Data, Biostatistics & Modeling Core
National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: Simon Cauchemez
2017 – 2024 Continue Reading Data, Biostatistics & Modeling Core
National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: Simon Cauchemez
2017 – 2024 Continue Reading Data, Biostatistics & Modeling Core
National Institutes of Health, National Institute of General Medical Sciences
People: Simon Cauchemez, James (Mac) Hyman, Steven Riley, Sze Man Leung, Neil Ferguson
2014 – 2019 Continue Reading Models for synthesising molecular, clinical and epidemiological data, and transla
Menezes A, Koffi D, Rice BL, Metcalf CJE, Graham AL, Cauchemez S, Peeters M, Toure AO, Dosso M, Ayouba A, Roche B. (2026). Seroprevalence of endemic and emergent coronaviruses among SARS-COV-2 patients and healthcare workers in Abidjan, Côte d'Ivoire. BMC infectious diseases
Ochida N, Ramassamy JL, Djuicy DD, Plancoulaine S, Mouinga-Ondémé A, Ndongo CB, Njouom R, Watanabe T, Einsiedel L, Metras R, Gessain A, Cauchemez S. (2026). Quantifying how multiple transmission routes contribute to the spread of HTLV-1 in different endemic foci: a mathematical modelling study. The Lancet. Infectious diseases
Shin MJY, Paireau J, Cauchemez S. (2026). Leveraging regularity in COVID-19 growth rate dynamics for epidemic wave forecasting. Epidemics, (55)
Yman V, Rosado J, Ochida N, Garcia L, Gasasira MF, Baudemont G, Cramer E, Dupont-Rouzeyrol M, Huet K, Douine M, Sanna A, Lambert Y, Carrasco-Escobar G, Nolasco O, Gamboa D, Fall G, Ndiaye O, Faye O, Loucoubar C, Toure-Balde A, Niang M, Vigan-Womas I, Cauchemez S, White MT. (2026). Investigating antibody cross-reactivity and transmission dynamics of alphaviruses and flaviviruses using a multiplex serological assay. Nature communications, 17(1)
Cortes-Azuero O, Vegvari C, Sutcliffe E, Roney E, Scarponi D, Mukandavire C, Cauchemez S, Gurley E, Salje H. (2026). Modeling optimal deployment strategies for Nipah vaccines and monoclonal antibodies. Vaccine, (84)
Hachid A, Benbetka C, Bouamra A, Bouredjoul N, Khardine FA, Ochida N, Garni R, Khaldi A, Seghier M, Charniga K, Cauchemez S. (2026). Patterns of emergence and circulation of West Nile Virus in Algeria. Nature communications
Khurana MP, Tsui JL, Gutierrez B, Chopra A, Scheidwasser N, Zhu HBH, Chang SY, Duchêne DA, Mills C, Inward RPD, Reddy B, Brittain J, Dasgupta A, Sheldon J, Githinji G, Brownstein JS, Monod M, Ferretti L, Bershan S, Tietze S, Ferres L, Argimón S, Dallman TJ, Koua E, Ratmann O, Cauchemez S, Meyers LA, Su L, Vespignani A, Pronyk P, O'Toole Á, Rambaut A, Loman NJ, Holmes EC, Flaxman S, Mulder N, Morgan OW, Tegally H, Gomez-Rodriguez M, Shadbolt N, Happi C, Chand M, Tessema SK, Mbala-Kingebeni P, Suchard MA, Pybus OG, Scarpino SV, Bhatt S, Kraemer MUG. (2026). Global approaches to infectious disease surveillance and modeling. Nature medicine, 32(5)
Ganser I, Paireau J, Buckeridge DL, Cauchemez S, Thiébaut R, Prague M. (2025). Comparative evaluation of methodologies for estimating the effectiveness of non-pharmaceutical interventions in the context of COVID-19: a simulation study. American journal of epidemiology
Perlant C, Weill FX, Paireau J, Scipioni M, Bosetti P, Cauchemez S. (2025). Modeling the spatio-temporal spread of cholera in France in 1892. Epidemics, (53)
O'Driscoll M, Hozé N, Lefrancq N, Ribeiro Dos Santos G, Hoinard D, Rahman MZ, Paul KK, Naser Titu AM, Alam MS, Hossain ME, Vanhomwegen J, Cauchemez S, Gurley ES, Salje H. (2025). Epidemiological and antigenic inferences from serological cross-reactivity among arboviruses. Science translational medicine, 17(826)
Bosetti P, Peckeu-Abboud L, Andrianasolo RM, Baguelin M, Fonteneau L, Deghamne AE, Taha MK, Barret AS, Grimprel E, Opatowski L, Levy-Bruhl D, Cauchemez S. (2025). Modelling the impact of a quadrivalent ACWY meningococcal vaccination and vaccination targeting serogroup B in France. Vaccine, (67)
Menezes A, Hay JA, Razafindratsimandresy R, Randriamanantena AH, Yang L, Héraud JM, Cauchemez S, Wesolowski A, Grenfell B, Graham AL, Metcalf CJE. (2025). Revealing trends in measles immunity during periods of varying measles circulation in Madagascar. American journal of epidemiology
Duque MP, Paul KK, Sultana R, Ribeiro Dos Santos G, O'Driscoll M, Naser AM, Rahman M, Alam MS, Al-Amin HM, Rahman MZ, Hossain ME, Paul RC, Krainski E, Luby SP, Cauchemez S, Vanhomwegen J, Gurley ES, Salje H. (2025). National burden of and optimal vaccine policy for Japanese encephalitis virus in Bangladesh: a seroprevalence and modelling study. The Lancet. Infectious diseases
Soussand F, Abdou AY, Sanchez M, Huynh BT, Giese C, Tran-Kiem C, Béraud G, Guillemot D, Cauchemez S, Opatowski L, Bosetti P. (2025). Evolution of social contacts patterns in France over the SARS-CoV-2 pandemic: results from the SocialCov survey. BMC infectious diseases, 25(1)
Rasoamalala F, Ramasindrazana B, Parany MJ, Rahajandraibe S, Randriantseheno L, Rahelinirina S, Gorgé O, Valade E, Harimalala M, Rajerison M, Cauchemez S, Brault A. (2025). Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar. Proceedings of the National Academy of Sciences of the United States of America, 122(24)
