LSHTM Organisational Structure (3751)
Faculty of Epidemiology and Population Health (2441)
Dept of Infectious Disease Epidemiology & Dynamics (2023-) (98)
Number of items at this level: 98.
vaccine-impact/hpv_vaccine_equity. (2024)
Abbas, Kaja M.; Vaccine Impact
lshtm-vimc/prime. (2024)
Abbas, Kaja M.; Vaccine Impact; Hadley, Liza
seabbs/badtobetter: Initial release. (2023)
Abbott, Sam
EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters. (2024)
Abbott, Sam; Hellewell, Joel; Sherratt, Katharine; Gostic, Katelyn; Hickson, Joe; Badr, Hamada S.; DeWitt, Michael; Azam, James M.; EpiForecasts; Funk, Sebastian
epinowcast/epidist. (2025)
Abbott, Sam; Howes, Adam; Park, Sang Woo; Funk, Sebastian; Bayer, Damon; DeWitt, Michael
thimotei/legacy_ct_modelling: Final version. (2023)
Abbott, Sam; Russell, Timothy W.; Hellewell, Joel; Kucharski, Adam J.
Dynamics of SARS-CoV-2 infection over two epidemic waves in Manaus, Brazil: a serological study of seven thousand blood donors. (2024)
Alexander, Neal; Dye, Christopher; Busch, Michael P.; Buss, Lewis; Prete Jr, Carlos A.; Brady, Oliver J.; Mee, Paul; Abrahim, Claudia M. M.; Crispim, Myuki A. E.; da Costa, Allyson G.; Salomon, Tassila; Mayaud, Philippe; Oikawa, Márcio K.; Faria, Nuno; Sabino, Ester C.
toshiakiasakura/polio_environmental_surveillance. (2025)
Asakura, Toshiaki R.
Association between HTLV-1/2 infection and COVID-19 severity in a migrant Shipibo-Konibo population in Lima, Peru: Database and dictionary. (2024)
Avila Dextre, Fátima; Morales Álvarez, Bryan; Aguirre Castañeda, Paulo; Alva, Isaac Efrain; López, Giovanni; Schwalb, Alvaro; Gotuzzo, Eduardo
epichains: Simulating and Analysing Transmission Chain Statistics Using Branching Process Models. (2024)
Azam, James M.; Funk, Sebastian; Finger, Flavio; Kamvar, Zhian N.; Gruson, Hugo; Mané, Karim; Gupte, Pratik; Lambert, Joshua W.
Data and code from: Estimating the burden of dengue and the impact of release of wMel Wolbachia infected mosquitoes in Indonesia: a modelling study. (2019)
Brady, Oliver J.
obrady/CATI_Vietnam. (2024)
Brady, Oliver J.
Transcripts of the COVID-19-related material from the focus group discussions and in-depth interviews. (2025)
Carwile, Madeline E.; Jain, Komal; Dauphinais, Madolyn R.; Narasimhan, Prakash Babu; Maloomian, Kimberly; Rajaram, Manju; Cintron, Chelsie; Mcquaid, C. Finn; Locks, Lindsey M.; Sabin, Lora L.; Lakshminarayanan, Subitha; Sinha, Pranay
anastasiachtz/COMMAND_stan/. (2019)
Chatzilena, Anastasia; Van Leeuwen, Edwin
lshtm-tbmg/tbmod-pub-funding-impacts. (2025)
Clark, Rebecca
lshtm-tbmg/tbmod-pub-undernutrition. (2024)
Clark, Rebecca
epiverse-trace/serofoi. (2024)
Domínguez, Nicolás Torres; Gruson, Hugo; Pavlich-Mariscal, Jaime; Gomez, Geraldine; Gámez López, Miguel Enrique; Cucunubá, Zulma M.; tracelac; Hartgerink, Chris; Azam, James; ben18785
Wastewater surveillance overcomes socio-economic limitations of laboratory-based surveillance when monitoring disease transmission: the South African experience during the COVID-19 pandemic. (2025)
Els, Fiona; Maree, Gillian; Naidoo, Yashena; Naidoo, Laven; Mahamuza, Phemelo; Macheke, Mokgaetji; Ndlovu, Nkosenhle; Iwu-Jaja, Chinwe; Taukobong, Setshaba; Maposa, Sibonginkosi; O'reilly, Kathleen M.; Yousif, Mukhlid; McCarthy, Kerrigan; Rachida, Said
DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. (2023)
Etienne, Rampal S.; Valente, Luis; Phillimore, Albert B.; Haegeman, Bart; Lambert, Joshua W.; Santos Neves, Pedro; Xie, Shu; Bilderbeek, Richèl J.C.; Hildenbrandt, Hanno; Hauffe, Torsten; Laudanno, Giovanni; Kristensen, Nadiah; Scherrer, Raphael
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.
Data and R code to accompany 'Compound and cascading effects of climatic extremes on dengue outbreak risk in the Caribbean: an impact-based modelling framework with long-lag and short-lag interactions'. (2025)
Fletcher, Chloe; Moirano, Giovenale; Alcayna, Tilly; Rollock, Leslie; Van Meerbeeck, Cédric J; Mahon, Roche; Trotman, Adrian; Boodram, Laura-Lee; Browne, Tia; Best, Sabu; Lührsen, Daniela; Díaz, Avriel R; Dunbar, Willy; Lippi, Catherine A; Ryan, Sadie J; Colón-González, Felipe J; Stewart-Ibarra, Anna M; Lowe, Rachel
Data and R code to accompany 'Compound and cascading effects of climatic extremes on dengue outbreak risk in the Caribbean: an impact-based modelling framework with long-lag and short-lag interactions'. (2025)
Fletcher, Chloe; Moirano, Giovenale; Alcayna, Tilly; Rollock, Leslie; Van Meerbeeck, Cédric J; Mahon, Roché; Trotman, Adrian; Boodram, Laura-Lee; Browne, Tia; Best, Sabu; Lührsen, Daniela; Diaz, Avriel R; Dunbar, Willy; Lippi, Catherine A; Ryan, Sadie J; Colón-González, Felipe J; Stewart-Ibarra, Anna M; Lowe, Rachel
TheYongjinChoi/NYS-COVID19-Disparities-Survey. (2021)
Fox, Ashley; Choi, Yongjin
lucy-gf/imd-covid. (2024)
Goodfellow, Lucy
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.
S1 Data for: "Impacts of climate change on diarrhoeal disease hospitalisations: How does the global warming targets of 1.5–2°C affect Dhaka, Bangladesh?". (2024)
Haque, Farhana; Lampe, Fiona C.; Hajat, Shakoor; Stavrianaki, Katerina; Hasan, S. M. Tafsir; Faruque, A. S. G.; Ahmed, Tahmeed; Jubayer, Shamim; Kelman, Ilan
numberize: Convert Words to Numbers in Multiple Languages. (2024)
Hartgerink, Chris; Lambert, Joshua W.; Mané, Karim; Gruson, Hugo; Ahadzie, Bankole
opensafely/openprompt-vaccine-long-covid. (2023)
Henderson, Alasdair D; Butler-Cole, Ben FC; Wiedemann, Milan; Evans, David; Smith, Rebecca
dchodge/nambcea. (2022)
Hodgson, David
seroanalytics/serojump. (2025)
Hodgson, David
Assessing the impact of the 2018 Changchun Changsheng vaccine incident on childhood vaccination in China. (2023)
Hou, Zhiyuan; Lai, Xiaozhen; Liu, Yang; Jit, Mark; Larson, Heidi; Hai, Fang
Social Mobilization Action Consortium: Community Engagement data from the 2014-2016 Sierra Leone Ebola outbreak. (2019)
Hébert-Dufresne, Laurent; Althouse, Benjamin M.; Skrip, Laura; Bedson, Jamie
Measles Seroprevalence Systematic Review and Bias Assessment 1962-2019. (2024)
Institute for Health Metrics and Evaluation (IHME); London School of Hygiene and Tropical Medicine
ZeinaJamaluddine/gaza_mortality_capture_recapture. (2024)
Jamaluddine, Zeina; Checchi, Francesco
CoMix data (last round in BE, CH, NL and UK). (2024)
Jarvis, Christopher I.; Coletti, Pietro; Backer, Jantien; Munday, James D.; Faes, Christel; Beutels, Philippe; Althaus, Christian; Low, Nicola; Wallinga, Jacco; Hens, Niel; Edmunds, John
Model for "Estimating the health and macroeconomic burdens of tuberculosis in India, 2021-2040". (2024)
Jensen, Henning Tarp
folder_zip
kaitejohnson/School_reopening. (2020)
Johnson, Kaitlyn E.
wastewater-informed-covid-forecasting. (2024)
Johnson, Kaitlyn E.
epinowcast/baselinenowcast-paper. (2025)
Johnson, Kaitlyn E.; Abbott, Sam; Bracher, Johannes
EpiFusion Analysis Framework Software Article. (2025)
Judge, Ciara
ciarajudge/EpiFusion. (2024)
Judge, Ciara
ciarajudge/EpiFusion: EpiFusionv1.0. (2025)
Judge, Ciara
ciarajudge/EpiFusionUtilities. (2025)
Judge, Ciara
ciarajudge/EpiFusion_PublicationRepo. (2024)
Judge, Ciara
ciarajudge/EpiFusion_Vignettes: F1000 Article Release. (2025)
Judge, Ciara
Replication Data for: Age-dependent acquisition of IgG antibodies to Shigella serotypes – a retrospective analysis of sero-prevalence in Kenyan children. (2023)
Kapulu, Melissa C; Muthumbi, Esther; Otieno, Edward; Rossi, Omar; Ferruzzi, Pietro; Necchi, Francesca; Acquaviva, Alessandra; Martin, Laura B; Orindi, Benedict; Mwai, Kennedy; Mwanzu, Alfred; Bigogo, Godfrey M; Verani, Jennifer R; Mbae, Cecilia; Nyundo, Christopher; Agoti, Charles N; Nakakana, Usman Nasir; Conti, Valentino; Bejon, Philip; Kariuki, Samuel; Scott, J Anthony G; Micoli, Francesca; Podda, Audino
ckim0509/amr_cost. (2025)
Kim, Chaelin
kingaa/pomp. (2025)
King, Aaron A; O'Dea, Eamon; Asfaw, Kidus; Wheeler, Jesse; Breto, Carles; Ionides, Edward; Akinshin, Andrey; Voipio, Timo; Funk, Sebastian
fkrauer/RSV-VACC-DE. (2024)
Krauer, Fabienne
joshwlambert/DAISIEprepExtra. (2024)
Lambert, Joshua W.
DAISIEmainland. (2024)
Lambert, Joshua W.; Bilderbeek, Richèl; Santos Neves, Pedro
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
epiparameterDB: Database of Epidemiological Parameters. (2024)
Lambert, Joshua W.; Kucharski, Adam J.; Tamayo, Carmen
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
AR.IA App all datasets. (2019)
Leclerc, Quentin J.; Naylor, Nichola R.; Aiken, Alexander M.; Coll, Francesc; Knight, Gwenan M.
AR.IA App drug breakdown. (2019)
Leclerc, Quentin J.; Naylor, Nichola R.; Aiken, Alexander M.; Coll, Francesc; Knight, Gwenan M.
AR.IA App economic data. (2019)
Leclerc, Quentin J.; Naylor, Nichola R.; Aiken, Alexander M.; Coll, Francesc; Knight, Gwenan M.
