-acquired SARS-CoV-2 in England. Nature, 623 (7985). pp. 132-138. ISSN 0028-0836 DOI: https://doi.org/10.1038/s41586-023-06634-z

Murayama, Hiroaki; Pearson, Carl AB; Abbott, Sam; Miura, Fuminari; Jung, Sung-Mok; Fearon, Elizabeth; Funk, Sebastian; Endo, Akira; (2023) Accumulation of Immunity in Heavy-Tailed Sexual Contact Networks Shapes Mpox Outbreak Sizes. The Journal of infectious diseases, 229 (1). pp. 59-63. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiad254

Park, Sang Woo; Sun, Kaiyuan; Abbott, Sam; Sender, Ron; Bar-On, Yinon M; Weitz, Joshua S; Funk, Sebastian; Grenfell, Bryan T; Backer, Jantien A; Wallinga, Jacco; +2 more... Viboud, Cecile; Dushoff, Jonathan; (2023) Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America, 120 (22). e2221887120-. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.2221887120

Abbott, Sam; Sherratt, Katharine; Gerstung, Moritz; Funk, Sebastian; (2022) Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England. DOI: https://doi.org/10.1101/2022.01.08.22268920

Bosse, Nikos I; Abbott, Sam; Bracher, Johannes; Hain, Habakuk; Quilty, Billy J; Jit, Mark; Centre for the Mathematical Modelling of Infectious Diseases COV; van Leeuwen, Edwin; Cori, Anne; Funk, Sebastian; (2022) Comparing human and model-based forecasts of COVID-19 in Germany and Poland. PLoS computational biology, 18 (9). e1010405-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1010405

Cramer, Estee Y; Ray, Evan L; Lopez, Velma K; Bracher, Johannes; Brennen, Andrea; Castro Rivadeneira, Alvaro J; Gerding, Aaron; Gneiting, Tilmann; House, Katie H; Huang, Yuxin; +285 more... Jayawardena, Dasuni; Kanji, Abdul H; Khandelwal, Ayush; Le, Khoa; Mühlemann, Anja; Niemi, Jarad; Shah, Apurv; Stark, Ariane; Wang, Yijin; Wattanachit, Nutcha; Zorn, Martha W; Gu, Youyang; Jain, Sansiddh; Bannur, Nayana; Deva, Ayush; Kulkarni, Mihir; Merugu, Srujana; Raval, Alpan; Shingi, Siddhant; Tiwari, Avtansh; White, Jerome; Abernethy, Neil F; Woody, Spencer; Dahan, Maytal; Fox, Spencer; Gaither, Kelly; Lachmann, Michael; Meyers, Lauren Ancel; Scott, James G; Tec, Mauricio; Srivastava, Ajitesh; George, Glover E; Cegan, Jeffrey C; Dettwiller, Ian D; England, William P; Farthing, Matthew W; Hunter, Robert H; Lafferty, Brandon; Linkov, Igor; Mayo, Michael L; Parno, Matthew D; Rowland, Michael A; Trump, Benjamin D; Zhang-James, Yanli; Chen, Samuel; Faraone, Stephen V; Hess, Jonathan; Morley, Christopher P; Salekin, Asif; Wang, Dongliang; Corsetti, Sabrina M; Baer, Thomas M; Eisenberg, Marisa C; Falb, Karl; Huang, Yitao; Martin, Emily T; McCauley, Ella; Myers, Robert L; Schwarz, Tom; Sheldon, Daniel; Gibson, Graham Casey; Yu, Rose; Gao, Liyao; Ma, Yian; Wu, Dongxia; Yan, Xifeng; Jin, Xiaoyong; Wang, Yu-Xiang; Chen, YangQuan; Guo, Lihong; Zhao, Yanting; Gu, Quanquan; Chen, Jinghui; Wang, Lingxiao; Xu, Pan; Zhang, Weitong; Zou, Difan; Biegel, Hannah; Lega, Joceline; McConnell, Steve; Nagraj, VP; Guertin, Stephanie L; Hulme-Lowe, Christopher; Turner, Stephen D; Shi, Yunfeng; Ban, Xuegang; Walraven, Robert; Hong, Qi-Jun; Kong, Stanley; van de Walle, Axel; Turtle, James A; Ben-Nun, Michal; Riley, Steven; Riley, Pete; Koyluoglu, Ugur; DesRoches, David; Forli, Pedro; Hamory, Bruce; Kyriakides, Christina; Leis, Helen; Milliken, John; Moloney, Michael; Morgan, James; Nirgudkar, Ninad; Ozcan, Gokce; Piwonka, Noah; Ravi, Matt; Schrader, Chris; Shakhnovich, Elizabeth; Siegel, Daniel; Spatz, Ryan; Stiefeling, Chris; Wilkinson, Barrie; Wong, Alexander; Cavany, Sean; España, Guido; Moore, Sean; Oidtman, Rachel; Perkins, Alex; Kraus, David; Kraus, Andrea; Gao, Zhifeng; Bian, Jiang; Cao, Wei; Lavista Ferres, Juan; Li, Chaozhuo; Liu, Tie-Yan; Xie, Xing; Zhang, Shun; Zheng, Shun; Vespignani, Alessandro; Chinazzi, Matteo; Davis, Jessica T; Mu, Kunpeng; Pastore Y Piontti, Ana; Xiong, Xinyue; Zheng, Andrew; Baek, Jackie; Farias, Vivek; Georgescu, Andreea; Levi, Retsef; Sinha, Deeksha; Wilde, Joshua; Perakis, Georgia; Bennouna, Mohammed Amine; Nze-Ndong, David; Singhvi, Divya; Spantidakis, Ioannis; Thayaparan, Leann; Tsiourvas, Asterios; Sarker, Arnab; Jadbabaie, Ali; Shah, Devavrat; Della Penna, Nicolas; Celi, Leo A; Sundar, Saketh; Wolfinger, Russ; Osthus, Dave; Castro, Lauren; Fairchild, Geoffrey; Michaud, Isaac; Karlen, Dean; Kinsey, Matt; Mullany, Luke C; Rainwater-Lovett, Kaitlin; Shin, Lauren; Tallaksen, Katharine; Wilson, Shelby; Lee, Elizabeth C; Dent, Juan; Grantz, Kyra H; Hill, Alison L; Kaminsky, Joshua; Kaminsky, Kathryn; Keegan, Lindsay T; Lauer, Stephen A; Lemaitre, Joseph C; Lessler, Justin; Meredith, Hannah R; Perez-Saez, Javier; Shah, Sam; Smith, Claire P; Truelove, Shaun A; Wills, Josh; Marshall, Maximilian; Gardner, Lauren; Nixon, Kristen; Burant, John C; Wang, Lily; Gao, Lei; Gu, Zhiling; Kim, Myungjin; Li, Xinyi; Wang, Guannan; Wang, Yueying; Yu, Shan; Reiner, Robert C; Barber, Ryan; Gakidou, Emmanuela; Hay, Simon I; Lim, Steve; Murray, Chris; Pigott, David; Gurung, Heidi L; Baccam, Prasith; Stage, Steven A; Suchoski, Bradley T; Prakash, B Aditya; Adhikari, Bijaya; Cui, Jiaming; Rodríguez, Alexander; Tabassum, Anika; Xie, Jiajia; Keskinocak, Pinar; Asplund, John; Baxter, Arden; Oruc, Buse Eylul; Serban, Nicoleta; Arik, Sercan O; Dusenberry, Mike; Epshteyn, Arkady; Kanal, Elli; Le, Long T; Li, Chun-Liang; Pfister, Tomas; Sava, Dario; Sinha, Rajarishi; Tsai, Thomas; Yoder, Nate; Yoon, Jinsung; Zhang, Leyou; Abbott, Sam; Bosse, Nikos I; Funk, Sebastian; Hellewell, Joel; Meakin, Sophie R; Sherratt, Katharine; Zhou, Mingyuan; Kalantari, Rahi; Yamana, Teresa K; Pei, Sen; Shaman, Jeffrey; Li, Michael L; Bertsimas, Dimitris; Skali Lami, Omar; Soni, Saksham; Tazi Bouardi, Hamza; Ayer, Turgay; Adee, Madeline; Chhatwal, Jagpreet; Dalgic, Ozden O; Ladd, Mary A; Linas, Benjamin P; Mueller, Peter; Xiao, Jade; Wang, Yuanjia; Wang, Qinxia; Xie, Shanghong; Zeng, Donglin; Green, Alden; Bien, Jacob; Brooks, Logan; Hu, Addison J; Jahja, Maria; McDonald, Daniel; Narasimhan, Balasubramanian; Politsch, Collin; Rajanala, Samyak; Rumack, Aaron; Simon, Noah; Tibshirani, Ryan J; Tibshirani, Rob; Ventura, Valerie; Wasserman, Larry; O'Dea, Eamon B; Drake, John M; Pagano, Robert; Tran, Quoc T; Ho, Lam Si Tung; Huynh, Huong; Walker, Jo W; Slayton, Rachel B; Johansson, Michael A; Biggerstaff, Matthew; Reich, Nicholas G; (2022) Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States. Proceedings of the National Academy of Sciences, 119 (15). e2113561119-. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.2113561119