Hoy G, Cortier T, Maier HE, Kuan G, Lopez R, Sanchez N, Ojeda S, Plazaola M, Stadlbauer D, Shotwell A, Balmaseda A, Krammer F, Cauchemez S, Gordon A. (2025). Anti-neuraminidase and anti-HA stalk antibodies reduce the susceptibility to and infectivity of influenza A/H3N2 virus. Nature communications, 16(1)
Ribeiro Dos Santos G, Jawed F, Mukandavire C, Deol A, Scarponi D, Mboera LEG, Seruyange E, Poirier MJP, Bosomprah S, Udeze AO, Dellagi K, Hozé N, Chilongola J, Nasrallah GK, Cauchemez S, Salje H. (2025). Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns. Nature medicine
Ribeiro Dos Santos G, Jawed F, Mukandavire C, Deol A, Scarponi D, Mboera LEG, Seruyange E, Poirier MJP, Bosomprah S, Udeze AO, Dellagi K, Hozé N, Chilongola J, Nasrallah GK, Cauchemez S, Salje H. (2025). Author Correction: Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns. Nature medicine
Cortier T, Gilboa M, Layan M, Joseph G, Meltzer L, Amit S, Rubin C, Lustig Y, Alroy-Preis S, Kreiss Y, Cauchemez S, Regev-Yochay G. (2025). Factors associated with the transmission of the delta SARS-CoV-2 variant in households: the Israeli COVID-19 Family Study (ICoFS). The Journal of infectious diseases
Duque MP, Paul KK, Sultana R, Ribeiro Dos Santos G, O'Driscoll M, Naser AM, Rahman M, Alam MS, Al-Amin HM, Rahman MZ, Hossain ME, Paul RC, Krainski E, Luby SP, Cauchemez S, Vanhomwegen J, Gurley ES, Salje H. (2025). National burden and optimal vaccine policy for Japanese encephalitis virus in Bangladesh. medRxiv : the preprint server for health sciences
Cauchemez S. (2025). Now is the time to integrate serology into routine infectious disease surveillance. The Lancet. Infectious diseases
Perlant C, Klitting R, Colizza V, Gaythorpe KAM, Gabiane G, Lamballerie X, Failloux AB, Cauchemez S, Bosetti P. (2025). A framework to assess the risk of Yellow Fever emergence. Journal of travel medicine
Cristancho-Fajardo L, Nkuba-Ndaye A, Simons E, Hozé N, Guichet E, Izia YA, Ndongo FA, Mbala-Kingebeni P, Soumah AA, Muzinga J, Tshiminyi-Munkamba P, Diallo MSK, Bissek AZ, Makiala-Mandanda S, Toure A, Ahuka-Mundeke S, Ayouba A, Etard JF, Peeters M, Roche B, Nikolay B, Delaporte E, Cauchemez S. (2025). Assessing SARS-CoV-2 transmission in African households from the reanalysis of serosurveys. American journal of epidemiology
Hozé N, Pons-Salort M, Metcalf CJE, White M, Salje H, Cauchemez S. (2025). RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies. PLoS computational biology, 21(2)
Brady OJ, Bastos LS, Caldwell JM, Cauchemez S, Clapham HE, Dorigatti I, Gaythorpe KAM, Hu W, Hussain-Alkhateeb L, Johansson MA, Lim A, Lopez VK, Maude RJ, Messina JP, Mordecai EA, Peterson AT, Rodriquez-Barraquer I, Rabe IB, Rojas DP, Ryan SJ, Salje H, Semenza JC, Tran QM. (2025). Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections. PLoS computational biology, 21(4)
Traore A, Charniga K, Grellet S, Terpant G, Da Cruz H, Lamy A, Thomas N, Gbaguidi G, Mercier A, Prudhomme J, Visseaux B, Vieillefond V, Haim-Boukobza S, Giannoli JM, , , Castro-Alvarez J, Kouamen AC, Rameix-Welti MA, Beirrera-Ibraim S, Destras G, Josset L, Cauchemez S, Lina B, Coignard B, Schaeffer J, Enouf V, Bal A, , . (2025). Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 30(1)
Pérez-Estigarribia PE, Ribeiro Dos Santos G, Cauchemez S, Vazquez C, Ibarrola-Vannucci AK, Sequera G, Villalba S, Ortega MJ, Di Fabio JL, Scarponi D, Mukandavire C, Deol A, Cabello Á, Vargas E, Fernández C, León L, Salje H. (2025). Modeling the impact of vaccine campaigns on the epidemic transmission dynamics of chikungunya virus outbreaks. Nature medicine
Chauvel C, Casalegno JS, Visseaux B, Vieillefond V, Haim-Boukozba S, Enouf V, Chanard E, Fabre M, Rameix-Welti MA, Oblette A, Giannoli JM, Paireau J, Josset L, Lina B, Gaymard A, Cauchemez S, Morfin F, Nunes MC, Bal A. (2025). Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023-2024 Season, Lyon, France. Journal of medical virology, 97(9)
Kraemer MUG, Tsui JL, Chang SY, Lytras S, Khurana MP, Vanderslott S, Bajaj S, Scheidwasser N, Curran-Sebastian JL, Semenova E, Zhang M, Unwin HJT, Watson OJ, Mills C, Dasgupta A, Ferretti L, Scarpino SV, Koua E, Morgan O, Tegally H, Paquet U, Moutsianas L, Fraser C, Ferguson NM, Topol EJ, Duchêne DA, Stadler T, Kingori P, Parker MJ, Dominici F, Shadbolt N, Suchard MA, Ratmann O, Flaxman S, Holmes EC, Gomez-Rodriguez M, Schölkopf B, Donnelly CA, Pybus OG, Cauchemez S, Bhatt S. (2025). Artificial intelligence for modelling infectious disease epidemics. Nature, 638(8051)
Funk A, Florin TA, Kuppermann N, Finkelstein Y, Kazakoff A, Baldovsky M, Tancredi DJ, Breslin K, Bergmann KR, Gardiner M, Pruitt CM, Liu DR, Neuman MI, Wilkinson M, Ambroggio L, Pang XL, Cauchemez S, Malley R, Klassen TP, Lee BE, Payne DC, Mahmud SM, Freedman SB. (2024). Household Transmission Dynamics of Asymptomatic SARS-CoV-2-Infected Children: A Multinational, Controlled Case-Ascertained Prospective Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Brault A, Pontais I, Enouf V, Debeuret C, Bloch E, Paireau J, Rameix-Welti MA, White M, Baudemont G, Lina B, Parent du Châtelet I, Casalegno JS, Vaux S, Cauchemez S. (2024). Effect of nirsevimab on hospitalisations for respiratory syncytial virus bronchiolitis in France, 2023-24: a modelling study. The Lancet. Child & adolescent health
Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, Salje H. (2024). Antigenic distance between primary and secondary dengue infections correlates with disease risk. Science translational medicine, 16(744)
Cuartero CT, Carnegie AC, Cucunuba ZM, Cori A, Hollis SM, Van Gaalen RD, Baidjoe AY, Spina AF, Lees JA, Cauchemez S, Santos M, Umaña JD, Chen C, Gruson H, Gupte P, Tsui J, Shah AA, Millan GG, Quevedo DS, Batra N, Torneri A, Kucharski AJ. (2024). From the 100 Day Mission to 100 lines of software development: how to improve early outbreak analytics. The Lancet. Digital health
Chen Y, Xu Y, Wang L, Liang Y, Li N, Lourenço J, Yang Y, Lin Q, Wang L, Zhao H, Cazelles B, Song H, Liu Z, Wang Z, Brady OJ, Cauchemez S, Tian H. (2024). Indian Ocean temperature anomalies predict long-term global dengue trends. Science (New York, N.Y.), 384(6696)
Galmiche S, Coustaury C, Charniga K, Grant R, Cauchemez S, Fontanet A, . (2024). Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries. BMC global and public health, 2(1)
Duque MP, Naser AM, Dos Santos GR, O'Driscoll M, Paul KK, Rahman M, Alam MS, Al-Amin HM, Rahman MZ, Hossain ME, Paul RC, Luby SP, Cauchemez S, Vanhomwegen J, Gurley ES, Salje H. (2024). Informing an investment case for Japanese encephalitis vaccine introduction in Bangladesh. Science advances, 10(32)
Tsang TK, Du RQR, Fang VJ, Lau EHY, Chan KH, Chu DKW, Ip DKM, Peiris JSM, Leung GM, Cauchemez S, Cowling BJ. (2024). Decreased risk of non-influenza respiratory infection after influenza B virus infection in children. Epidemiology and infection, (152)
Macaux L, Rasolofo V, Eyangoh S, N'Guessan KR, Tejiokem MC, Rakotosamimanana N, Soumahoro MK, , Cauchemez S, Randremanana RV. (2024). Accuracy of Xpert and alternative sampling methods to diagnose childhood pulmonary tuberculosis, a prospective cohort study. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Nunes MC, Thommes E, Fröhlich H, Flahault A, Arino J, Baguelin M, Biggerstaff M, Bizel-Bizellot G, Borchering R, Cacciapaglia G, Cauchemez S, Barbier-Chebbah A, Claussen C, Choirat C, Cojocaru M, Commaille-Chapus C, Hon C, Kong J, Lambert N, Lauer KB, Lehr T, Mahe C, Marechal V, Mebarki A, Moghadas S, Niehus R, Opatowski L, Parino F, Pruvost G, Schuppert A, Thiébaut R, Thomas-Bachli A, Viboud C, Wu J, Crépey P, Coudeville L. (2024). Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report. Infectious Disease Modelling, 9(2)
Layan M, Hens N, de Hoog MLA, Bruijning-Verhagen PCJL, Cowling BJ, Cauchemez S. (2024). Addressing current limitations of household transmission studies by collecting contact data. American journal of epidemiology
Andronico A, Paireau J, Cauchemez S. (2024). Integrating information from historical data into mechanistic models for influenza forecasting. PLoS computational biology, 20(10)
Charniga K, Park SW, Akhmetzhanov AR, Cori A, Dushoff J, Funk S, Gostic KM, Linton NM, Lison A, Overton CE, Pulliam JRC, Ward T, Cauchemez S, Abbott S. (2024). Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. PLoS computational biology, 20(10)
Roux J, Massonnaud CR, Colizza V, Cauchemez S, Crépey P. (2023). Modeling the impact of national and regional lockdowns on the 2020 spring wave of COVID-19 in France. Scientific reports, 13(1)
Woudenberg T, Pinaud L, Garcia L, Tondeur L, Pelleau S, De Thoisy A, Donnadieu F, Backovic M, Attia M, Hozé N, Duru C, Koffi AD, Castelain S, Ungeheuer MN, Fernandes Pellerin S, Planas D, Bruel T, Cauchemez S, Schwartz O, Fontanet A, White M. (2023). Estimated protection against COVID-19 based on predicted neutralisation titres from multiple antibody measurements in a longitudinal cohort, France, April 2020 to November 2021. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 28(25)
Paireau J, Charpignon ML, Larrieu S, Calba C, Hozé N, Boëlle PY, Thiebaut R, Prague M, Cauchemez S. (2023). Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France. BMC infectious diseases, 23(1)
Gallian P, Hozé N, Brisbarre N, Saba Villarroel PM, Nurtop E, Isnard C, Pastorino B, Richard P, Morel P, Cauchemez S, de Lamballerie X. (2023). SARS-CoV-2 IgG seroprevalence surveys in blood donors before the vaccination campaign, France 2020-2021. iScience, 26(4)
Hozé N, Salje H, Rousset D, Fritzell C, Vanhomwegen J, Bailly S, Najm M, Enfissi A, Manuguerra JC, Flamand C, Cauchemez S. (2023). Author Correction: Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers. Nature communications, 14(1)
Tsang TK, Perera RAPM, Fang VJ, Wong JY, Shiu EY, So HC, Ip DKM, Malik Peiris JS, Leung GM, Cowling BJ, Cauchemez S. (2023). Author Correction: Reconstructing antibody dynamics to estimate the risk of influenza virus infection. Nature communications, 14(1)
Galmiche S, Cortier T, Charmet T, Schaeffer L, Chény O, von Platen C, Lévy A, Martin S, Omar F, David C, Mailles A, Carrat F, Cauchemez S, Fontanet A. (2023). SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study. The Lancet. Microbe, 4(6)
Andronico A, Menudier L, Salje H, Vincent M, Paireau J, de Valk H, Gallian P, Pastorino B, Brady O, de Lamballerie X, Lazarus C, Paty MC, Vilain P, Noel H, Cauchemez S. (2023). Comparing the Performance of Three Models Incorporating Weather Data to Forecast Dengue Epidemics in Reunion Island, 2018-2019. The Journal of infectious diseases
Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, , Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG. (2023). Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science (New York, N.Y.), 381(6655)
Laydon DJ, Cauchemez S, Hinsley WR, Bhatt S, Ferguson NM. (2023). Impact of proactive and reactive vaccination strategies for health-care workers against MERS-CoV: a mathematical modelling study. The Lancet. Global health, 11(5)
Bauzile B, Durand B, Lambert S, Rautureau S, Fourtune L, Guinat C, Andronico A, Cauchemez S, Paul MC, Vergne T. (2023). Impact of palmiped farm density on the resilience of the poultry sector to highly pathogenic avian influenza H5N8 in France. Veterinary research, 54(1)
Tan-Lhernould L, Tamandjou C, Deschamps G, Platon J, Sommen C, Chereau F, Parent du Châtelet I, Cauchemez S, Vaux S, Paireau J. (2023). Impact of vaccination against severe COVID-19 in the French population aged 50 years and above: a retrospective population-based study. BMC medicine, 21(1)
Tsang TK, Wang C, Fang VJ, Perera RAPM, So HC, Ip DKM, Leung GM, Peiris JSM, Cauchemez S, Cowling BJ. (2023). Reconstructing household transmission dynamics to estimate the infectiousness of asymptomatic influenza virus infections. Proceedings of the National Academy of Sciences of the United States of America, 120(33)
Tsang TK, Huang X, Wang C, Chen S, Yang B, Cauchemez S, Cowling BJ. (2023). The effect of variation of individual infectiousness on SARS-CoV-2 transmission in households. eLife, (12)
Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. (2023). Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus evolution, 9(1)
Cauchemez S, Bosetti P, Cowling BJ. (2023). Managing sources of error during pandemics. Science (New York, N.Y.), 379(6631)
Bhatia S, Imai N, Watson OJ, Abbood A, Abdelmalik P, Cornelissen T, Ghozzi S, Lassmann B, Nagesh R, Ragonnet-Cronin ML, Schnitzler JC, Kraemer MU, Cauchemez S, Nouvellet P, Cori A. (2023). Lessons from COVID-19 for rescalable data collection. The Lancet. Infectious diseases
Hozé N, Diarra I, Sangaré AK, Pastorino B, Pezzi L, Kouriba B, Sagara I, Dabo A, Djimdé A, Thera MA, Doumbo OK, de Lamballerie X, Cauchemez S. (2023). Author Correction: Model-based assessment of Chikungunya and O'nyong-nyong virus circulation in Mali in a serological cross-reactivity context. Nature communications, 14(1)
Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead S, Cauchemez S, Cummings DAT, Salje H. (2023). Antigenic diversity and dengue disease risk. Research square
Colosi E, Bassignana G, Contreras DA, Poirier C, Boëlle PY, Cauchemez S, Yazdanpanah Y, Lina B, Fontanet A, Barrat A, Colizza V. (2022). Screening and vaccination against COVID-19 to minimise school closure: a modelling study. The Lancet. Infectious diseases
Paireau J, Mailles A, Eisenhauer C, de Laval F, Delon F, Bosetti P, Salje H, Pontiès V, Cauchemez S. (2022). Early chains of transmission of COVID-19 in France, January to March 2020. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 27(6)
Bailly S, Hozé N, Bisser S, Zhu-Soubise A, Fritzell C, Fernandes-Pellerin S, Mbouangoro A, Rousset D, Djossou F, Cauchemez S, Flamand C. (2022). Transmission dynamics of Q fever in French Guiana: A population-based cross-sectional study. Lancet regional health. Americas, (16)
Paireau J, Andronico A, Hozé N, Layan M, Crépey P, Roumagnac A, Lavielle M, Boëlle PY, Cauchemez S. (2022). An ensemble model based on early predictors to forecast COVID-19 health care demand in France. Proceedings of the National Academy of Sciences of the United States of America, 119(18)
Lefrancq N, Bouchez V, Fernandes N, Barkoff AM, Bosch T, Dalby T, Åkerlund T, Darenberg J, Fabianova K, Vestrheim DF, Fry NK, González-López JJ, Gullsby K, Habington A, He Q, Litt D, Martini H, Piérard D, Stefanelli P, Stegger M, Zavadilova J, Armatys N, Landier A, Guillot S, Hong SL, Lemey P, Parkhill J, Toubiana J, Cauchemez S, Salje H, Brisse S. (2022). Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis. Science translational medicine, 14(642)
Sofonea MT, Cauchemez S, Boëlle PY. (2022). Epidemic models: why and how to use them. Anaesthesia, critical care & pain medicine
Yang J, Liao Q, Luo K, Liu F, Zhou Y, Zou G, Huang W, Yu S, Wei X, Zhou J, Dai B, Qiu Q, Altmeyer R, Hu H, Paireau J, Luo L, Gao L, Nikolay B, Hu S, Xing W, Wu P, van Doorn HR, Horby PW, Simmonds P, Leung GM, Cowling BJ, Cauchemez S, Yu H. (2022). Seroepidemiology of enterovirus A71 infection in prospective cohort studies of children in southern China, 2013-2018. Nature communications, 13(1)
Bosetti P, Tran Kiem C, Andronico A, Colizza V, Yazdanpanah Y, Fontanet A, Benamouzig D, Cauchemez S. (2022). Epidemiology and control of SARS-CoV-2 epidemics in partially vaccinated populations: a modeling study applied to France. BMC medicine, 20(1)
Tsang TK, Perera RAPM, Fang VJ, Wong JY, Shiu EY, So HC, Ip DKM, Malik Peiris JS, Leung GM, Cowling BJ, Cauchemez S. (2022). Reconstructing antibody dynamics to estimate the risk of influenza virus infection. Nature communications, 13(1)
Brault A, Tran-Kiem C, Couteaux C, Olié V, Paireau J, Yazdanpanah Y, Ghosn J, Martin-Blondel G, Bosetti P, Cauchemez S. (2022). Modelling the end of a Zero-COVID strategy using nirmatrelvir/ritonavir, vaccination and NPIs in Wallis and Futuna. The Lancet regional health. Western Pacific, (30)
Tsang TK, Wang C, Fang VJ, Perera RAPM, So HC, Ip DKM, Peiris JSM, Leung GM, Cauchemez S, Cowling BJ. (2022). Indirect Protection from Vaccinating Children against Influenza A Virus Infection in Households. Viruses, 14(10)
Blanquart F, Hozé N, Cowling BJ, Débarre F, Cauchemez S. (2022). Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants. eLife, (11)
Faucher B, Assab R, Roux J, Levy-Bruhl D, Tran Kiem C, Cauchemez S, Zanetti L, Colizza V, Boëlle PY, Poletto C. (2022). Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19. Nature communications, 13(1)
Ten Bosch Q, Andrianaivoarimanana V, Ramasindrazana B, Mikaty G, Rakotonanahary RJL, Nikolay B, Rahajandraibe S, Feher M, Grassin Q, Paireau J, Rahelinirina S, Randremanana R, Rakotoarimanana F, Melocco M, Rasolofo V, Pizarro-Cerdá J, Le Guern AS, Bertherat E, Ratsitorahina M, Spiegel A, Baril L, Rajerison M, Cauchemez S. (2022). Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. PLoS biology, 20(8)
Razafimahatratra SL, Menezes A, Wesolowski A, Rafetrarivony L, Cauchemez S, Razafindratsimandresy R, Harimanana A, Crucitti T, Collard JM, Metcalf CJE. (2022). Leveraging serology to titrate immunisation programme functionality for diphtheria in Madagascar. Epidemiology and infection, (150)
Kraemer MUG, Pybus OG, Fraser C, Cauchemez S, Rambaut A, Cowling BJ. (2022). Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission. Nature medicine
Zhou J, Zhou Y, Luo K, Liao Q, Zheng W, Gong H, Shi H, Zhao S, Wang K, Qiu Q, Dai B, Ren L, Wang L, Gao L, Xu M, Liu N, Lu W, Zheng N, Chen X, Chen Z, Yang J, Cauchemez S, Yu H. (2022). The transfer of maternal antibodies and dynamics of maternal and natural infection-induced antibodies against coxsackievirus A16 in Chinese children 0-13 years of age: a longitudinal cohort study. BMC medicine, 20(1)
Christofferson RC, Wearing HJ, Turner EA, Walsh CS, Salje H, Tran-Kiem C, Cauchemez S. (2022). How do i bite thee? let me count the ways: Exploring the implications of individual biting habits of Aedes aegypti for dengue transmission. PLoS neglected tropical diseases, 16(10)
Nemoto T, Aubry M, Teissier Y, Paul R, Cao-Lormeau VM, Salje H, Cauchemez S. (2022). Reconstructing long-term dengue virus immunity in French Polynesia. PLoS neglected tropical diseases, 16(10)
Layan M, Gilboa M, Gonen T, Goldenfeld M, Meltzer L, Andronico A, Hozé N, Cauchemez S, Regev-Yochay G. (2022). Impact of BNT162b2 vaccination and isolation on SARS-CoV-2 transmission in Israeli households: an observational study. American journal of epidemiology
Metcalf CJE, Paireau J, O'Driscoll M, Pivette M, Hubert B, Pontais I, Nickbakhsh S, Cummings DAT, Cauchemez S, Salje H. (2022). Comparing the age and sex trajectories of SARS-CoV-2 morbidity and mortality with other respiratory pathogens. Royal Society open science, 9(6)
Tran Kiem C, Crépey P, Bosetti P, Levy Bruhl D, Yazdanpanah Y, Salje H, Boelle PY, Cauchemez S. (2021). Lockdown as a last resort option in case of COVID-19 epidemic rebound: a modelling study. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26(22)
Bosetti P, Tran Kiem C, Andronico A, Paireau J, Lévy-Bruhl D, Alter L, Fontanet A, Cauchemez S. (2021). Impact of booster vaccination on the control of COVID-19 Delta wave in the context of waning immunity: application to France in the winter 2021/22. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 27(1)
Bosetti P, Huynh BT, Abdou AY, Sanchez M, Eisenhauer C, Courtejoie N, Accardo J, Salje H, Guillemot D, Moslonka-Lefebvre M, Boëlle PY, Béraud G, Cauchemez S, Opatowski L. (2021). Lockdown impact on age-specific contact patterns and behaviours, France, April 2020. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26(48)
Tran Kiem C, Andronico A, Bosetti P, Paireau J, Alter L, Boelle PY, Fontanet A, Lévy-Bruhl D, Cauchemez S. (2021). Benefits and risks associated with different uses of the COVID-19 vaccine Vaxzevria: a modelling study, France, May to September 2021. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26(26)
Travier L, Alonso M, Andronico A, Hafner L, Disson O, Lledo PM, Cauchemez S, Lecuit M. (2021). Neonatal susceptibility to meningitis results from the immaturity of epithelial barriers and gut microbiota. Cell reports, 35(13)
Gaymard A, Bosetti P, Feri A, Destras G, Enouf V, Andronico A, Burrel S, Behillil S, Sauvage C, Bal A, Morfin F, Van Der Werf S, Josset L, , , Blanquart F, Coignard B, Cauchemez S, Lina B. (2021). Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26(9)
Layan M, Dellicour S, Baele G, Cauchemez S, Bourhy H. (2021). Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review. PLoS neglected tropical diseases, 15(5)
Grant R, Charmet T, Schaeffer L, Galmiche S, Madec Y, Von Platen C, Chény O, Omar F, David C, Rogoff A, Paireau J, Cauchemez S, Carrat F, Septfons A, Levy-Bruhl D, Mailles A, Fontanet A. (2021). Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France. The Lancet regional health. Europe
Tran Kiem C, Bosetti P, Paireau J, Crépey P, Salje H, Lefrancq N, Fontanet A, Benamouzig D, Boëlle PY, Desenclos JC, Opatowski L, Cauchemez S. (2021). SARS-CoV-2 transmission across age groups in France and implications for control. Nature communications, 12(1)
Salje H, Alera MT, Chua MN, Hunsawong T, Ellison D, Srikiatkhachorn A, Jarman RG, Gromowski GD, Rodriguez-Barraquer I, Cauchemez S, Cummings DAT, Macareo L, Yoon IK, Fernandez S, Rothman AL. (2021). Evaluation of the extended efficacy of the Dengvaxia vaccine against symptomatic and subclinical dengue infection. Nature medicine
Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A, , Volz E, Faria NR, Aanensen D, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science (New York, N.Y.)
Salje H, Wesolowski A, Brown TS, Kiang MV, Berry IM, Lefrancq N, Fernandez S, Jarman RG, Ruchusatsawat K, Iamsirithaworn S, Vandepitte WP, Suntarattiwong P, Read JM, Klungthong C, Thaisomboonsuk B, Engø-Monsen K, Buckee C, Cauchemez S, Cummings DAT. (2021). Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nature communications, 12(1)
Charmet T, Schaeffer L, Grant R, Galmiche S, Chény O, Von Platen C, Maurizot A, Rogoff A, Omar F, David C, Septfons A, Cauchemez S, Gaymard A, Lina B, Lefrancois LH, Enouf V, van der Werf S, Mailles A, Levy-Bruhl D, Carrat F, Fontanet A. (2021). Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France. The Lancet regional health. Europe, (8)
Nikolay B, Ribeiro Dos Santos G, Lipsitch M, Rahman M, Luby SP, Salje H, Gurley ES, Cauchemez S. (2021). Assessing the feasibility of Nipah vaccine efficacy trials based on previous outbreaks in Bangladesh. Vaccine
Tran Kiem C, Massonnaud CR, Levy-Bruhl D, Poletto C, Colizza V, Bosetti P, Fontanet A, Gabet A, Olié V, Zanetti L, Boëlle PY, Crépey P, Cauchemez S. (2021). A modelling study investigating short and medium-term challenges for COVID-19 vaccination: From prioritisation to the relaxation of measures. EClinicalMedicine, (38)
Hozé N, Diarra I, Sangaré AK, Pastorino B, Pezzi L, Kouriba B, Sagara I, Dabo A, Djimdé A, Thera MA, Doumbo OK, de Lamballerie X, Cauchemez S. (2021). Model-based assessment of Chikungunya and O'nyong-nyong virus circulation in Mali in a serological cross-reactivity context. Nature communications, 12(1)
Paireau J, Guillot S, Aït El Belghiti F, Matczak S, Trombert-Paolantoni S, Jacomo V, Taha MK, Salje H, Brisse S, Lévy-Bruhl D, Cauchemez S, Toubiana J. (2021). Effect of change in vaccine schedule on pertussis epidemiology in France: a modelling and serological study. The Lancet. Infectious diseases
Lapidus N, Paireau J, Lévy-Bruhl D, de Lamballerie X, Severi G, Touvier M, Zins M, Cauchemez S, Carrat F, . (2021). Do not neglect SARS-CoV-2 hospitalization and fatality risks in the middle-aged adult population. Infectious diseases now
Landier J, Paireau J, Rebaudet S, Legendre E, Lehot L, Fontanet A, Cauchemez S, Gaudart J. (2021). Cold and dry winter conditions are associated with greater SARS-CoV-2 transmission at regional level in western countries during the first epidemic wave. Scientific reports, 11(1)
Galmiche S, Charmet T, Schaeffer L, Paireau J, Grant R, Chény O, Von Platen C, Maurizot A, Blanc C, Dinis A, Martin S, Omar F, David C, Septfons A, Cauchemez S, Carrat F, Mailles A, Levy-Bruhl D, Fontanet A. (2021). Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study. The Lancet regional health. Europe, (7)
Cauchemez S, Bosetti P, Kiem CT, Mouro V, Consoli A, Fontanet A. (2021). Education and mental health: good reasons to vaccinate children. Lancet
Flamand C, Alves Sarmento C, Enfissi A, Bailly S, Beillard E, Gaillet M, Michaud C, Servas V, Clement N, Perilhou A, Carage T, Musso D, Carod JF, Eustache S, Tourbillon C, Boizon E, James S, Djossou F, Salje H, Cauchemez S, Rousset D. (2021). Seroprevalence of anti-SARS-CoV-2 IgG at the first epidemic peak in French Guiana, July 2020. PLoS neglected tropical diseases, 15(11)
Andronico A, Tran Kiem C, Paireau J, Succo T, Bosetti P, Lefrancq N, Nacher M, Djossou F, Sanna A, Flamand C, Salje H, Rousseau C, Cauchemez S. (2021). Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana. Nature communications, 12(1)
Cauchemez S, Kiem CT. (2021). Managing COVID-19 importation risks in a heterogeneous world. The Lancet. Public health
Andrianaivoarimanana V, Wagner DM, Birdsell DN, Nikolay B, Rakotoarimanana F, Randriantseheno LN, Vogler AJ, Sahl JW, Hall CM, Somprasong N, Cauchemez S, Schweizer HP, Razafimandimby H, Rogier C, Rajerison M. (2021). Transmission of antimicrobial resistant Yersinia pestis during a pneumonic plague outbreak. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Hozé N, Paireau J, Lapidus N, Tran Kiem C, Salje H, Severi G, Touvier M, Zins M, de Lamballerie X, Lévy-Bruhl D, Carrat F, Cauchemez S. (2021). Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalisation and serological data: a modelling study. The Lancet. Public health
Kraemer MUG, Pybus OG, Fraser C, Cauchemez S, Rambaut A, Cowling BJ. (2021). Monitoring key epidemiological parameters of SARS-CoV-2 transmission. Nature medicine
Ukita M, Hozé N, Nemoto T, Cauchemez S, Asakura S, Makingi G, Kazwala R, Makita K. (2021). Quantitative evaluation of the infection dynamics of bovine brucellosis in Tanzania. Preventive veterinary medicine, (194)
Di Domenico L, Sabbatini CE, Boëlle PY, Poletto C, Crépey P, Paireau J, Cauchemez S, Beck F, Noel H, Lévy-Bruhl D, Colizza V. (2021). Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic. Communications medicine, (1)
Tsang TK, Wang C, Yang B, Cauchemez S, Cowling BJ. (2021). Using secondary cases to characterize the severity of an emerging or re-emerging infection. Nature communications, 12(1)
Moura A, Lefrancq N, Wirth T, Leclercq A, Borges V, Gilpin B, Dallman TJ, Frey J, Franz E, Nielsen EM, Thomas J, Pightling A, Howden BP, Tarr CL, Gerner-Smidt P, Cauchemez S, Salje H, Brisse S, Lecuit M, . (2021). Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Science advances, 7(49)
Bailly S, Rousset D, Fritzell C, Hozé N, Ben Achour S, Berthelot L, Enfissi A, Vanhomwegen J, Salje H, Fernandes-Pellerin S, Saout M, Lavergne A, Manuguerra JC, Carod JF, Djossou F, Cauchemez S, Flamand C. (2021). Spatial Distribution and Burden of Emerging Arboviruses in French Guiana. Viruses, 13(7)
Lefrancq N, Paireau J, Hozé N, Courtejoie N, Yazdanpanah Y, Bouadma L, Boelle PY, Chereau F, Salje H, Cauchemez S. (2021). Evolution of outcomes for patients hospitalised during the first 9 months of the SARS-CoV-2 pandemic in France: A retrospective national surveillance data analysis. The Lancet regional health. Europe, (5)
Capai L, Hozé N, Chiaroni J, Gross S, Djoudi R, Charrel R, Izopet J, Bosseur F, Priet S, Cauchemez S, de Lamballerie X, Falchi A, Gallian P. (2020). Seroprevalence of hepatitis E virus among blood donors on Corsica, France, 2017. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(5)
Bosetti P, Kiem CT, Yazdanpanah Y, Fontanet A, Lina B, Colizza V, Cauchemez S. (2020). Impact of mass testing during an epidemic rebound of SARS-CoV-2: a modelling study using the example of France. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 26(1)
Kraemer MUG, Pigott DM, Hill SC, Vanderslott S, Reiner RC Jr., Stasse S, Brownstein JS, Gutierrez B, Dennig F, Hay SI, Wint GRW, Pybus OG, Castro MC, Vinck P, Pham PN, Nilles EJ, Cauchemez S. (2020). Dynamics of conflict during the Ebola outbreak in the Democratic Republic of the Congo 2018-2019. BMC medicine, 18(1)
Diarra I, Nurtop E, Sangaré AK, Sagara I, Pastorino B, Sacko S, Zeguimé A, Coulibaly D, Fofana B, Gallian P, Priet S, Drexler JF, Failloux AB, Dabo A, Thera MA, Djimdé A, Kouriba B, Cauchemez S, de Lamballerie X, Hozé N, Doumbo OK. (2020). Zika Virus Circulation in Mali. Emerging infectious diseases, 26(5)
Du Z, Wang L, Cauchemez S, Xu X, Wang X, Cowling BJ, Meyers LA. (2020). Risk for Transportation of 2019 Novel Coronavirus (COVID-19) from Wuhan to Cities in China. medRxiv : the preprint server for health sciences
Adam DC, Wu P, Wong JY, Lau EHY, Tsang TK, Cauchemez S, Leung GM, Cowling BJ. (2020). Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong. Nature medicine
Razafimahatratra SL, Wesolowski A, Rafetrarivony L, Heraud JM, Jones FK, Cauchemez S, Razafindratsimandresy R, Raharinantoanina SJ, Harimanana A, Collard JM, Metcalf C. (2020). Seroprevalence of pertussis in Madagascar and implications for vaccination. Epidemiology and infection
Pellis L, Cauchemez S, Ferguson NM, Fraser C. (2020). Systematic selection between age and household structure for models aimed at emerging epidemic predictions. Nature communications, 11(1)
Du Z, Wang L, Cauchemez S, Xu X, Wang X, Cowling BJ, Meyers LA. (2020). Risk for Transportation of 2019 Novel Coronavirus Disease from Wuhan to Other Cities in China. Emerging infectious diseases, 26(5)
Salje H, Tran Kiem C, Lefrancq N, Courtejoie N, Bosetti P, Paireau J, Andronico A, Hozé N, Richet J, Dubost CL, Le Strat Y, Lessler J, Lévy-Bruhl D, Fontanet A, Opatowski L, Boelle PY, Cauchemez S. (2020). Estimating the burden of SARS-CoV-2 in France. Science (New York, N.Y.)
Nikolay B, Salje H, Khan AKMD, Sazzad HMS, Satter SM, Rahman M, Doan S, Knust B, Flora MS, Luby SP, Cauchemez S, Gurley ES. (2020). A Framework to Monitor Changes in Transmission and Epidemiology of Emerging Pathogens: Lessons From Nipah Virus. The Journal of infectious diseases, 221(Supplement_4)
Sow A, Nikolay B, Faye O, Cauchemez S, Cano J, Diallo M, Faye O, Sadio B, Ndiaye O, Weaver SC, Dia AT, Sall AA, Malvy D. (2020). Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal. Viruses, 12(2)
Fontanet A, Cauchemez S. (2020). COVID-19 herd immunity: where are we?. Nature reviews. Immunology
Wei X, Yang J, Gao L, Wang L, Liao Q, Qiu Q, Luo K, Yu S, Zhou Y, Liu F, Chen Q, Zhang J, Dai B, Yang H, Zhou J, Xing W, Chen X, He M, Ren L, Guo J, Luo L, Wu P, Chen Z, van Doorn HR, Cauchemez S, Cowling BJ, Yu H. (2020). The transfer and decay of maternal antibodies against enterovirus A71, and dynamics of antibodies due to later natural infections in Chinese infants: a longitudinal, paired mother-neonate cohort study. The Lancet. Infectious diseases
Hozé N, Salje H, Rousset D, Fritzell C, Vanhomwegen J, Bailly S, Najm M, Enfissi A, Manuguerra JC, Flamand C, Cauchemez S. (2020). Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers. Nature communications, 11(1)
Cauchemez S, Kiem CT, Paireau J, Rolland P, Fontanet A. (2020). Lockdown impact on COVID-19 epidemics in regions across metropolitan France. Lancet, 396(10257)
O'Driscoll M, Ribeiro Dos Santos G, Wang L, Cummings DAT, Azman AS, Paireau J, Fontanet A, Cauchemez S, Salje H. (2020). Age-specific mortality and immunity patterns of SARS-CoV-2. Nature
Raherindrasana A, Metcalf CJ, Heraud JM, Cauchemez S, Winter A, Wesolowski A, Razafindratsimandresy R, Randriamampionona L, Rafalimanantsoa SA, Masembe Y, Ndiaye C, Rakotonirina J. (2020). Towards better targeting: lessons from a posthoneymoon measles outbreak in Madagascar, 2018-2019. BMJ global health, 5(10)
Lee KH, Nikolay B, Sazzad HMS, Hossain MJ, Khan AKMD, Rahman M, Satter SM, Nichol ST, Klena JD, Pulliam JRC, Kilpatrick AM, Sultana S, Afroj S, Daszak P, Luby S, Cauchemez S, Salje H, Gurley E. (2020). Changing contact patterns over disease progression: Nipah virus as a case study. The Journal of infectious diseases
Churakov M, Villabona-Arenas CJ, Kraemer MUG, Salje H, Cauchemez S. (2019). Spatio-temporal dynamics of dengue in Brazil: Seasonal travelling waves and determinants of regional synchrony. PLoS neglected tropical diseases, 13(4)
Cousien A, Abel S, Monthieux A, Andronico A, Calmont I, Cervantes M, Césaire R, Gallian P, de Lamballerie X, Laouénan C, Najioullah F, Pierre-François S, Pircher M, Salje H, Ten Bosch QA, Cabié A, Cauchemez S. (2019). Assessing Zika Virus Transmission Within Households During an Outbreak in Martinique, 2015-2016. American journal of epidemiology, 188(7)
Cauchemez S, Hoze N, Cousien A, Nikolay B, Ten Bosch Q. (2019). How Modelling Can Enhance the Analysis of Imperfect Epidemic Data. Trends in parasitology, 35(5)
Tsang TK, Fang VJ, Ip DKM, Perera RAPM, So HC, Leung GM, Peiris JSM, Cowling BJ, Cauchemez S. (2019). Indirect protection from vaccinating children against influenza in households. Nature communications, 10(1)
Nikolay B, Salje H, Hossain MJ, Khan AKMD, Sazzad HMS, Rahman M, Daszak P, Ströher U, Pulliam JRC, Kilpatrick AM, Nichol ST, Klena JD, Sultana S, Afroj S, Luby SP, Cauchemez S, Gurley ES. (2019). Transmission of Nipah Virus - 14 Years of Investigations in Bangladesh. The New England journal of medicine, 380(19)
Andronico A, Courcoul A, Bronner A, Scoizec A, Lebouquin-Leneveu S, Guinat C, Paul MC, Durand B, Cauchemez S. (2019). Highly pathogenic avian influenza H5N8 in south-west France 2016-2017: A modeling study of control strategies. