Item Type Date Title No Grouping

A

akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. (2022) Endo, Akira, Uchida, Mitsuo, Liu, Yang, Atkins, Katherine E., Kucharski, Adam J., Funk, Sebastian

akira-endo/schooldynamics_FluMatsumoto14-15: Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. (2021) Endo, Akira, Uchida, Mitsuo, Hayashi, Naoki, Liu, Yang, Atkins, Katherine E., Kucharski, Adam J., Funk, Sebastian

adamkucharski/covid-import-model. (2021) Kucharski, Adam J.

Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". (2021) Davies, Nicholas G., Abbott, Sam, Barnard, Rosanna C., Jarvis, Christopher I., Kucharski, Adam J., Munday, James, Pearson, Carl A. B., Russell, Timothy W., Tully, Damien C., Washburne, Alex D., 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

Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 Variant of Concern 202012/01 in England". (2021) Davies, Nicholas G., Abbott, Sam, Barnard, Rosanna C., Jarvis, Christopher I., Kucharski, Adam J., Munday, James, Pearson, Carl A. B., Russell, Timothy W., Tully, Damien C., Washburne, Alex D., 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

akira-endo/COVID19_backwardtracing. (2020) Endo, Akira, Kucharski, Adam J.

akira-endo/COVID19_clustersize: Estimating the amount of superspreading using outbreak sizes of COVID-19 outside China. (2020) Endo, Akira, Abbott, Sam, Kucharski, Adam J., Funk, Sebastian

Age-structured SEIR model for COVID-19 outbreak in Wuhan, China. (2020) Prem, Kiesha, Liu, Yang, Russell, Timothy W, Kucharski, Adam J, Eggo, Rosalind M, Davies, Nicholas G, Jit, Mark, Klepac, Petra, Flasche, Stefan, Clifford, Samuel, Pearson, Carl A B, Munday, James D, Abbott, Sam, Gibbs, Hamish, Rosello, Alicia, Quilty, Billy J, Jombart, Thibaut, Sun, Fiona, Diamond, Charlie, Gimma, Amy, Van zandvoort, Kevin, Funk, Sebastian, Jarvis, Christopher I, Edmunds, W John, Bosse, Nikos I, Hellewell, Joel

Additional file 2: of Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. (2019) Finger, Flavio, Funk, Sebastian, White, Kate, Siddiqui, M. Ruby, Edmunds, W. John, Kucharski, Adam J.

adamkucharski/fiji-denv3-2014. (2018) 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, Edmunds, W John, Aaskov, John, Nilles, Eric James, Cao-Lormeau, Van-Mai, Hue, Stephane, Hibberd, Martin L

B

Bed capacity for Ebola patients in Sierra Leone. (2015) Camacho, Anton, Kucharski, Adam J., Aki-Sawyerr, Y, White, M A, Flasche, Stefan, Baguelin, Marc, Pollington, T M, Carney, J, Glover, Rebecca, Smout, E, Tiffany, A, Edmunds, W. John, Funk, Sebastian

C

cfr: Estimate Disease Severity and Case Ascertainment. (2024) Gupte, Pratik R., Kucharski, Adam J., Russell, Timothy W., Lambert, Joshua W., Gruson, Hugo, Taylor, Tim, Azam, James M., Degoot, Abdoelnaser M., Funk, Sebastian

cmmid/SA2UK: CEA submission. (2022) Pearson, Carl A. B., Russell, Timothy W., Kucharski, Adam J.

cmmid/SA2UK. (2021) Pearson, Carl A. B., Russell, Timothy W., Kucharski, Adam J.

cmmid/pcr-profile. (2020) Hellewell, Joel, Russell, Timothy W., The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group, Beale, Rupert, Kelly, Gavin, Houlihan, Catherine, Nastouli, Eleni, Kucharski, Adam J.

cmmid/covid-uk. (2020) Davies, Nicholas G, Kucharski, Adam J., Eggo, Rosalind M, Gimma, Amy, COVID-19 Working Group, Edmunds, W. John

Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project. (2020) Klepac, Petra, Kucharski, Adam J, Conlan, Andrew JK, Kissler, Stephen, Tang, Maria, Fry, Hannah, Gog, Julia R

Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks: Simulation and Inference code. (2015) Kucharski, Adam, Edmunds, John description

D

Data and R-code to accompany 'Towards an Early Warning System for Leptospirosis in North-Eastern Argentina'. (2023) Lotto Batista, Martín, Rees, Eleanor M., Gómez, Andrea, López, Soledad, Castell, Stefanie, Kucharski, Adam J., Ghozzi, Stéphane, Müller, Gabriela V, Lowe, Rachel

Data for: Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections. (2018) le Polain de Waroux, Olivier, Flasche, Stefan, Kucharski, Adam J, Langendorf, Celine, Ndazima, Donny, Mwanga-Amumpaire, Juliet, Grais, Rebecca F, Cohuet, Sandra, Edmunds, W John

Data from: Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data. (2015) Kucharski, Adam, Mills, Harriet, Pinsent, Amy, Fraser, Christophe, Kerkhove, Maria Van, Riley, Steven

