Item Type Date Title No Grouping

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

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.

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

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

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

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

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

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.

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

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

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

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

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

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.

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

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.

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

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

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.

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

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

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

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

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

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.

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

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

o2geosocial. (2020) Robert, Alexis; Funk, Sebastian; 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.

akira-endo/COVID19_backwardtracing. (2020) Endo, Akira; 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

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

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

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

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

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.

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.

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

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

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

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

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.

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.

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.

scrapR. (2018) Kucharski, Adam

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

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

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.

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

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

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

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

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

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

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

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

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