LSHTM Organisational Structure (3724)

Faculty of Epidemiology and Population Health (2426)

Dept of Infectious Disease Epidemiology (-2023) (826) Data Creators(s) Title Item Type No Grouping

A

vaccine-impact/epi_covid. (2020) Abbas, Kaja M.

seabbs/getTBinR. (2020) Abbott, Sam, Bekker-Nielsen Dunbar, Maria, Smith, Arfon

Collated Results of the National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Tests, Hospital Admissions and Deaths. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

Continent Summary Reproduction Number (R) Based on Reported Deaths. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National Reproduction Number (R) Based on Reported Cases. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National Reproduction Number (R) Estimates Based on Reported Deaths. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results. (2020) Abbott, Sam, Bennett, Christopher, Hickson, Joe, Allen, Jamie, Sherratt, Katharine, Funk, Sebastian

epiforecasts/EpiSoon. (2020) Abbott, Sam, Bosse, Nikos, DeWitt, Michael, Rau, Andrea, Chateigner, Aurelien, Mareschal, Sylvain, Hellewell, Joel

idmodelr: Infectious Disease Model Library and Utilities. (2020) Abbott, Sam, Endo, Akira

Pathways to Low Fertility. (2020) Abbott, Sam, Funk, Sebastian, Munday, James D., Hellewell, Joel

Wuhan Seeding Vs Transmission. (2020) Abbott, Sam, Funk, Sebastian, Munday, James D., Hellewell, Joel

epiforecasts/WuhanSeedingVsTransmission: Resubmission to Wellcome Open Research. (2020) Abbott, Sam, Funk, Sebastian, Munday, James D., Hellewell, Joel

seabbs/CovidInterventionReview: CC0 license. (2020) Abbott, Sam, Gaythorpe, Katy A.M., Imai, Natsuko, Liu, Yang

epiforecasts/covid: Submission release. (2020) Abbott, Sam, Sherratt, Katharine, Funk, Sebastian, Hellewell, Joel

epiforecasts/NCoVUtils. (2020) Abbott, Sam, Sherratt, Katharine, Gibbs, Hamish, Finger, Flavio, Campbell, Paul, Hellewell, Joel, Barks, Patrick, Meakin, Sophie, Lee, Haze

Dataset: Seasonality and immunity to laboratory-confirmed seasonal coronaviruses (HCoV-NL63, HCoV-OC43, and HCoV-229E): results from the Flu Watch cohort study. (2020) Aldridge, Robert W., Lewer, Dan, Beale, Sarah, Johnson, Anne M., Zambon, Maria, Hayward, Andrew C., Fragaszy, Ellen

B

Household Transmission of Seasonal Coronavirus Infections: Results from the Flu Watch cohort study. (2020) Beale, Sarah, Lewer, Dan, Aldridge, Robert W., Johnson, Anne M., Zambon, Maria, Hayward, Andrew, Fragaszy, Ellen

Parents’ and guardians’ views on the acceptability of a future COVID-19 vaccine for themselves and their children: cross-sectional survey and qualitative interview data. (2020) Bell, Sadie, Clarke, Richard, Mounier-Jack, Sandra, Paterson, Pauline

Data for: "Boosting understanding of Lassa Fever virus epidemiology: field testing a novel assay to identify past Lassa Fever virus infection in blood and oral fluids of survivors and unexposed controls in Sierra Leone". (2020) Bower, Hilary, Akpogheneta, Onome, Kanneh, Zainab, Jusu, Brima, Kanneh, Lansana, Alhasan, Foday, Gbakie, Michael, Shieffelin, John description

C

Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil. (2020) Candido, Darlan S., Claro, Ingra M., de Jesus, Jaqueline G., Souza, William M., Moreira, Filipe R. R., Dellicour, Simon, Mellan, Thomas A., du Plessis, Louis, Pereira, Rafael H. M., Sales, Flavia C. S., Manuli, Erika R., Thézé, Julien, Almeida, Luiz, Menezes, Mariane T., Voloch, Carolina M., Fumagalli, Marcilio J., Coletti, Thaís M., da Silva, Camila A. M., Ramundo, Mariana S., Amorim, Mariene R., Hoeltgebaum, Henrique H., Mishra, Swapnil, Gill, Mandev S., Carvalho, Luiz M., Buss, Lewis F., Prete, Carlos A., Ashworth, Jordan, Nakaya, Helder I., Peixoto, Pedro S., Brady, Oliver J., Nicholls, Samuel M., Tanuri, Amilcar, Rossi, Átila D., Braga, Carlos K.V., Gerber, Alexandra L., de C. Guimarães, Ana Paula, Gaburo, Nelson, Alencar, Cecila Salete, Ferreira, Alessandro C.S., Lima, Cristiano X., Levi, José Eduardo, Granato, Celso, Ferreira, Giulia M., Francisco, Ronaldo S., Granja, Fabiana, Garcia, Marcia T., Moretti, Maria Luiza, Perroud, Mauricio W., Castiñeiras, Terezinha M. P. P., Lazari, Carolina S., Hill, Sarah C., de Souza Santos, Andreza Aruska, Simeoni, Camila L., Forato, Julia, Sposito, Andrei C., Schreiber, Angelica Z., Santos, Magnun N. N., de Sá, Camila Zolini, Souza, Renan P., Resende-Moreira, Luciana C., Teixeira, Mauro M., Hubner, Josy, Leme, Patricia A. F., Moreira, Rennan G, Nogueira, Maurício L., Ferguson, Neil M, Costa, Silvia F., Proenca-Modena, José Luiz, Vasconcelos, Ana Tereza R., Bhatt, Samir, Lemey, Philippe, Wu, Chieh-Hsi, Rambaut, Andrew, Loman, Nick J., Aguiar, Renato S., Pybus, Oliver G., Sabino, Ester C., Faria, Nuno Rodrigues

Evolution and epidemic spread of SARS-CoV-2 in Brazil. (2020) Candido, Darlan S., Claro, Ingra M., de Jesus, Jaqueline G., Souza, William M., Moreira, Filipe R. R., Dellicour, Simon, Mellan, Thomas A., du Plessis, Louis, Pereira, Rafael H. M., Sales, Flavia C. S., Manuli, Erika R., Thézé, Julien, Almeida, Luiz, Menezes, Mariane T., Voloch, Carolina M., Fumagalli, Marcilio J., Coletti, Thaís M., da Silva, Camila A. M., Ramundo, Mariana S., Amorim, Mariene R., Hoeltgebaum, Henrique H., Mishra, Swapnil, Gill, Mandev S., Carvalho, Luiz M., Buss, Lewis F., Prete, Carlos A., Ashworth, Jordan, Nakaya, Helder I., Peixoto, Pedro S., Brady, Oliver J., Nicholls, Samuel M., Tanuri, Amilcar, Rossi, Átila D., Braga, Carlos K.V., Gerber, Alexandra L., de C. Guimarães, Ana Paula, Gaburo, Nelson, Alencar, Cecila Salete, Ferreira, Alessandro C.S., Lima, Cristiano X., Levi, José Eduardo, Granato, Celso, Ferreira, Giulia M., Francisco, Ronaldo S., Granja, Fabiana, Garcia, Marcia T., Moretti, Maria Luiza, Perroud, Mauricio W., Castiñeiras, Terezinha M. P. P., Lazari, Carolina S., Hill, Sarah C., de Souza Santos, Andreza Aruska, Simeoni, Camila L., Forato, Julia, Sposito, Andrei C., Schreiber, Angelica Z., Santos, Magnun N. N., de Sá, Camila Zolini, Souza, Renan P., Resende-Moreira, Luciana C., Teixeira, Mauro M., Hubner, Josy, Leme, Patricia A. F., Moreira, Rennan G, Nogueira, Maurício L., Ferguson, Neil M, Costa, Silvia F., Proenca-Modena, José Luiz, Vasconcelos, Ana Tereza R., Bhatt, Samir, Lemey, Philippe, Wu, Chieh-Hsi, Rambaut, Andrew, Loman, Nick J., Aguiar, Renato S., Pybus, Oliver G., Sabino, Ester C., Faria, Nuno Rodrigues

Dengue and microcephaly cases in Brazil used in Carvalho et al. (2020) Carvalho, Marilia Sá, Freitas, Laís Picinini, Cruz, Oswaldo Gonçalves, Brasil, Patrícia, Bastos, Leonardo Soares