E

epiparameterDB: Database of Epidemiological Parameters. (2024) Lambert, Joshua W., Kucharski, Adam J., Tamayo, Carmen

enilles1/immunoepidemiology. (2024) Nilles, Eric J., Kucharski, Adam J.

epiverse-trace/simulist. (2024) Lambert, Joshua, Gruson, Hugo, Kucharski, Adam J., Tamayo Cuartero, Carmen

epiverse-trace/epiparameter. (2023) Lambert, Joshua, Gruson, Hugo, Kucharski, Adam J., Gupte, Pratik, Salmon, Maëlle, Campos, Andree Valle, Monticone, Pietro

epiverse-trace. (2023) Pavlich-Mariscal, Jaime, Eggo, Rosalind M., Kucharski, Adam J., Gruson, Hugo, Russell, Timothy W., Valle Campos, Andree, Cucunubá, Zulma M., Santos-Vega, Mauricio, Gupte, Pratik, Azam, James, Torres Domínguez, Nicolás, Lambert, Joshua, Gomez, Geraldine, Umaña, Juan D., Quevedo-Vega, David Santiago, Gámez López, Miguel Enrique, Carnegie, Anna

EmilieFinch/covid-reinfection. (2022) Finch, Emilie, Kucharski, Adam J.

Extended data: Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. (2020) Endo, Akira, Abbott, Sam, Kucharski, Adam J., Funk, Sebastian

Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship. (2020) Russell, Timothy W., Hellewell, Joel, Jarvis, Christopher I., Van-Zandvoort, Kevin, Abbott, Sam, Ratnayake, Ruwan, Flasche, Stefan, Eggo, Rosalind M, Kucharski, Adam J.

Ebola Dataset for "Learning Clinical Epidemiology with R" tutorial. (2017) Marks, Michael, Camacho, Anton, Kucharski, Adam, Funk, Sebastian, Edmunds, John, Piot, Peter description

Ebola virus disease in the Democratic Republic of the Congo, 1976-2014: Figures and Data. (2015) Rosello, Alicia, Mossoko, Mathias, Flasche, Stefan, Vanhoek, Albert, Mbala, Placide, Camacho, Anton, Funk, Sebastian, Kucharski, Adam, Ilunga, Benoit Kebela, Edmunds, John, Piot, Peter, Baguelin, Marc, Tamfum, Jean-Jacques Muyembe description

F

finalsize: Calculate the Final Size of an Epidemic. (2024) Gupte, Pratik, Van Leeuwen, Edwin, Kucharski, Adam, Eggo, Rosalind M., Gruson, Hugo, Jombart, Thibaut, Valle Campos, Andree, Lambert, Joshua W.

Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. (2020) Hellewell, Joel, Abbott, Sam, Gimma, Amy, Bosse, Nikos, Jarvis, Christopher, Russell, Timothy, Munday, James, Kucharski, Adam, Edmunds, W John, Funk, Sebastian, Eggo, Rosalind, Sun, Fiona, Flasche, Stefan, Quilty, Billy, Davies, Nicholas, Liu, Yang, Clifford, Samuel, Klepac, Petra, Jit, Mark, Diamond, Charlie, Gibbs, Hamish, Van Zandvoort, Kevin

G

Geospatial analysis of leptospirosis clusters and risk factors in two provinces of the Dominican Republic. (2025) Martin, Beatris Mario, Sartorius, Benn, Mayfield, Helen J., Cadavid Restrepo, Angela M., Kiani, Behzad, Then Paulino, Cecilia J., Etienne, Marie Caroline, Skewes-Ramm, Ronald, de St. Aubin, Michael, Dumas, Devan, Garnier, Salomé, Duke, William, Peña, Farah, Abdalla, Gabriela, de la Cruz, Lucia, Henríquez, Bernarda, Baldwin, Margaret, Kucharski, Adam J., Nilles, Eric J., Lau, Colleen L.

H

hamishgibbs/facebook_population_2020_2021. (2022) Gibbs, Hamish, Waterlow, Naomi R., Cheshire, James, Danon, Leon, Liu, Yang, Grundy, Chris, Kucharski, Adam J., Eggo, Rosalind M.

I

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. (2023) Chapman, Lloyd A.C., Aubry, Maite, Maset, Noemie, Russell, Timothy, Knock, Edward S, Lees, John A, Mallet, Henri-Pierre, Cao-Lormeau, Van-Mai, Kucharski, Adam J.

Inferring COVID-19 cases from deaths of confirmed cases. (2020) Jombart, Thibaut, Abbott, Sam, Gimma, Amy, Zandvoort, Kevin, Clifford, Samuel, Jarvis, Christopher, Russell, Timothy, Funk, Sebastian, Gibbs, Hamish, Eggo, Rosalind M., Kucharski, Adam J., CMMID COVID-19 Working Group, Edmunds, W. John

O

o2geosocial: Reconstruction of Transmission Chains from Surveillance Data. (2021) Robert, Alexis, Funk, Sebastian, Kucharski, Adam J., Jombart, Thibaut

o2geosocial. (2020) Robert, Alexis, Funk, Sebastian, Kucharski, Adam J.

P

Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic - Estimates for Local Authority Districts. (2021) Gibbs, Hamish, Waterlow, Naomi R., Cheshire, James, Danon, Leon, Liu, Yang, Grundy, Chris, Kucharski, Adam J., Eggo, Rosalind M.

Probability of a large 2019-nCoV outbreak following introduction of cases. (2020) Kucharski, Adam J., Russell, Timothy W., Diamond, Charlie, CMMID nCoV working group, Funk, Sebastian, Eggo, Rosalind M.

Potential for large outbreaks of Ebola virus disease: Supplementary Data. (2014) Camacho, Anton, Kucharski, Adam, Funk, Sebastian, Breman, J, Piot, Peter, Edmunds, John

R

rachaelpung/temporal_networks. (2024) Pung, Rachael, Kucharski, Adam J., Firth, Josh, Russell, Timothy W., Rogers, Tim, Lee, Vernon

Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study. (2023) Pung, Rachael, Clapham, Hannah E, Russell, Timothy W., Lee, Vernon J., Kucharski, Adam J.

Reconstructing the global dynamics of unreported COVID-19 cases and infections. (2020) Russell, Timothy W., Golding, Nick, Hellewell, Joel, Abbott, Sam, Pearson, Carl A B, Van zandvoort, Kevin, Jarvis, Christopher I, Gibbs, Hamish, Liu, Yang, Eggo, Rosalind M., Edmunds, W. John, Kucharski, Adam J., CMMID COVID-19 working group

Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. (2019) Finger, Flavio, Funk, Sebastian, White, Kate, Siddiqui, M. Ruby, Edmunds, W. John, Kucharski, Adam J.

Reported contacts dataset for "Structure and consistency of self-reported social contact networks in British secondary schools". (2018) Kucharski, Adam J., Wenham, Clare, Brownlee, Polly, Racon, Lucie, Widmer, Natasha, Eames, Ken T. D., Conlan, Andrew J. K.

S

superspreading: Understand Individual-Level Variation in Infectious Disease Transmission. (2025) Lambert, Joshua W., Kucharski, Adam J., Adam, Dillon C., Funk, Sebastian, Gupte, Pratik, Gruson, Hugo, Azam, James M., Hartgerink, Chris

simulist: Simulate Disease Outbreak Line List and Contacts Data. (2025) Lambert, Joshua W., Tamayo, Carmen, Gruson, Hugo, Gupte, Pratik R., Kucharski, Adam J., Hartgerink, Chris, Funk, Sebastian

scrapR. (2018) Kucharski, Adam

Social mixing in Fiji: Who-eats-with-whom contact patterns and the implications of age and ethnic heterogeneity for disease dynamics in the Pacific Islands. (2017) Watson, Conall H., Coriakula, Jeremaia, Ngoc, Dung Tran Thi, Flasche, Stefan, Kucharski, Adam J., Lau, Colleen L., Thieu, Nga Tran Vu, le Polain de Waroux, Olivier, Rawalai, Kitione, Van, Tan Trinh, Taufa, Mere, Baker, Stephen, Nilles, Eric J., Kama, Mike, Edmunds, W. John

S1 Dataset for "Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013–14 French Polynesia Outbreak". (2016) Kucharski, Adam J., Funk, Sebastian, Eggo, Rosalind M., Mallet, Henri-Pierre, Edmunds, W. John, Nilles, Eric J. description

School's Out: Seasonal Variation in the Movement Patterns of School Children. S1 Dataset. Reported individual travel patterns. (2015) Kucharski, Adam, Conlan, Andrew J. K., Eames, Ken grid_on

T

thimotei/legacy_nAb_kinetics. (2024) Russell, Timothy W., Kucharski, Adam J.

thimotei/legacy_ct_modelling: Final version. (2023) Abbott, Sam, Russell, Timothy W., Hellewell, Joel, Kucharski, Adam J.

The importance of fine-scale predictors of wild boar habitat use in an isolated population. (2022) Bacigalupo, Sonny, Ruby Chang, Yu-Mei, Dixon, Linda, Gubbins, Simon, Kucharski, Adam J., Drewe, Julian

thimotei/covid_travel_restrictions. (2020) Russell, Timothy W., Wu, Joseph T, Clifford, Samuel, CMMID COVID-19 working group, Edmunds, W John, Kucharski, Adam J., Jit, Mark

thimotei/CFR_calculation. (2020) Russell, Timothy W., Hellewell, Joel, Abbott, Sam, Jarvis, Christopher, Zandvoort, Kevin van, Ratnayake, Ruwan, CMMID nCov working group, Flasche, Stefan, Eggo, Rosalind M., Edmunds, W. John, Kucharski, Adam J.

U

Unexposed populations and potential COVID-19 burden in European countries as of 21st November 2021. (2021) Chapman, Lloyd A C, Barnard, Rosanna C, Russell, Timothy W, Abbott, Sam, Van Zandvoort, Kevin, Davies, Nicholas G, Kucharski, Adam J

UK Colocation Dashboard. (2020) Gibbs, Hamish, CMMID nCov Working Group, Eggo, Rosalind M., Grundy, Chris, Kucharski, Adam J.