Endo 遠藤彰, Akira; CMMID COVID-19 Working Group; Uchida 内田満夫, Mitsuo; Liu 刘扬, Yang; Atkins, Katherine E; Kucharski, Adam J; Funk, Sebastian; (2022) Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. Proceedings of the National Academy of Sciences of the United States of America, 119 (37). e2203019119-. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.2203019119

Endo, Akira; Murayama, Hiroaki; Abbott, Sam; Ratnayake, Ruwan; Pearson, Carl AB; Edmunds, W John; Fearon, Elizabeth; Funk, Sebastian; (2022) Heavy-tailed sexual contact networks and monkeypox epidemiology in the global outbreak, 2022. Science (New York, N.Y.), 378 (6615). pp. 90-94. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.add4507

Funk, Sebastian; Abbott, Sam; Bracher, Johannes; (2022) Sebastian Funk, Sam Abbott and Johannes Bracher’s Discussion Contribution to the Papers in Session 2 of The Royal Statistical Society’s Special Topic Meeting on Covid-19 Transmission: 11 June 2021. Journal of the Royal Statistical Society Series A: Statistics in Society, 185 (Supple). S103-S104. ISSN 0964-1998 DOI: https://doi.org/10.1111/rssa.12974

Gimma, Amy; Munday, James D; Wong, Kerry LM; Coletti, Pietro; van Zandvoort, Kevin; Prem, Kiesha; CMMID COVID-19 working group; Klepac, Petra; Rubin, G James; Funk, Sebastian; +2 more... Edmunds, W John; Jarvis, Christopher I; (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 DOI: https://doi.org/10.1371/journal.pmed.1003907

Hart, William S; Abbott, Sam; Endo, Akira; Hellewell, Joel; Miller, Elizabeth; Andrews, Nick; Maini, Philip K; Funk, Sebastian; Thompson, Robin N; (2022) Inference of the SARS-CoV-2 generation time using UK household data. eLife, 11. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.70767

Hart, William S; Miller, Elizabeth; Andrews, Nick J; Waight, Pauline; Maini, Philip K; Funk, Sebastian; Thompson, Robin N; (2022) Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis. The Lancet. Infectious diseases, 22 (5). pp. 603-610. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(22)00001-9

Jarvis, Christopher I; Gimma, Amy; Finger, Flavio; Morris, Tim P; Thompson, Jennifer A; le Polain de Waroux, Olivier; Edmunds, W John; Funk, Sebastian; Jombart, Thibaut; (2022) Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics. PLoS Computational Biology, 18 (5). e1008800-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008800

Knight, Gwenan M; Pham, Thi Mui; Stimson, James; Funk, Sebastian; Jafari, Yalda; Pople, Diane; Evans, Stephanie; Yin, Mo; Brown, Colin S; Bhattacharya, Alex; +7 more... Hope, Russell; Semple, Malcolm G; ISARIC4C Investigators; CMMID COVID-19 Working Group; Read, Jonathan M; Cooper, Ben S; Robotham, Julie V; (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 DOI: https://doi.org/10.1186/s12879-022-07490-4

Meakin, Sophie; Abbott, Sam; Bosse, Nikos; Munday, James; Gruson, Hugo; Hellewell, Joel; Sherratt, Katharine; CMMID COVID-19 Working Group; 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-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-022-02271-x

Nyberg, Tommy; Ferguson, Neil M; Nash, Sophie G; Webster, Harriet H; Flaxman, Seth; Andrews, Nick; Hinsley, Wes; Bernal, Jamie Lopez; Kall, Meaghan; Bhatt, Samir; +17 more... Blomquist, Paula; Zaidi, Asad; Volz, Erik; Aziz, Nurin Abdul; Harman, Katie; Funk, Sebastian; Abbott, Sam; COVID-19 Genomics UK (COG-UK) consortium; Hope, Russell; Charlett, Andre; Chand, Meera; Ghani, Azra C; Seaman, Shaun R; Dabrera, Gavin; De Angelis, Daniela; Presanis, Anne M; Thelwall, Simon; (2022) Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. Lancet (London, England), 399 (10332). pp. 1303-1312. ISSN 0140-6736 DOI: https://doi.org/10.1016/S0140-6736(22)00462-7

Park, Sang Woo; Bolker, Benjamin M; Funk, Sebastian; Metcalf, C Jessica E; Weitz, Joshua S; Grenfell, Bryan T; Dushoff, Jonathan; (2022) The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants. Journal of the Royal Society. Interface, 19 (191). 20220173-. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2022.0173

Ray, Evan L; Brooks, Logan C; Bien, Jacob; Biggerstaff, Matthew; Bosse, Nikos I; Bracher, Johannes; Cramer, Estee Y; Funk, Sebastian; Gerding, Aaron; Johansson, Michael A; +5 more... Rumack, Aaron; Wang, Yijin; Zorn, Martha; Tibshirani, Ryan J; Reich, Nicholas G; (2022) Comparing trained and untrained probabilistic ensemble forecasts of COVID-19 cases and deaths in the United States. International Journal of Forecasting, 39 (3). pp. 1366-1383. ISSN 0169-2070 DOI: https://doi.org/10.1016/j.ijforecast.2022.06.005

Robert, Alexis; Kucharski, Adam J; Funk, Sebastian; (2022) The impact of local vaccine coverage and recent incidence on measles transmission in France between 2009 and 2018. BMC Medicine, 20 (1). 77-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-022-02277-5

Biggs, Joseph R; Sy, Ava Kristy; Brady, Oliver J; Kucharski, Adam J; Funk, Sebastian; Tu, Yun-Hung; Reyes, Mary Anne Joy; Quinones, Mary Ann; Jones-Warner, William; Ashall, James; +8 more... Avelino, Ferchito L; Sucaldito, Nemia L; Tandoc, Amado O; Cutiongco-de la Paz, Eva; Capeding, Maria Rosario Z; Padilla, Carmencita D; Hibberd, Martin L; Hafalla, Julius Clemence R; (2021) Serological Evidence of Widespread Zika Transmission across the Philippines. Viruses, 13 (8). p. 1441. DOI: https://doi.org/10.3390/v13081441

Biggs, Joseph R; Sy, Ava Kristy; Sherratt, Katharine; Brady, Oliver J; Kucharski, Adam J; Funk, Sebastian; Reyes, Mary Anne Joy; Quinones, Mary Ann; Jones-Warner, William; Avelino, Ferchito L; +7 more... Sucaldito, Nemia L; Tandoc, Amado O; la Paz, Eva Cutiongco-de; Capeding, Maria Rosario Z; Padilla, Carmencita D; Hafalla, Julius Clemence R; Hibberd, Martin L; (2021) Estimating the annual dengue force of infection from the age of reporting primary infections across urban centres in endemic countries. BMC medicine, 19 (1). 217-. DOI: https://doi.org/10.1186/s12916-021-02101-6

Bracher, J; Wolffram, D; Deuschel, J; Görgen, K; Ketterer, JL; Ullrich, A; Abbott, S; Barbarossa, MV; Bertsimas, D; Bhatia, S; +29 more... Bodych, M; Bosse, NI; Burgard, JP; Castro, L; Fairchild, G; Fuhrmann, J; Funk, S; Gogolewski, K; Gu, Q; Heyder, S; Hotz, T; Kheifetz, Y; Kirsten, H; Krueger, T; Krymova, E; Li, ML; Meinke, JH; Michaud, IJ; Niedzielewski, K; Ożański, T; Rakowski, F; Scholz, M; Soni, S; Srivastava, A; Zieliński, J; Zou, D; Gneiting, T; Schienle, M; List of Contributors by Team; List of Contributors by Team; (2021) A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave. Nature communications, 12 (1). 5173-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-25207-0

Brady, Oliver J; Kucharski, Adam J; Funk, Sebastian; Jafari, Yalda; Loock, Marnix Van; Herrera-Taracena, Guillermo; Menten, Joris; Edmunds, W John; Sim, Shuzhen; Ng, Lee-Ching; +2 more... Hué, Stéphane; Hibberd, Martin L; (2021) Case-area targeted interventions (CATI) for reactive dengue control: Modelling effectiveness of vector control and prophylactic drugs in Singapore. PLoS neglected tropical diseases, 15 (8). e0009562-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0009562

Coughlan de Perez, Erin; Stephens, Elisabeth; van Aalst, Maarten; Bazo, Juan; Fournier-Tombs, Eleonore; Funk, Sebastian; Hess, Jeremy J; Ranger, Nicola; Lowe, Rachel; (2021) Epidemiological versus meteorological forecasts: Best practice for linking models to policymaking. International Journal of Forecasting, 38 (2). pp. 521-526. ISSN 0169-2070 DOI: https://doi.org/10.1016/j.ijforecast.2021.08.003

Davies, Nicholas G; Abbott, Sam; Barnard, Rosanna C; Jarvis, Christopher I; Kucharski, Adam J; Munday, James D; Pearson, Carl AB; Russell, Timothy W; Tully, Damien C; Washburne, Alex D; +15 more... Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D; CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M; Funk, Sebastian; Jit, Mark; Atkins, Katherine E; Edmunds, W John; (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, N.Y.), 372 (6538). 149-+. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abg3055

Docherty, Annemarie B; Mulholland, Rachel H; Lone, Nazir I; Cheyne, Christopher P; De Angelis, Daniela; Diaz-Ordaz, Karla; Donegan, Cara; Drake, Thomas M; Dunning, Jake; Funk, Sebastian; +20 more... García-Fiñana, Marta; Girvan, Michelle; Hardwick, Hayley E; Harrison, Janet; Ho, Antonia; Hughes, David M; Keogh, Ruth H; Kirwan, Peter D; Leeming, Gary; Nguyen Van-Tam, Jonathan S; Pius, Riinu; Russell, Clark D; Spencer, Rebecca G; Tom, Brian Dm; Turtle, Lance; Openshaw, Peter Jm; Baillie, J Kenneth; Harrison, Ewen M; Semple, Malcolm G; ISARIC4C Investigators; ISARIC4C Investigators; (2021) Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK. The Lancet. Respiratory medicine, 9 (7). pp. 773-785. ISSN 2213-2600 DOI: https://doi.org/10.1016/S2213-2600(21)00175-2

Endo, A; (2021) Roles of heterogeneity in infectious disease epidemiology: implications on dynamics, inference and control of influenza and COVID-19. PhD (research paper style) thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04661974

Endo, Akira; Centre for the Mathematical Modelling of Infectious Diseases COV; Leclerc, Quentin J; Knight, Gwenan M; Medley, Graham F; Atkins, Katherine E; Funk, Sebastian; Kucharski, Adam J; (2021) Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome Open Research, 5. 239-. DOI: https://doi.org/10.12688/wellcomeopenres.16344.3

Endo, Akira; Uchida, Mitsuo; Hayashi, Naoki; Liu, Yang; Atkins, Katherine E; Kucharski, Adam J; Funk, Sebastian; (2021) Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. Proc Natl Acad Sci U S A, 118 (46). e2112605118-e2112605118. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.2112605118

Gostic, Katelyn M; McGough, Lauren; Baskerville, Edward B; Abbott, Sam; Joshi, Keya; Tedijanto, Christine; Kahn, Rebecca; Niehus, Rene; Hay, James A; De Salazar, Pablo M; +15 more... Hellewell, Joel; Meakin, Sophie; Munday, James D; Bosse, Nikos I; Sherrat, Katharine; Thompson, Robin N; White, Laura F; Huisman, Jana S; Scire, Jérémie; Bonhoeffer, Sebastian; Stadler, Tanja; Wallinga, Jacco; Funk, Sebastian; Lipsitch, Marc; Cobey, Sarah; (2021) Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Computational Biology, 17 (12). e1009679-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1009679 Item availability may be restricted.

Henderson, Alasdair D; Kama, Mike; Aubry, Maite; Hue, Stephane; Teissier, Anita; Naivalu, Taina; Bechu, Vinaisi D; Kailawadoko, Jimaima; Rabukawaqa, Isireli; Sahukhan, Aalisha; +9 more... Hibberd, Martin L; Nilles, Eric J; Funk, Sebastian; Whitworth, Jimmy; Watson, Conall H; Lau, Colleen L; Edmunds, W John; Cao-Lormeau, Van-Mai; Kucharski, Adam J; (2021) Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji. Nature communications, 12 (1). 1671-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-21788-y

Lovell-Read, Francesca A; Funk, Sebastian; Obolski, Uri; Donnelly, Christl A; Thompson, Robin N; (2021) Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study. Journal of the Royal Society, Interface, 18 (178). 20201014-. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2020.1014

Mburu, CN; Ojal, J; Chebet, R; Akech, D; Karia, B; Tuju, J; Sigilai, A; Abbas, K; Jit, M; Funk, S; +9 more... Smits, G; van Gageldonk, PGM; van der Klis, FRM; Tabu, C; Nokes, DJ; LSHTM CMMID COVID-19 Working Group; Scott, Jag; Flasche, S; Adetifa, Imo; (2021) The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya. BMC medicine, 19 (1). 35-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-021-01906-9

Mburu, CN; Ojal, J; Chebet, R; Akech, D; Karia, B; Tuju, J; Sigilai, A; Abbas, K; Jit, M; Funk, S; +8 more... Smits, G; van Gageldonk, PGM; van der Klis, FRM; Tabu, C; Nokes, DJ; Scott, JAG; Flasche, S; Adetifa, IMO; (2021) The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya. BMC medicine. ISSN 1741-7015 DOI: https://doi.org/10.1101/2020.08.25.20181198

Munday, James D; I Jarvis, Christopher; Gimma, Amy; Wong, Kerry LM; Zandvoort, Kevin van; Funk, Sebastian; 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. BMJ Yale - medRxiv preprint. DOI: https://doi.org/10.1101/2021.03.06.21252964

Munday, James D; Jarvis, Christopher I; Gimma, Amy; Wong, Kerry LM; van Zandvoort, Kevin; CMMID COVID-19 Working Group; Funk, Sebastian; 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 DOI: https://doi.org/10.1186/s12916-021-02107-0

Munday, James D; Sherratt, Katharine; Meakin, Sophie; Endo, Akira; Pearson, Carl AB; Hellewell, Joel; Abbott, Sam; Bosse, Nikos I; CMMID COVID-19 Working Group; Atkins, Katherine E; +4 more... Wallinga, Jacco; Edmunds, W John; van Hoek, Albert Jan; 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-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-22213-0

Palmer, Joseph; Sherratt, Katharine; Martin-Nielsen, Richard; Bevan, Jonnie; Gibbs, Hamish; Group, Cmmid; Funk, Sebastian; Abbott, Sam; (2021) covidregionaldata: Subnational data for COVID-19 epidemiology. Journal of Open Source Software, 6 (63). p. 3290. DOI: https://doi.org/10.21105/joss.03290

Pavelka, Martin; Van-Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; CMMID COVID-19 working group; Inštitút Zdravotných Analýz; Jarčuška, Pavol; Krajčí, Marek; Flasche, Stefan; +1 more... Funk, Sebastian; CMMID COVID-19 working group, In�titút Zdravotných Analýz; (2021) The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. Science (New York, N.Y.), 372 (6542). pp. 635-641. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abf9648

Read, Jonathan M; Green, Chris A; Harrison, Ewen M; Docherty, Annemarie B; Funk, Sebastian; Harrison, Janet; Girvan, Michelle; Hardwick, Hayley E; Turtle, Lance; Dunning, Jake; +5 more... Nguyen-Van-Tam, Jonathan S; Openshaw, Peter Jm; Baillie, J Kenneth; Semple, Malcolm G; ISARIC4C investigators; (2021) Hospital-acquired SARS-CoV-2 infection in the UK's first COVID-19 pandemic wave. Lancet, 398 (10305). pp. 1037-1038. ISSN 0140-6736 DOI: https://doi.org/10.1016/S0140-6736(21)01786-4

Robert, A; (2021) Modelling the Risks of Measles Outbreaks Near Elimination. PhD (research paper style) thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04664163

Robert, Alexis; Funk, Sebastian; Kucharski, Adam J; (2021) <i>o2geosocial</i>: Reconstructing who-infected-whom from routinely collected surveillance data. F1000Research, 10. 31-. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.28073.2

Robert, Alexis; Funk, Sebastian; Kucharski, Adam J; (2021) o2geosocial: Reconstructing who-infected-whom from routinely collected surveillance data. F1000Research, 10. p. 31. DOI: https://doi.org/10.12688/f1000research.28073.1

Robert, Alexis; Funk, Sebastian; Kucharski, Adam J; (2021) o2geosocial: Reconstructing who-infected-whom from routinely collected surveillance data. F1000Research, 10. p. 31. DOI: https://doi.org/10.12688/f1000research.28073.2