Database for pay-it-forward to reduce HPV vaccine delay and increase uptake. (2025)
Li, Jing; Li, Yifan; Qin, Chuanyu; He, Yu; Lu, Haidong; Xie, Yewei; Ong, Jason J.; Lu, Yajiao; Yang, Ying; Yang, Fan; Du, Heng; Gong, Wenfeng; Zou, Fei; Larson, Heidi J.; Jit, Mark; Lin, Leesa; Smith, Jennifer S.; Geng, Elvin H.; Xu, Dong; Tang, Weiming; Tang, Shenglan; Tucker, Joseph D.; Wu, Dan
ahyoung-lim/Arbo_riskmaps_public. (2025)
Lim, Ahyoung
OpenDengue/master-repo. (2024)
Lim, Ahyoung; Brady, Oliver J
Data and code from "The overlapping global distribution of dengue, chikungunya, Zika and yellow fever". (2025)
Lim, Ahyoung; Brady, Oliver J.
Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. (2023)
London School of Hygiene & Tropical Medicine
Data and R-code to accompany 'Modelling the impact of climate and the environment on the spatiotemporal dynamics of Lyme borreliosis in Germany'. (2025)
Lotto Batista, Martín; Carvalho, Bruno; Gibb, Rory; Solaraju-Murali, Balakrishnan; Flasche, Stefan; Castell, Stefanie; Ghozzi, Stéphane; Lowe, Rachel
Contexts, Facilitators, and Barriers to Integrating Portable Genomic Sequencing in Outbreak Response: A Qualitative Study from Coastal Kenya. (2025)
Makena, Evelyn; Wang, Ling; Okanda, Dorcas; Carter, Daniel; Leggio, Cristina; Odhiambo, Juliet; Munyoki, Catherine; Abdalla, Abbbas; Agoti, Charles N.; Gatie, Victor; Adam, Ahmed; Wasike, Hildergard; Kassim, Salim; Onwonga, Vera; Robaa, Abdi; Ndia, Millicent; Kiiru, John; Kingwara, Leonard; Madada, Rukia; Lang'at, Paul; Hargreaves, James R.; Hughes, Gwenda; Eunice Wangeci, Kagucia; Haque, Farhana; Githinji, George
cleanepi: Clean and Standardize Epidemiological Data. (2024)
Mané, Karim; Jombart, Thibaut; Bah, Bubacarr; Ahadzie, Bankolé; Mohammed, Nuredin; Degoot, Abdoelnaser M.; Gruson, Hugo; Gupte, Pratik R.; Azam, James M.; Lambert, Joshua W.; 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.
Household fuel use and adverse pregnancy outcomes. (2024)
Mezmur, Haymanot; Tefera, Maleda; Jemal, Mohamed; Kahsay, Bersabeh; Assefa, Nega
ghr/wnv_casecrossover. (2024)
Moirano, Giovenale; Fletcher, Chloe; Semenza, Jan C.; Lowe, Rachel
NikkiR08/AMR-UCR. (2025)
Naylor, Nichola R.
NikkiR08/VAF_AMR_EconBurden. (2025)
Naylor, Nichola R.
rsetienne/DAISIE. (2023)
Neves, Pedro Santos; Lambert, Joshua W.; Etienne, Rampal S.; Bilderbeek, Richel; Xie, Shu; Valente, Luis; Hildenbrandt, H; Scherrer, Raphaël; Yangshen0325
esnightingale/vl-collection-methods-xm. (2023)
Nightingale, Emily
esnightingale/vl-disaggregation. (2024)
Nightingale, Emily
esnightingale/vl-spatial-diagnosis-delay. (2025)
Nightingale, Emily
enilles1/immunoepidemiology. (2024)
Nilles, Eric J.; Kucharski, Adam J.