AZ-SMC Trial - School child parasitaemia dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ogobara, Jean-Bosco, Greenwood, Brian description

AZ-SMC Trial - In vivo treatment efficacy dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco description

AZ-SMC Trial - Cross-sectional dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco, Greenwood, Brian description

AZ-SMC Trial - Drug administration dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco, Greenwood, Brian description

AZ-SMC Trial - Person-Time dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco, Greenwood, Brian description

AZ-SMC Trial - Weekly survey dataset. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco, Greenwood, Brian description

Data repository for AZ-SMC - a trial of seasonal malaria chemoprevention combined with azithromycin in African children. (2020) Chandramohan, Daniel, Dicko, Alassane, Zongo, Issaka, Sagara, Issaka, Cairns, Matthew, Kuepfer, Irene, Diarra, Modibo, Barry, Amadou, Tapily, Amadou, Nikiema, Frederic, Yerbanga, Serge, Coumare, Samba, Thera, Ismaila, Traore, Abdourhamane, Milligan, Paul, Tinto, Halidou, Doumbo, Ogobara, Ouedraogo, Jean-Bosco, Greenwood, Brian

francescochecchi/aden_covid. (2020) Checchi, Francesco

cmmid/pcr_test_trace. (2020) Clifford, Samuel, Quilty, Billy

cmmid/travel_screening_strategies. (2020) Clifford, Samuel, Quilty, Billy J., Russell, Timothy W., Liu, Yang, Chan, Yung-Wai Desmond, Pearson, Carl A. B., Eggo, Rosalind M., Endo, Akira, CMMID COVID-19 Working Group, Flasche, Stefan, Edmunds, W. John

Effectiveness of airport-based interventions at detecting travellers and delaying an outbreak of COVID-19 (formerly 2019-nCoV). (2020) Clifford, Samuel, Quilty, Billy, CMMID nCoV working group, Pearson, Carl, Flasche, Stefan, Eggo, Rosalind M.

ptti/ptti: Modelling the health and economic impacts of different testing and tracing strategies for COVID-19 in the UK. (2020) Colbourn, Tim, Waites, William, Manheim, David, Sturniolo, Simone, Kerr, Cliff C., Panovska-Griffiths, Jasmina, Colbourn, Greg

CoMix social contact data (Belgium). (2020) Coletti, Pietro, Wambua, James, Gimma, Amy, Willem, Lander, Vercruysse, Sarah, Vanhoutte, Bieke, Jarvis, Christopher I., Van zandvoort, Kevin, Edmunds, W. John, Beutels, Philippe, Hens, Niel

Social contact data from CoMix survey (Belgium). (2020) Coletti, Pietro, Wambua, James, Gimma, Amy, Willem, Lander, Vercruysse, Sarah, Vanhoutte, Bieke, Jarvis, Christopher I, Van Zandvoort, Kevin, Edmunds, John, Beutels, Philippe, Hens, Niel

Co-morbidities (malnutrition, diabetes, anaemia, HIV, hypertension) and quality of life in persons with tuberculosis in the Philippines. (2020) Cox, Sharon E., White, Laura V., Faguer, Benjamin, Edwards, Tansy, Lee, Nathaniel, Solon, Juan, Ariyoshi, Koya, Castro, Mary Christine, Saludar, Naomi R., Saito, Nobuo, Calapis, Rugaiya W

D

cmmid/covid-age. (2020) Davies, Nicholas G.

nicholasdavies/covidm-alpha. (2020) Davies, Nicholas G.

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

Additional file 3 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. (2020) Dawa, Jeanette, Emukule, Gideon O., Barasa, Edwine, Widdowson, Marc Alain, Anzala, Omu, Van Leeuwen, Edwin, Baguelin, Marc, Chaves, Sandra S., Eggo, Rosalind M.

Additional file 1 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. (2020) Dawa, Jeanette, Emukule, Gideon O., Barasa, Edwine, Widdowson, Marc Alain, Anzala, Omu, Van leeuwen, Edwin, Baguelin, Marc, Chaves, Sandra S., Eggo, Rosalind M.

E

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

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

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

Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK. (2020) Enria, Luisa, Waterlow, Naomi, Rogers, Nina, Brindle, Hannah, Lal, Sham, Eggo, Rosalind M., Lees, Shelley, Roberts, Chrissy

Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Qualitative Data. (2020) Enria, Luisa, Waterlow, Naomi, Rogers, Nina, Brindle, Hannah, Lal, Sham, Eggo, Rosalind M., Lees, Shelley, Roberts, Chrissy description

F

Global Retinoblastoma Presentation 2017 data, on behalf of the Global Retinoblastoma Study Group. (2020) Fabian, Ido Didi, Stacey, Andrew, Foster, Allen, Kivelä, Tero T., Munier, Francis, Cassoux, Nathalie, Bowman, Richard

Data set for the comparison of the performance of QuantiFERON-TB Gold Plus with QuantiFERON-T Gold in-tube among highly TB exposed gold miners in South Africa. (2020) Fielding, Katherine description

StefanFlasche/Pneumo_Trans_Inf. (2020) Flasche, Stefan

Wasting prevention CHNRI dataset. (2020) Frison, Severine

sbfnk/rbi.helpers. (2020) Funk, Sebastian, Finger, Flavio

G

RtD3. (2020) Gibbs, Hamish, Abbott, Sam, Funk, Sebastian

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

Systematic analysis of infectious disease outcomes by age. (2020) Glynn, Judith grid_on

CLEAN study dataset. (2020) Gon, Giorgia grid_on

Data for "HANDS project - Hand-hygiene of Attendants for Newborn Deliveries and Survival". (2020) Gon, Giorgia description

H

cmmid/ringbp. (2020) Hellewell, Joel

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

timcdlucas/ringbp: Code as used in the paper "Engagement and adherence trade-offs for SARS-CoV-2 contact tracing". (2020) Hellewell, Joel, Lucas, Tim, Davis, Emma, Abbott, Sam, Gimma, Amy, Thompson, Robin

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.

The Nairobi Early Childcare in Slums (NECS) Study. (2020) Hughes, Robert, Kitsao-Wekulo, Patricia, Bhopal, Sunil, Kimani-Murage, Elizabeth, Hill, Zelee, Kirkwood, Betty

J

Inferring COVID-19 cases from recent death. (2020) Jombart, Thibaut, Abbott, Sam, Gimma, Amy, Van zandvoort, Kevin, Jarvis, Christopher

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

thibautjombart/covid19_bed_occupancy: Second major release. (2020) Jombart, Thibaut, Clifford, Samuel, Pearson, Carl A. B. Pearson, Rees, Eleanor, Nightingale, Emily, Procter, Simon, Knight, Gwen

adegenet: Exploratory Analysis of Genetic and Genomic Data. (2020) Jombart, Thibaut, Kamvar, Zhian N., Collins, Caitlin, Luštrik, Roman, Beugin, Marie-Pauline, Knaus, Brian J, Solymos, Peter, Mikryukov, Vladimir, Schliep, Klaus, Maié, Tiago, Morkovsky, Libor, Ahmed, Ismail, Cori, Anne, Calboli, Federico, Ewing, RJ, Michaud, Frédéric, DeCamp, Rebecca, Courtiol, Alexandre

projections: Project Future Case Incidence. (2020) Jombart, Thibaut, Nouvellet, Pierre, Bhatia, Sangeeta, Kamvar, Zhian N., Taylor, Tim, Ghozzi, Stephane

trendbreaker 0.1.0: Detect Changes in Temporal Trends. (2020) Jombart, Thibaut, Schumacher, Dirk

K

Effect of repeat BCG on all-cause mortality: a double-blind randomised placebe-controlled trial in Malawi. (2020) Kanjala, Chifundo, Glynn, Judith R., Fine, Paul

skissler/haslemere. (2020) Kissler, Stephen M., Klepac, Petra, Tang, Maria, Conlan, Andrew J.K., Gog, Julia R.

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

sysbio-curie/exact-stoch-log-mod. (2020) Koltai, Mihály

Evaluating the informed push model intervention in Senegal. (2020) Krug, Catarina, Lynch, Caroline, Cavallaro, Francesca, Wong, Kerry folder_zip

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.

L

Every Newborn INDEPTH (EN-INDEPTH) Study - Additional Materials. (2020) Lawn, Joy E., Waiswa, Peter, Waiswa, Joseph Akuze, Kwesiga, Doris, Blencowe, Hannah, Baschieri, Angela, Gordeev, Vladimir S., EN-INDEPTH Collaborator Group grid_on

COVID-SCORE: A global survey to assess public perceptions of government responses to COVID-19 (COVID-SCORE-10). (2020) Lazarus, Jeffrey V., Ratzan, Scott, Palayew, Adam, Billari, Francesco C., Binagwaho, Agnes, Kimball, Spencer, Larson, Heidi J., Melegaro, Alessia, Rabin, Kenneth, White, Trenton M., El-Mohandes, Ayman

COVID19 settings of transmission - collected reports database. (2020) Leclerc, Quentin J., Fuller, Naomi M., Knight, Lisa E., Funk, Sebastian, Knight, Gwenan M.

qleclerc/nhs_pathways_report. (2020) Leclerc, Quentin J., Nightingale, Emily, Abbott, Sam

tsleng93/SocialBubble: Social Bubble (including density dependence). (2020) Leng, Trystan, Flasche, Stefan

The impact of insecticide treated curtains on dengue virus transmission: A cluster randomized trial in Iquitos, Peru. (2020) Lenhart, Audrey, Morrison, Amy C., Paz-Soldan, Valerie A., Forshey, Brett M., Cordova-Lopez, Jhonny J., Astete, Helvio, Elder, John P., Sihuincha, Moises, Gotlieb, Esther E., Halsey, Eric S., Kochel, Tadeusz J., Scott, Thomas W., Alexander, Neal, McCall, Philip J.

Social contact data for Hong Kong. (2020) Leung, Kathy, Jit, Mark, Lau, Eric H. Y., Wu, Joseph T.

yangclaraliu/COVID19_NPIs_vs_Rt. (2020) Liu, Yang

yangclaraliu/2019nCoV_proportion_asym: WOR Submission. (2020) Liu, Yang, Funk, Sebastian, Flasche, Stefan

yangclaraliu/covid_surveillance_strategy: WOR Submission. (2020) Liu, Yang, Gong, Wenfeng, Clifford, Samuel, Sundaram, Maria E, CMMID COVID-19 Working Group, Jit, Mark, Flasche, Stefan, Klepac, Petra

M

Clinical risk groups for Pneumococcal Polysaccharide Vaccine. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara

Immunisation risk group - Cardiac disease. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara code

Immunisation risk group - Diabetes. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara code

Immunisation risk group - chronic kidney disease. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara description

Immunisation risk group - chronic respiratory disease without asthma. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara description

Immunisation risk group - liver disease. (2020) Mcdonald, Helen, Evans, Dai, Clay, Simon, Edelstein, Michael, Thomas, Sara description

Data_Sheet_2_Natural Killer Cells Dampen the Pathogenic Features of Recall Responses to Influenza Infection. (2020) Mooney, Jason P., Qendro, Tedi, Keith, Marianne, Philbey, Adrian W., Groves, Helen T., Tregoning, John S., Goodier, Martin R., Riley, Eleanor M.

SONA Project - Anxiety Disorders and Asthma Dataset. (2020) Mpairwe, Harriet, Webb, Emily html

SONA project - Risk factors for allergy-related diseases among schoolchildren in Uganda. (2020) Mpairwe, Harriet, Webb, Emily description

The patient costs of care for those with TB and HIV: a cross-sectional study from South Africa. (2020) Mudzengi, Don, Sweeney, Sedona, Hippner, Piotr, Kufa, Tendesayi, Fielding, Katherine, Grant, Alison D., Churchyard, Gavin J., Vassall, Anna description

N

Mongolia MDR-TB contact e-registry ODK 2017. (2020) Naker, Kush

Effect of intensive versus standard anthelminthic treatment on growth and cognition among children living in a high Schistosoma mansoni transmission setting - Supporting Information. (2020) Nampijja, Margaret, Lubyayi, Lawrence, Tumusiime, Josephine, Nabulime, Juliet, Kizindo, Robert, Kabuubi, Prossy, Sanya, Richard E., Kabagenyi, Joyce, Akurut, Hellen, Muhangi, Lawrence, Webb, Emily L., Alcock, Katie, Elliott, Alison M., LaVIISWA Trial Team description

CLAN: Stata module to perform cluster-level analysis of cluster randomised trials. (2020) Nash, Stephen, Thompson, Jennifer, Leurent, Baptiste

COVID-19 length of hospital stay. (2020) Nightingale, Emily, Waterlow, Naomi, Clifford, Samuel, Rees, Eleanor

Supplementary files 2 and 3 for "Linking health facility data from young adults aged 18-24 years to longitudinal demographic data: Experience from The Kilifi Health and Demographic Surveillance System". (2020) Nyundo, Christopher, Doyle, Aoife M., Walumbe, David, Otiende, Mark, Kinuthia, Michael, Amadi, David, Jibendi, Boniface, Mochamah, George, Kihuha, Norbert, Williams, Thomas, Ross, David A., Bauni, Evasius

O

Replication Data for: Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data. (2020) Ojal, John, Brand, Samuel P. C., Were, Vincent, Okiro, Emelda A., Kombe, Ivy K., Mburu, Caroline, Aziza, Rabia, Ogero, Morris, Agweyu, Ambrose, Warimwe, George M., Uyoga, Sophie, Adetifa, Ifedayo M.O., Scott, J. Anthony G., Otieno, Edward, Ochola-Oyier, Lynette Isabella, Agoti, Charles N., Kasera, Kadondi, Amoth, Patrick, Mwangangi, Mercy, Aman, Rashid, Ng’ang’a, Wangari, Tsofa, Benjamin, Bejon, Philip, Barasa, Edwine, Keeling, Matt. J., Nokes, David James

The global scientific research response to the public health emergency of Zika virus infection. S1 Data. (2020) Oliveira, Juliane Fonseca de, Pescarini, Julia Moreira, Rodrigues, Moreno de Souza, Almeida, Bethania de Araujo, Henriques, Claudio Maierovitch Pessanha, Gouveia, Fabio Castro, Rabello, Elaine Teixeira, Matta, Gustavo Correa, Barreto, Mauricio L., Sampaio, Ricardo Barros

deworm3 Electronic Treatment Register. (2020) Oswald, William E., Kennedy, David S., Farzana, Jasmine, Kaliappan, Saravanakumar Puthupalayam, Atindegla, Eloic, Houngbégnon, Parfait, Chisambi, Alvin, Witek-mcmanus, Stefan, Galagan, Sean R., Emmanuel-Fabula, Mira, Gwayi-Chore, Marie-Claire, Legge, Hugo, Yard, Elodie, Kalua, Khumbo, Ibikounlé, Moudachirou, Ajjampur, Sitara Swarna Rao, Means, Arianna Rubin, Ásbjörnsdóttir, Kristjana H., Halliday, Katherine E., Walson, Judd L.

Replication Data for: Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. (2020) Otieno, Grieven P., Murunga, Nickson, Agoti, Charles N., Gallagher, Katherine E., Awori, Juliet O., Nokes, D. James

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pegas: Population and Evolutionary Genetics Analysis System. (2020) Paradis, Emmanuel, Kamvar, Zhian N., Jombart, Thibaut, Brian, Knaus, Frederic, Michaud

Projections of COVID-19 epidemics in LMIC countries. (2020) Pearson, Carl A. B., Van zandvoort, Kevin, Jarvis, Christopher I., Davies, Nicholas G., Thompson, Sam, Checchi, Francesco, Jit, Mark, Eggo, Rosalind M., LSHTM CMMID COVID-19 Working Group

Clinical codelist - Congenital malformation codes. (2020) Peppa, Maria, Thomas, Sara, Kempley, Steve, Mangtani, Punam description

HES diagnosis codelist - Congenital malformation codes. (2020) Peppa, Maria, Thomas, Sara, Kempley, Steve, Mangtani, Punam description

HES procedures codelist - Congenital malformation codes. (2020) Peppa, Maria, Thomas, Sara, Kempley, Steve, Mangtani, Punam code

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

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ruwanepi/Detection-analysis. (2020) Ratnayake, Ruwan

Additional file 2 of COVID-19 length of hospital stay: a systematic review and data synthesis. (2020) Rees, Eleanor M., Nightingale, Emily S., Jafari, Yalda, Waterlow, Naomi R., Clifford, Samuel, B. Pearson, Carl A., CMMID Working Group, Jombart, Thibaut, Procter, Simon R., Knight, Gwenan M.

geosocial-outbreaker: Integrating geographical and social contact data to reconstruct transmission chains. (2020) Robert, Alexis

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

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/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

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epiforecasts/rt-comparison-uk-public: v1.0.0. (2020) Sherratt, Katharine

Crimean-congo haemorrhagic fever virus detected in Rhipicephalus ticks feeding on cattle in an abattoir, Uganda. (2020) Stubbs, Sam

BILHIV acceptability dataset. (2020) Sturt, Amy, Bustinduy, Amaya, Phiri, Comfort description

tomsumner/Latency_Model_Comparison_Public. (2020) Sumner, Tom

Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic. (2020) Sun, Haoyang, Dickens, Borame L., Jit, Mark, Cook, Alex R., Carrasco, L. Roman

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deusthindwa/Electronic-Data-Capture-for-Large-Scale-Typhoid-Surveillance---STRATAA: edc. (2020) Thindwa, Deus, Oxford Vaccine Group, Mujadidi, Yama Farooq

COVID-19 risk group - Neurological disease codelist. (2020) Thomas, Sara description

Code lists for: "Social determinants of pertussis and influenza vaccine uptake in pregnancy: a national cohort study using electronic health records". (2020) Thomas, Sara

Influenza clinical risk groups 2017 version - Asthma. (2020) Thomas, Sara description

Influenza clinical risk groups 2017 version - Chronic cardiac conditions. (2020) Thomas, Sara description

Influenza clinical risk groups 2017 version - Chronic renal disease diagnoses. (2020) Thomas, Sara description

Influenza clinical risk groups 2017 version - Chronic respiratory disease (not asthma). (2020) Thomas, Sara description

Influenza clinical risk groups 2017 version - Diabetes. (2020) Thomas, Sara code

Influenza risk groups 2017 version - Chronic liver disease. (2020) Thomas, Sara description

Comparison of small-sample standard-error corrections for generalised estimating equations in stepped wedge cluster randomised trials with a binary outcome: A simulation study. (2020) Thompson, Jennifer

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COVID-19 vaccine development pipeline. (2020) Vaccine Centre

Epigenome-wide association study for perceived discrimination among sub-Saharan African migrants in Europe - the RODAM study. (2020) van der Laan, Loes C., Meeks, Karlijn A. C., Chilunga, Felix P., Agyemang, Charles, Venema, Andrea, Mannens, Marcel M. A. M., Zafarmand, Mohammad H., Klipstein-Grobusch, Kerstin, Smeeth, Liam, Adeyemo, Adebowale, Henneman, Peter

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LaVIISWA Round 1 and 2 Dataset. (2020) Webb, Emily, Nampijja, Margaret grid_on

Social Contact Rates (SOCRATES) Data Tool. (2020) Willem, Lander, Hoang, Van Thang, Funk, Sebastian, Coletti, Pietro, Beutels, Philippe, Hens, Niel

Multi-Country Model Application for RSV Cost-Effectiveness Policy (McMarcel). (2020) Willem, Lander, Xiao, Li, Antillon, Marina, Bilcke, Joke, Jit, Mark, Beutels, Philippe

opensafely/risk-factors-research. (2020) Williamson, Elizabeth, Walker, Alex J, Bhaskaran, Krishnan J, Bacon, Seb, Bates, Chris, Morton, Caroline E, Curtis, Helen J, Mehrkar, Amir, Evans, David, Inglesby, Peter, Cockburn, Jonathan, Mcdonald, Helen I, MacKenna, Brian, Tomlinson, Laurie, Douglas, Ian J, Rentsch, Christopher T, Mathur, Rohini, Wong, Angel, Grieve, Richard, Harrison, David, Forbes, Harriet, Schultze, Anna, Croker, Richard T, Parry, John, Hester, Frank, Harper, Sam, Perera, Rafael, Evans, Stephen, Smeeth, Liam, Goldacre, Ben

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Transmission analysis of a large TB outbreak in London: a mathematical modelling study using genomic data. (2020) Xu, Yuanwei, Stockdale, Jessica E, Naidu, Vijay, Hatherell, Hollie, Stimson, James, Stagg, Helen R, Abubakar, Ibrahim, Colijn, Caroline