Sherratt, Katharine; Abbott, Sam; Meakin, Sophie R; Hellewell, Joel; Munday, James D; Bosse, Nikos; CMMID COVID-19 Working Group; Jit, Mark; Funk, Sebastian; (2021) Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 376 (1829). 20200283-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2020.0283

Sherratt, Katharine; Abbott, Sam; Meakin, Sophie R; Hellewell, Joel; Munday, James D; Bosse, Nikos; Jit, Mark; Funk, Sebastian; (2021) Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of Covid-19 in England. Philosophical transactions of the Royal Society of London Series B, Biological sciences, 376 (1829). ISSN 0962-8436 DOI: https://doi.org/10.1101/2020.10.18.20214585

Vöhringer, Harald S; Sanderson, Theo; Sinnott, Matthew; De Maio, Nicola; Nguyen, Thuy; Goater, Richard; Schwach, Frank; Harrison, Ian; Hellewell, Joel; Ariani, Cristina V; +19 more... Gonçalves, Sonia; Jackson, David K; Johnston, Ian; Jung, Alexander W; Saint, Callum; Sillitoe, John; Suciu, Maria; Goldman, Nick; Panovska-Griffiths, Jasmina; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Genomics UK (COG-UK) Consortium*; Birney, Ewan; Volz, Erik; Funk, Sebastian; Kwiatkowski, Dominic; Chand, Meera; Martincorena, Inigo; Barrett, Jeffrey C; Gerstung, Moritz; (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. NATURE, 600 (7889). pp. 506-511. ISSN 0028-0836 DOI: https://doi.org/10.1038/s41586-021-04069-y

Abbas, Kaja; Procter, Simon R; van Zandvoort, Kevin; Clark, Andrew; Funk, Sebastian; Mengistu, Tewodaj; Hogan, Dan; Dansereau, Emily; Jit, Mark; Flasche, Stefan; +1 more... LSHTM CMMID COVID-19 Working Group; (2020) Routine childhood immunisation during the COVID-19 pandemic in Africa: a benefit-risk analysis of health benefits versus excess risk of SARS-CoV-2 infection. The Lancet Global Health, 8 (10). e1264-e1272. DOI: https://doi.org/10.1016/S2214-109X(20)30308-9

Abbott, Sam; Hellewell, Joel; Munday, James; CMMID nCoV working group; Funk, Sebastian; (2020) The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis. Wellcome open research, 5. 17-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15718.1

Abbott, Sam; Hellewell, Joel; Thompson, Robin N; Sherratt, Katharine; Gibbs, Hamish P; Bosse, Nikos I; Munday, James D; Meakin, Sophie; Doughty, Emma L; Chun, June Young; +11 more... Chan, Yung-Wai Desmond; Finger, Flavio; Campbell, Paul; Endo, Akira; Pearson, Carl AB; Gimma, Amy; Russell, Tim; Flasche, Stefan; Kucharski, Adam J; Eggo, Rosalind M; Funk, Sebastian; (2020) Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Research, 5. p. 112. DOI: https://doi.org/10.12688/wellcomeopenres.16006.1

Abbott, Sam; Hellewell, Joel; Thompson, Robin N; Sherratt, Katharine; Gibbs, Hamish P; Bosse, Nikos I; Munday, James D; Meakin, Sophie; Doughty, Emma L; Chun, June Young; +11 more... Chan, Yung-Wai Desmond; Finger, Flavio; Campbell, Paul; Endo, Akira; Pearson, Carl AB; Gimma, Amy; Russell, Tim; Flasche, Stefan; Kucharski, Adam J; Eggo, Rosalind M; Funk, Sebastian; (2020) Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Research, 5. p. 112. DOI: https://doi.org/10.12688/wellcomeopenres.16006.2

Biggs, Joseph R; Sy, Ava Kristy; Brady, Oliver J; Kucharski, Adam J; Funk, Sebastian; Reyes, Mary Anne Joy; Quinones, Mary Ann; Jones-Warner, William; Tu, Yun-Hung; Avelino, Ferchito L; +15 more... Sucaldito, Nemia L; Mai, Huynh Kim; Lien, Le Thuy; Do Thai, Hung; Nguyen, Hien Anh Thi; Anh, Dang Duc; Iwasaki, Chihiro; Kitamura, Noriko; Yoshida, Lay-Myint; Tandoc, Amado O; la Paz, Eva Cutiongco-de; Capeding, Maria Rosario Z; Padilla, Carmencita D; Hafalla, Julius Clemence R; Hibberd, Martin L; (2020) A serological framework to investigate acute primary and post-primary dengue cases reporting across the Philippines. BMC medicine, 18 (1). 364-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-020-01833-1

Davies, Nicholas G; Abbott, Sam; Barnard, Rosanna C; Jarvis, Christopher I; Kucharski, Adam J; Munday, James D; Pearson, Carl AB; Russell, Timothy W; Tully, Damien C; Washburne, Alex D; +13 more... Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M; Funk, Sebastian; Jit, Mark; Atkins, Katherine E; Edmunds, W John; (2020) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. MedRxiv. DOI: https://doi.org/10.1101/2020.12.24.20248822 Item availability may be restricted.

Eggo, Rosalind M; Hellewell, Joel; Funk, Sebastian; (2020) Feasibility of controlling COVID-19 - Authors' reply. The Lancet. Global health, 8 (6). e775-. ISSN 2214-109X DOI: https://doi.org/10.1016/S2214-109X(20)30128-5

Emery, Jon C; Russell, Timothy W; Liu, Yang; Hellewell, Joel; Pearson, Carl Ab; CMMID COVID-19 Working Group; Knight, Gwenan M; Eggo, Rosalind M; Kucharski, Adam J; Funk, Sebastian; +2 more... Flasche, Stefan; Houben, Rein Mgj; (2020) The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship. eLife, 9. e58699-. DOI: https://doi.org/10.7554/eLife.58699

Endo, A; Funk, S; Kucharski, AJ; (2020) Bias correction methods for test-negative designs in the presence of misclassification. EPIDEMIOLOGY AND INFECTION, 148. e216-. ISSN 0950-2688 DOI: https://doi.org/10.1017/S0950268820002058

Endo, Akira; Centre for the Mathematical Modelling of Infectious Diseases COV; Abbott, Sam; Kucharski, Adam J; Funk, Sebastian; (2020) Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Research, 5. 67-. DOI: https://doi.org/10.12688/wellcomeopenres.15842.3

Endo, Akira; Centre for the Mathematical Modelling of Infectious Diseases COV; Leclerc, Quentin J; Knight, Gwenan M; Medley, Graham F; Atkins, Katherine E; Funk, Sebastian; Kucharski, Adam J; (2020) Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome open research, 5. 239-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.16344.1

Endo, Akira; Centre for the Mathematical Modelling of Infectious Diseases COV; Leclerc, Quentin J; Knight, Gwenan M; Medley, Graham F; Atkins, Katherine E; Funk, Sebastian; Kucharski, Adam J; (2020) Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome Open Res, 5. 239-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.16344.2

Funk, S; Abbott, S; Atkins, BD; Baguelin, M; Baillie, JK; Birrell, P; Blake, J; Bosse, NI; Burton, J; Carruthers, J; +37 more... Davies, NG; De Angelis, D; Dyson, L; Edmunds, WJ; Eggo, RM; Ferguson, NM; Gaythorpe, K; Gorsich, E; Guyver-Fletcher, G; Hellewell, J; Hill, EM; Holmes, A; House, TA; Jewell, C; Jit, M; Jombart, T; Joshi, I; Keeling, MJ; Kendall, E; Knock, ES; Kucharski, AJ; Lythgoe, KA; Meakin, SR; Munday, JD; Openshaw, PJM; Overton, CE; Pagani, F; Pearson, J; Perez-Guzman, PN; Pellis, L; Scarabel, F; Semple, MG; Sherratt, K; Tang, M; Tildesley, MJ; Van Leeuwen, E; Whittles, LK; (2020) Short-term forecasts to inform the response to the Covid-19 epidemic in the UK. medRxiv preprint - BMJ Yale. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.11.11.20220962

Gostic, Katelyn M; McGough, Lauren; Baskerville, Edward B; Abbott, Sam; Joshi, Keya; Tedijanto, Christine; Kahn, Rebecca; Niehus, Rene; Hay, James A; De Salazar, Pablo M; +15 more... Hellewell, Joel; Meakin, Sophie; Munday, James D; Bosse, Nikos I; Sherrat, Katharine; Thompson, Robin N; White, Laura F; Huisman, Jana S; Scire, Jérémie; Bonhoeffer, Sebastian; Stadler, Tanja; Wallinga, Jacco; Funk, Sebastian; Lipsitch, Marc; Cobey, Sarah; (2020) Practical considerations for measuring the effective reproductive number, Rt. PLOS COMPUTATIONAL BIOLOGY, 16 (12). e1008409-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008409

Gostic, Katelyn M; McGough, Lauren; Baskerville, Edward B; Abbott, Sam; Joshi, Keya; Tedijanto, Christine; Kahn, Rebecca; Niehus, Rene; Hay, James; De Salazar, Pablo M; +15 more... Hellewell, Joel; Meakin, Sophie; Munday, James; Bosse, Nikos I; Sherrat, Katharine; Thompson, Robin N; White, Laura F; Huisman, Jana S; Scire, Jérémie; Bonhoeffer, Sebastian; Stadler, Tanja; Wallinga, Jacco; Funk, Sebastian; Lipsitch, Marc; Cobey, Sarah; (2020) Practical considerations for measuring the effective reproductive number, R t. medRxiv preprint. ISSN 1468-5833 DOI: https://doi.org/10.1101/2020.06.18.20134858

Hellewell, Joel; Abbott, Sam; Gimma, Amy; Bosse, Nikos I; Jarvis, Christopher I; Russell, Timothy W; Munday, James D; Kucharski, Adam J; Edmunds, W John; Centre for the Mathematical Modelling of Infectious Diseases COV; +2 more... Funk, Sebastian; Eggo, Rosalind M; (2020) Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. The Lancet. Global health, 8 (4). e488-e496. ISSN 2214-109X DOI: https://doi.org/10.1016/S2214-109X(20)30074-7

Hellewell, Joel; Abbott, Sam; Gimma, Amy; Bosse, Nikos I; Jarvis, Christopher I; Russell, Timothy W; Munday, James D; Kucharski, Adam J; Edmunds, W John; Funk, Sebastian; +1 more... Eggo, Rosalind M; (2020) Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts. DOI: https://doi.org/10.1101/2020.02.08.20021162

Hellewell, Joel; Funk, Sebastian; Eggo, Rosalind M; (2020) On the fallibility of simulation models in informing pandemic responses - Authors' reply. LANCET GLOBAL HEALTH, 8 (6). e778-e779. ISSN 2214-109X DOI: https://doi.org/10.1016/S2214-109X(20)30217-5

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; Centre for the Mathematical Modelling of Infectious Diseases COV; (2020) Inferring the number of COVID-19 cases from recently reported deaths. Wellcome Open Res, 5. 78-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.15786.1

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. medRxiv. DOI: https://doi.org/10.1101/2020.03.10.20033761

Jombart, Thibaut; van Zandvoort, Kevin; Russell, Timothy W; Jarvis, Christopher I; Gimma, Amy; Abbott, Sam; Clifford, Sam; Funk, Sebastian; Gibbs, Hamish; Liu, Yang; +6 more... Pearson, Carl AB; Bosse, Nikos I; Centre for the Mathematical Modelling of Infectious Diseases COV; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; (2020) Inferring the number of COVID-19 cases from recently reported deaths. Wellcome open research, 5. 78-. DOI: https://doi.org/10.12688/wellcomeopenres.15786.1

Kucharski, Adam J; Funk, Sebastian; Eggo, Rosalind M; (2020) The COVID-19 response illustrates that traditional academic reward structures and metrics do not reflect crucial contributions to modern science. PLOS BIOLOGY, 18 (10). e3000913-. ISSN 1544-9173 DOI: https://doi.org/10.1371/journal.pbio.3000913

Kucharski, Adam J; Russell, Timothy W; Diamond, Charlie; Liu, Yang; Edmunds, John; Funk, Sebastian; Eggo, Rosalind M; (2020) Early dynamics of transmission and control of COVID-19: a mathematical modelling study. DOI: https://doi.org/10.1101/2020.01.31.20019901

Kucharski, Adam J; Russell, Timothy W; Diamond, Charlie; Liu, Yang; Edmunds, John; Funk, Sebastian; Eggo, Rosalind M; Centre for Mathematical Modelling of Infectious Diseases COVID-1; (2020) Early dynamics of transmission and control of COVID-19: a mathematical modelling study. The Lancet. Infectious diseases, 20 (5). pp. 553-558. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(20)30144-4

Leclerc, Quentin J; Fuller, Naomi M; Knight, Lisa E; CMMID COVID-19 Working Group; Funk, Sebastian; Knight, Gwenan M; (2020) What settings have been linked to SARS-CoV-2 transmission clusters? Wellcome Open Research, 5. 83-. DOI: https://doi.org/10.12688/wellcomeopenres.15889.2

Liu, Yang; Centre for Mathematical Modelling of Infectious Diseases nCoV Wo; Funk, Sebastian; Flasche, Stefan; (2020) The contribution of pre-symptomatic infection to the transmission dynamics of COVID-2019. Wellcome Open Research, 5. 58-. DOI: https://doi.org/10.12688/wellcomeopenres.15788.1

Musa, Sanjin; Bach Habersaat, Katrine; Jackson, Cath; Kulo, Aida; Primorac, Emilija; Smjecanin, Mirsad; Funk, Sebastian; (2020) Tailoring Immunization Programmes: using patient file data to explore vaccination uptake and associated factors. HUMAN VACCINES & IMMUNOTHERAPEUTICS, 17 (1). pp. 228-236. ISSN 2164-5515 DOI: https://doi.org/10.1080/21645515.2020.1769396

Métras, Raphaëlle; Edmunds, W John; Youssouffi, Chouanibou; Dommergues, Laure; Fournié, Guillaume; Camacho, Anton; Funk, Sebastian; Cardinale, Eric; Le Godais, Gilles; Combo, Soihibou; +3 more... Filleul, Laurent; Youssouf, Hassani; Subiros, Marion; (2020) Estimation of Rift Valley fever virus spillover to humans during the Mayotte 2018-2019 epidemic. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117 (39). pp. 24567-24574. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.2004468117

Pavelka, Martin; Van-Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; Analýz, Inštitút Zdravotných; Jarčuška, Pavol; Krajčí, Marek; Flasche, Stefan; Funk, Sebastian; (2020) The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia. MedRxiv. DOI: https://doi.org/10.1101/2020.12.02.20240648

Ratnayake, Ruwan; Finger, Flavio; Azman, Andrew S; Lantagne, Daniele; Funk, Sebastian; Edmunds, W John; Checchi, Francesco; (2020) Highly targeted spatiotemporal interventions against cholera epidemics, 2000-19: a scoping review. Lancet Infectious Diseases, 21 (3). e37-e48. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(20)30479-5

Robert, Alexis; Kucharski, Adam J; Gastañaduy, Paul A; Paul, Prabasaj; Funk, Sebastian; (2020) Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data. Journal of the Royal Society, Interface, 17 (168). 20200084-. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2020.0084

Thompson, Robin N; Hollingsworth, T Déirdre; Isham, Valerie; Arribas-Bel, Daniel; Ashby, Ben; Britton, Tom; Challenor, Peter; Chappell, Lauren HK; Clapham, Hannah; Cunniffe, Nik J; +33 more... Dawid, A Philip; Donnelly, Christl A; Eggo, Rosalind M; Funk, Sebastian; Gilbert, Nigel; Glendinning, Paul; Gog, Julia R; Hart, William S; Heesterbeek, Hans; House, Thomas; Keeling, Matt; Kiss, István Z; Kretzschmar, Mirjam E; Lloyd, Alun L; McBryde, Emma S; McCaw, James M; McKinley, Trevelyan J; Miller, Joel C; Morris, Martina; O'Neill, Philip D; Parag, Kris V; Pearson, Carl AB; Pellis, Lorenzo; Pulliam, Juliet RC; Ross, Joshua V; Tomba, Gianpaolo Scalia; Silverman, Bernard W; Struchiner, Claudio J; Tildesley, Michael J; Trapman, Pieter; Webb, Cerian R; Mollison, Denis; Restif, Olivier; (2020) Key questions for modelling COVID-19 exit strategies. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 287 (1932). 20201405-. ISSN 0962-8452 DOI: https://doi.org/10.1098/rspb.2020.1405

Tvermosegaard, KT; (2020) Computational Methods for D-optimal Design in Nonlinear Mixed Effects Models. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04657431

Willem, Lander; Van Hoang, Thang; Funk, Sebastian; Coletti, Pietro; Beutels, Philippe; Hens, Niel; (2020) SOCRATES: an online tool leveraging a social contact data sharing initiative to assess mitigation strategies for COVID-19. BMC research notes, 13 (1). 293-. ISSN 1756-0500 DOI: https://doi.org/10.1186/s13104-020-05136-9