Interview Questions for WW Dashboards. (2024)
O'reilly, Kathleen M.
tjhladish/AbcSmc. (2023)
Pearson, Carl A. B.; Hladish, Thomas
tjhladish/dengue-abm. (2023)
Pearson, Carl A. B.; Hladish, Thomas; Pillai, Alexander N.; Chao, Dennis
cmmid/comix_mobility. (2025)
Prestige, Em
rachaelpung/temporal_networks. (2024)
Pung, Rachael; Kucharski, Adam J.; Firth, Josh; Russell, Timothy W.; Rogers, Tim; Lee, Vernon
alexandrasrichards/natural_history_tb_disease. (2023)
Richards, Alexandra S
alxsrobert/measles_england_sir. (2024)
Robert, Alexis; Suffel, Anne Marie
S1 Table for "Assessing vulnerability for future Zika virus outbreaks using seroprevalence data and environmental suitability maps". (2024)
Roell, Yannik; Pezzi, Laura; Lozano-Parra, Anyela; Olson, Daniel; Messina, Jane; Quandelacy, Talia; Drexler, Jan Felix; Brady, Oliver; Karimzadeh, Morteza; Jaenisch, Thomas
Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants". (2023)
Russell, Timothy W.
thimotei/legacy_nAb_kinetics. (2024)
Russell, Timothy W.; Kucharski, Adam J.
Data from: Global yellow fever vaccination coverage from 1970 to 2016: an adjusted retrospective analysis. (2018)
Shearer, Freya M; Moyes, Catherine L; Pigott, David M; Brady, Oliver J.; Marinho, Fatima; Deshpande, Aniruddha; Longbottom, Joshua; Browne, Annie J; Kraemer, Moritz U G; O'reilly, Kathleen M.; Hombach, Joachim; Yactayo, Sergio; de Araújo, Valdelaine E M; da Nóbrega, Aglaêr A; Mosser, Jonathan F; Stanaway, Jeffrey D; Lim, Stephen S; Hay, Simon I; Golding, Nick; Reiner, Robert C
Improving modelling for epidemic responses: reflections. (2023)
Sherratt, Katharine; Abbott, Sam; Carnegie, Anna; Liu, Yang
epiforecasts/eval-by-method. (2025)
Sherratt, Katharine; Funk, Sebastian
epiforecasts/multi-model-information: Publication release. (2024)
Sherratt, Katharine; Funk, Sebastian
Dataset for "Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity". (2020)
Simpson, Kelly M J; Mor, Siobhan M; Ward, Michael P; Collins, Julie; Flint, James; Hill-Cawthorne, Grant A; El Ghany, Moataz Abd
Data collection tools and dataset from tracer study of Q4D Lab, a locally developed and owned coding and biostatistics program in Liberia. (2024)
Skrip, Laura; Barcon, Snoyonoh; Davis, George; Yeabah, Trokon O.; Kromah, Mulbah
Structural and social factors affecting COVID-19 vaccine uptake among healthcare workers and older people in Uganda: A qualitative analysis. Data file. (2024)
Sliversteri, Sande; Ssali, Agnes; Bahemuka, Ubaldo M.; Nsubuga, Denis; Muwanga, Moses; Nsereko, Chris; Ssemwanga, Edward; Robert, Asaba; Seeley, Janet; Elliott, Alison; Ruzagira, Eugene
tomsumner/Timing_of_vaccination. (2025)
Sumner, Tom
katietiley/Wolbachia_TPP_PPC. (2024)
Tiley, Katherine
Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland. Data and analyses. (2024)
Van zandvoort, Kevin; Hassan, Abdirahman Ibrahim; Bobe, Mohamed Omer; Pell, Casey L; Ahmed, Mohamed Saed; Ortika, Belinda D; Ibrahim, Saed; Abdi, Mohamed Ismail; Karim, Mustapha A; Eggo, Rosalind M.; Yusuf, Sulieman; Hinds, Jason; Soleman, Saeed Mohamood; Cummings, Rachael; Mcgowan, Catherine R; Mulholland, E Kim; Satzke, Catherine; Hergeeye, Mohamed Abdi; Checchi, Francesco; Flasche, Stefan
gwenknight/ecdc_data_age_sex. (2024)
Waterlow, Naomi; Knight, Gwen
xiangfstats/GenieR: A final release. (2019)
Xiang, Fei; Frost, Simon