Chun, June Young; Park, Wan Beom; Kim, Nam Joong; Choi, Eun Hwa; Funk, Sebastian; Oh, Myoung-Don; (2019) Estimating contact-adjusted immunity levels against measles in South Korea and prospects for maintaining elimination status. Vaccine, 38 (2). pp. 107-111. ISSN 0264-410X DOI: https://doi.org/10.1016/j.vaccine.2019.10.040

Endo, Akira; Uchida, Mitsuo; Kucharski, Adam J; Funk, Sebastian; (2019) Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15. PLoS computational biology, 15 (12). e1007589-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1007589

Finger, Flavio; Funk, Sebastian; White, Kate; Siddiqui, M Ruby; Edmunds, W John; Kucharski, Adam J; (2019) Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. BMC medicine, 17 (1). 58-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-019-1288-7

Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Lowe, Rachel; Eggo, Rosalind M; Edmunds, W John; (2019) Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15. PLoS computational biology, 15 (2). e1006785-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006785

Funk, Sebastian; King, Aaron A; (2019) Choices and trade-offs in inference with infectious disease models. Epidemics, 30. 100383-. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2019.100383

Funk, Sebastian; Knapp, Jennifer K; Lebo, Emmaculate; Reef, Susan E; Dabbagh, Alya J; Kretsinger, Katrina; Jit, Mark; Edmunds, W John; Strebel, Peter M; (2019) Combining serological and contact data to derive target immunity levels for achieving and maintaining measles elimination. BMC medicine, 17 (1). 180-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-019-1413-7

Gastañaduy, Paul A; Funk, Sebastian; Lopman, Benjamin A; Rota, Paul A; Gambhir, Manoj; Grenfell, Bryan; Paul, Prabasaj; (2019) Factors Associated With Measles Transmission in the United States During the Postelimination Era. JAMA Pediatrics, 174 (1). pp. 56-62. ISSN 2168-6203 DOI: https://doi.org/10.1001/jamapediatrics.2019.4357

Polonsky, Jonathan A; Baidjoe, Amrish; Kamvar, Zhian N; Cori, Anne; Durski, Kara; Edmunds, W John; Eggo, Rosalind M; Funk, Sebastian; Kaiser, Laurent; Keating, Patrick; +9 more... de Waroux, Olivier le Polain; Marks, Michael; Moraga, Paula; Morgan, Oliver; Nouvellet, Pierre; Ratnayake, Ruwan; Roberts, Chrissy H; Whitworth, Jimmy; Jombart, Thibaut; (2019) Outbreak analytics: a developing data science for informing the response to emerging pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 374 (1776). 20180276-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2018.0276

Robert, Alexis; Funk, Sebastian; Kucharski, Adam J; (2019) The measles crisis in Europe-the need for a joined-up approach. The Lancet, 393 (10185). 2033-. ISSN 0140-6736 DOI: https://doi.org/10.1016/S0140-6736(19)31039-6

Checchi, Francesco; Funk, Sebastian; Chandramohan, Daniel; Chappuis, François; Haydon, Daniel T; (2018) The impact of passive case detection on the transmission dynamics of gambiense Human African Trypanosomiasis. PLoS neglected tropical diseases, 12 (4). e0006276-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0006276

Faria, NR; Kraemer, MUG; Hill, SC; Goes de Jesus, J; Aguiar, RS; Iani, FCM; Xavier, J; Quick, J; du Plessis, L; Dellicour, S; +71 more... Thézé, J; Carvalho, RDO; Baele, G; Wu, C-H; Silveira, PP; Arruda, MB; Pereira, MA; Pereira, GC; Lourenço, J; Obolski, U; Abade, L; Vasylyeva, TI; Giovanetti, M; Yi, D; Weiss, DJ; Wint, GRW; Shearer, FM; Funk, S; Nikolay, B; Fonseca, V; Adelino, TER; Oliveira, MAA; Silva, MVF; Sacchetto, L; Figueiredo, PO; Rezende, IM; Mello, EM; Said, RFC; Santos, DA; Ferraz, ML; Brito, MG; Santana, LF; Menezes, MT; Brindeiro, RM; Tanuri, A; Dos Santos, FCP; Cunha, MS; Nogueira, JS; Rocco, IM; da Costa, AC; Komninakis, SCV; Azevedo, V; Chieppe, AO; Araujo, ESM; Mendonça, MCL; Dos Santos, CC; Dos Santos, CD; Mares-Guia, AM; Nogueira, RMR; Sequeira, PC; Abreu, RG; Garcia, MHO; Abreu, AL; Okumoto, O; Kroon, EG; de Albuquerque, CFC; Lewandowski, K; Pullan, ST; Carroll, M; de Oliveira, T; Sabino, EC; Souza, RP; Suchard, MA; Lemey, P; Trindade, GS; Drumond, BP; Filippis, AMB; Loman, NJ; Cauchemez, S; Alcantara, LCJ; Pybus, OG; (2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science (New York, NY), 361 (6405). pp. 894-899. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aat7115

Finger, F; Kucharski, A; Funk, S; Siddiqui, R; White, K; Edmunds, J; (2018) Real-time analysis of the diphtheria outbreak amongst forcibly displaced Myanmar nationals in Bangladesh. F1000Research, F1000Research. DOI: https://doi.org/10.7490/f1000research.1115484.1

Gastañaduy, Paul A; Funk, Sebastian; Paul, Prabasaj; Tatham, Lilith; Fisher, Nicholas; Budd, Jeremy; Fowler, Brian; de Fijter, Sietske; DiOrio, Mary; Wallace, Gregory S; +1 more... Grenfell, Bryan; (2018) Impact of Public Health Responses During a Measles Outbreak in an Amish Community in Ohio: Modeling the Dynamics of Transmission. American journal of epidemiology, 187 (9). pp. 2002-2010. ISSN 0002-9262 DOI: https://doi.org/10.1093/aje/kwy082

Gilligan, Peter H; Downey, Damian G; Elborn, J Stuart; Flume, Patrick A; Funk, Sebastian; Gilpin, Deirdre; Kidd, Timothy J; McCaughan, John; Millar, B Cherie; Murphy, Philip G; +3 more... Rendall, Jacqueline C; Tunney, Michael M; Moore, John E; (2018) "Pathogen Eradication" and "Emerging Pathogens": Difficult Definitions in Cystic Fibrosis. Journal of clinical microbiology, 56 (9). ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.00193-18

Knight, Gwenan M; Zimic, Mirko; Funk, Sebastian; Gilman, Robert H; Friedland, Jon S; Grandjean, Louis; (2018) The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. JOURNAL OF THE ROYAL SOCIETY INTERFACE, 15 (143). p. 20180025. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2018.0025

Kraemer, MUG; Cummings, DAT; Funk, S; Reiner, RC; Faria, NR; Pybus, OG; Cauchemez, S; (2018) Reconstruction and prediction of viral disease epidemics. Epidemiology and infection, 147. e34-. ISSN 0950-2688 DOI: https://doi.org/10.1017/S0950268818002881

Kucharski, Adam J; Kama, Mike; Watson, Conall H; Aubry, Maite; Funk, Sebastian; Henderson, Alasdair D; Brady, Oliver J; Vanhomwegen, Jessica; Manuguerra, Jean-Claude; Lau, Colleen L; +6 more... Edmunds, W John; Aaskov, John; Nilles, Eric James; Cao-Lormeau, Van-Mai; Hué, Stéphane; Hibberd, Martin L; (2018) Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji. eLife, 7. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.34848

O'Reilly, Kathleen M; Lowe, Rachel; Edmunds, W John; Mayaud, Philippe; Kucharski, Adam; Eggo, Rosalind M; Funk, Sebastian; Bhatia, Deepit; Khan, Kamran; Kraemer, Moritz UG; +8 more... Wilder-Smith, Annelies; Rodrigues, Laura C; Brasil, Patricia; Massad, Eduardo; Jaenisch, Thomas; Cauchemez, Simon; Brady, Oliver J; Yakob, Laith; (2018) Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis. BMC medicine, 16 (1). 180-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-018-1158-8

Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Lowe, Rachel; Eggo, Rosalind M; Edmunds, W John; (2017) Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area Region of Sierra Leone, 2014–15. bioRxiv. DOI: https://doi.org/10.1101/177451 (Unpublished)

Funk, Sebastian; Ciglenecki, Iza; Tiffany, Amanda; Gignoux, Etienne; Camacho, Anton; Eggo, Rosalind M; Kucharski, Adam J; Edmunds, W John; Bolongei, Josephus; Azuma, Phillip; +9 more... Clement, Peter; Alpha, Tamba S; Sterk, Esther; Telfer, Barbara; Engel, Gregory; Parker, Lucy Anne; Suzuki, Motoi; Heijenberg, Nico; Reeder, Bruce; (2017) The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia. Philosophical transactions of the Royal Society of London Series B, Biological sciences, 372 (1721). p. 20160302. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2016.0302

Funk, Sebastian; Knapp, Jennifer K; Lebo, Emmaculate; Reef, Susan E; Dabbagh, Alya J; Kretsinger, Katrina; Jit, Mark; Edmunds, W John; Strebel, Peter M; (2017) Combining serological and contact data to derive target immunity levels for achieving and maintaining measles elimination. bioRxiv. DOI: https://doi.org/10.1101/201574 (Unpublished)

Lau, Max SY; Dalziel, Benjamin Douglas; Funk, Sebastian; McClelland, Amanda; Tiffany, Amanda; Riley, Steven; Metcalf, C Jessica E; Grenfell, Bryan T; (2017) Spatial and temporal dynamics of superspreading events in the 2014-2015 West Africa Ebola epidemic. Proceedings of the National Academy of Sciences of the United States of America, 114 (9). pp. 2337-2342. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1614595114

Lau, Max SY; Gibson, Gavin J; Adrakey, Hola; McClelland, Amanda; Riley, Steven; Zelner, Jon; Streftaris, George; Funk, Sebastian; Metcalf, Jessica; Dalziel, Benjamin D; +1 more... Grenfell, Bryan T; (2017) A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak. PLoS computational biology, 13 (10). e1005798-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005798

Marks, Michael; Mitjà, Oriol; Fitzpatrick, Christopher; Asiedu, Kingsley; Solomon, Anthony W; Mabey, David CW; Funk, Sebastian; (2017) Mathematical Modeling of Programmatic Requirements for Yaws Eradication. Emerging infectious diseases, 23 (1). pp. 22-28. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2301.160487

Netto, Eduardo Martins; Moreira-Soto, Andres; Pedroso, Celia; Höser, Christoph; Funk, Sebastian; Kucharski, Adam J; Rockstroh, Alexandra; Kümmerer, Beate M; Sampaio, Gilmara Souza; Luz, Estela; +13 more... Vaz, Sara Nunes; Dias, Juarez Pereira; Bastos, Fernanda Anjos; Cabral, Renata; Kistemann, Thomas; Ulbert, Sebastian; de Lamballerie, Xavier; Jaenisch, Thomas; Brady, Oliver J; Drosten, Christian; Sarno, Manoel; Brites, Carlos; Drexler, Jan Felix; (2017) High Zika Virus Seroprevalence in Salvador, Northeastern Brazil Limits the Potential for Further Outbreaks. mBio, 8 (6). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.01390-17

Peppa, Maria; John Edmunds, W; Funk, Sebastian; (2017) Disease severity determines health-seeking behaviour amongst individuals with influenza-like illness in an internet-based cohort. BMC infectious diseases, 17 (1). 238-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-017-2337-5

Yakob, Laith; Funk, Sebastian; Camacho, Anton; Brady, Oliver; Edmunds, W John; (2017) Aedes aegypti Control Through Modernized, Integrated Vector Management. PLoS currents, 9. ecurrents.outbreaks.45deb8e03a438c4d088afb4fafae87-. ISSN 2157-3999 DOI: https://doi.org/10.1371/currents.outbreaks.45deb8e03a438c4d088afb4fafae8747

Camacho, A; Eggo, RM; Goeyvaerts, N; Vandebosch, A; Mogg, R; Funk, S; Kucharski, AJ; Watson, CH; Vangeneugden, T; Edmunds, WJ; (2016) Real-time dynamic modelling for the design of a cluster-randomized phase 3 Ebola vaccine trial in Sierra Leone. Vaccine, 35 (4). pp. 544-551. ISSN 0264-410X DOI: https://doi.org/10.1016/j.vaccine.2016.12.019

Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Eggo, Rosalind M; Edmunds, W John; (2016) Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model. Epidemics, 22. pp. 56-61. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2016.11.003

Funk, Sebastian; Kucharski, Adam J; Camacho, Anton; Eggo, Rosalind M; Yakob, Laith; Murray, Lawrence M; Edmunds, W John; (2016) Comparative Analysis of Dengue and Zika Outbreaks Reveals Differences by Setting and Virus. PLoS neglected tropical diseases, 10 (12). e0005173-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005173

Kucharski, Adam J; Eggo, Rosalind M; Watson, Conall H; Camacho, Anton; Funk, Sebastian; Edmunds, W John; (2016) Effectiveness of Ring Vaccination as Control Strategy for Ebola Virus Disease. Emerging infectious diseases, 22 (1). pp. 105-108. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2201.151410

Kucharski, Adam J; Funk, Sebastian; Eggo, Rosalind M; Mallet, Henri-Pierre; Edmunds, W John; Nilles, Eric J; (2016) Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013-14 French Polynesia Outbreak. PLoS neglected tropical diseases, 10 (5). e0004726-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0004726

Camacho, A; Kucharski, A; Aki-Sawyerr, Y; White, MA; Flasche, S; Baguelin, M; Pollington, T; Carney, JR; Glover, R; Smout, E; +3 more... Tiffany, A; Edmunds, WJ; Funk, S; (2015) Temporal changes in ebola transmission in sierra leone and implications for control requirements: A real-time modelling study. PLoS Currents, 7 (OUTBRE). 55052-. DOI: https://doi.org/10.1371/currents.outbreaks.406ae55e83ec0b5193e3085

Camacho, Anton; Eggo, Rosalind M; Funk, Sebastian; Watson, Conall H; Kucharski, Adam J; Edmunds, W John; (2015) Estimating the probability of demonstrating vaccine efficacy in the declining Ebola epidemic: a Bayesian modelling approach. BMJ open, 5 (12). e009346-. ISSN 2044-6055 DOI: https://doi.org/10.1136/bmjopen-2015-009346

Camacho, Anton; Kucharski, Adam; Aki-Sawyerr, Yvonne; White, Mark A; Flasche, Stefan; Baguelin, Marc; Pollington, Timothy; Carney, Julia R; Glover, Rebecca; Smout, Elizabeth; +3 more... Tiffany, Amanda; Edmunds, W John; Funk, Sebastian; (2015) Temporal Changes in Ebola Transmission in Sierra Leone and Implications for Control Requirements: a Real-time Modelling Study. PLoS currents, 7. ecurrents.outbreaks.406ae55e83ec0b5193e30856b9235e-. ISSN 2157-3999 DOI: https://doi.org/10.1371/currents.outbreaks.406ae55e83ec0b5193e30856b9235ed2

Checchi, Francesco; Funk, Sebastian; Chandramohan, Daniel; Haydon, Daniel T; Chappuis, François; (2015) Updated estimate of the duration of the meningo-encephalitic stage in gambiense human African trypanosomiasis. BMC research notes, 8 (1). 292-. ISSN 1756-0500 DOI: https://doi.org/10.1186/s13104-015-1244-3

Eggo, Rosalind M; Watson, Conall H; Camacho, Anton; Kucharski, Adam J; Funk, Sebastian; Edmunds, W John; (2015) Duration of Ebola virus RNA persistence in semen of survivors: population-level estimates and projections. Euro surveillance, 20 (48). 30083-. ISSN 1025-496X DOI: https://doi.org/10.2807/1560-7917.ES.2015.20.48.30083

Heesterbeek, Hans; Anderson, Roy M; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken TD; Edmunds, W John; Frost, Simon DW; Funk, Sebastian; +13 more... Hollingsworth, T Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James O; Metcalf, C Jessica E; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet RC; Roberts, Mick G; Viboud, Cecile; Isaac Newton Institute IDD Collaboration; (2015) Modeling infectious disease dynamics in the complex landscape of global health. Science (New York, NY), 347 (6227). aaa4339-. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aaa4339 Full text not available from this repository.

Kucharski, Adam J; Camacho, Anton; Checchi, Francesco; Waldman, Ron; Grais, Rebecca F; Cabrol, Jean-Clement; Briand, Sylvie; Baguelin, Marc; Flasche, Stefan; Funk, Sebastian; +1 more... Edmunds, W John; (2015) Evaluation of the benefits and risks of introducing Ebola community care centers, Sierra Leone. Emerging infectious diseases, 21 (3). pp. 393-399. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2103.141892

Kucharski, Adam J; Camacho, Anton; Flasche, Stefan; Glover, Rebecca E; Edmunds, W John; Funk, Sebastian; (2015) Measuring the impact of Ebola control measures in Sierra Leone. Proceedings of the National Academy of Sciences of the United States of America, 112 (46). pp. 14366-14371. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1508814112

Rosello, Alicia; Mossoko, Mathias; Flasche, Stefan; Van Hoek, Albert Jan; Mbala, Placide; Camacho, Anton; Funk, Sebastian; Kucharski, Adam; Ilunga, Benoit Kebela; Edmunds, W John; +3 more... Piot, Peter; Baguelin, Marc; Tamfum, Jean-Jacques Muyembe; (2015) Ebola virus disease in the Democratic Republic of the Congo, 1976-2014. eLife, 4 (NOVEMB). ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.09015

Adler, Alma J; Eames, Ken TD; Funk, Sebastian; Edmunds, W John; (2014) Incidence and risk factors for influenza-like-illness in the UK: online surveillance using Flusurvey. BMC infectious diseases, 14 (1). 232-. ISSN 1471-2334 DOI: https://doi.org/10.1186/1471-2334-14-232

Bajardi, Paolo; Paolotti, Daniela; Vespignani, Alessandro; Eames, Ken; Funk, Sebastian; Edmunds, W John; Turbelin, Clement; Debin, Marion; Colizza, Vittoria; Smallenburg, Ronald; +9 more... Koppeschaar, Carl; Franco, Ana O; Faustino, Vitor; Carnahan, AnnaSara; Rehn, Moa; Merletti, Franco; Douwes, Jeroen; Firestone, Ridvan; Richiardi, Lorenzo; (2014) Association between recruitment methods and attrition in Internet-based studies. PloS one, 9 (12). e114925-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0114925

Bajardi, Paolo; Vespignani, Alessandro; Funk, Sebastian; Eames, Ken Td; Edmunds, W John; Turbelin, Clément; Debin, Marion; Colizza, Vittoria; Smallenburg, Ronald; Koppeschaar, Carl E; +5 more... Franco, Ana O; Faustino, Vitor; Carnahan, Annasara; Rehn, Moa; Paolotti, Daniela; (2014) Determinants of follow-up participation in the Internet-based European influenza surveillance platform Influenzanet. Journal of medical Internet research, 16 (3). e78-. ISSN 1439-4456 DOI: https://doi.org/10.2196/jmir.3010

Blumberg, Seth; Funk, Sebastian; Pulliam, Juliet RC; (2014) Detecting differential transmissibilities that affect the size of self-limited outbreaks. PLoS pathogens, 10 (10). e1004452-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1004452

Camacho, A; Kucharski, AJ; Funk, S; Breman, J; Piot, P; Edmunds, WJ; (2014) Potential for large outbreaks of Ebola virus disease. Epidemics, 9. pp. 70-78. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.09.003

Funk, Sebastian; Bansal, Shweta; Bauch, Chris T; Eames, Ken TD; Edmunds, W John; Galvani, Alison P; Klepac, Petra; (2014) Nine challenges in incorporating the dynamics of behaviour in infectious diseases models. Epidemics, 10. pp. 21-25. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.09.005

Funk, Sebastian; Knight, Gwenan M; Jansen, Vincent AA; (2014) Ebola: the power of behaviour change. Nature, 515 (7528). 492-. ISSN 0028-0836 DOI: https://doi.org/10.1038/515492b Full text not available from this repository.

Funk, Sebastian; Piot, Peter; (2014) Mapping Ebola in wild animals for better disease control. eLife, 3. e04565-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.04565

Hollingsworth, T Déirdre; Pulliam, Juliet RC; Funk, Sebastian; Truscott, James E; Isham, Valerie; Lloyd, Alun L; (2014) Seven challenges for modelling indirect transmission: vector-borne diseases, macroparasites and neglected tropical diseases. Epidemics, 10. pp. 16-20. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.08.007

Klepac, Petra; Funk, Sebastian; Hollingsworth, T Deirdre; Metcalf, C Jessica E; Hampson, Katie; (2014) Six challenges in the eradication of infectious diseases. Epidemics, 10. pp. 97-101. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.12.001

Lloyd-Smith, James O; Funk, Sebastian; McLean, Angela R; Riley, Steven; Wood, James LN; (2014) Nine challenges in modelling the emergence of novel pathogens. Epidemics, 10. pp. 35-39. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.09.002

Metcalf, CJE; Andreasen, V; Bjørnstad, ON; Eames, K; Edmunds, WJ; Funk, S; Hollingsworth, TD; Lessler, J; Viboud, C; Grenfell, BT; (2014) Seven challenges in modeling vaccine preventable diseases. Epidemics, 10. pp. 11-15. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.08.004

Metcalf, CJE; Birger, RB; Funk, S; Kouyos, RD; Lloyd-Smith, JO; Jansen, VAA; (2014) Five challenges in evolution and infectious diseases. Epidemics, 10. pp. 40-44. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.12.003

LSHTM; (2013) LSHTM - May 2013 podcast - Measles, vaccine concerns, and mosquito manipulation. [Podcast] http://soundcloud.com/lshtm/lshtm-may-2013-podcast...

LSHTM; (2013) John Edmunds and Sebastian Funk - measles outbreak. [Podcast] http://soundcloud.com/lshtm/john-edmunds-and-sebas...

Bogich, Tiffany L; Funk, Sebastian; Malcolm, Trent R; Chhun, Nok; Epstein, Jonathan H; Chmura, Aleksei A; Kilpatrick, A Marm; Brownstein, John S; Hutchison, O Clyde; Doyle-Capitman, Catherine; +4 more... Deaville, Robert; Morse, Stephen S; Cunningham, Andrew A; Daszak, Peter; (2013) Using network theory to identify the causes of disease outbreaks of unknown origin. Journal of the Royal Society, Interface / the Royal Society, 10 (81). 20120904-. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2012.0904

Bryden, John; Funk, Sebastian; Jansen, Vincent AA; (2013) Word usage mirrors community structure in the online social network Twitter. EPJ data science, 2 (1). pp. 1-9. ISSN 2193-1127 DOI: https://doi.org/10.1140/epjds15

Funk, S; Jansen, VAA; (2013) The Talk of the Town: Modelling the Spread of Information and Changes in Behaviour. In: Manfredi, P; D'Onofrio, A, (eds.) Modeling the Interplay Between Human Behavior and the Spread of Infectious Diseases. Springer, pp. 93-102. ISBN 1461454735 https://researchonline.lshtm.ac.uk/id/eprint/856835 Full text not available from this repository.

Funk, Sebastian; Bogich, Tiffany L; Jones, Kate E; Kilpatrick, A Marm; Daszak, Peter; (2013) Quantifying trends in disease impact to produce a consistent and reproducible definition of an emerging infectious disease. PloS one, 8 (8). e69951-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0069951

Funk, Sebastian; Nishiura, Hiroshi; Heesterbeek, Hans; Edmunds, W John; Checchi, Francesco; (2013) Identifying transmission cycles at the human-animal interface: the role of animal reservoirs in maintaining gambiense human african trypanosomiasis. PLoS computational biology, 9 (1). e1002855-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002855

Edmunds, W John; Funk, Sebastian; (2012) Using the internet to estimate influenza vaccine effectiveness. Expert review of vaccines, 11 (9). pp. 1027-1029. ISSN 1476-0584 DOI: https://doi.org/10.1586/erv.12.88 Full text not available from this repository.

Bryden, John; Funk, Sebastian; Geard, Nicholas; Bullock, Seth; Jansen, Vincent AA; (2011) Stability in flux: community structure in dynamic networks. Journal of the Royal Society, Interface / the Royal Society, 8 (60). pp. 1031-1040. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2010.0524

Funk, S; Gilad, E; Jansen, VAA; (2010) Endemic disease, awareness, and local behavioural response. Journal of theoretical biology, 264 (2). pp. 501-509. ISSN 0022-5193 DOI: https://doi.org/10.1016/j.jtbi.2010.02.032

Funk, Sebastian; Jansen, Vincent AA; (2010) Interacting epidemics on overlay networks. Physical review E, Statistical, nonlinear, and soft matter physics, 81 (3 Pt 2). 036118-. ISSN 1539-3755 DOI: https://doi.org/10.1103/PhysRevE.81.036118

Funk, Sebastian; Salathé, Marcel; Jansen, Vincent AA; (2010) Modelling the influence of human behaviour on the spread of infectious diseases: a review. Journal of the Royal Society, Interface / the Royal Society, 7 (50). pp. 1247-1256. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2010.0142

Funk, Sebastian; Gilad, Erez; Watkins, Chris; Jansen, Vincent AA; (2009) The spread of awareness and its impact on epidemic outbreaks. Proceedings of the National Academy of Sciences of the United States of America, 106 (16). pp. 6872-6877. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.0810762106 Full text not available from this repository.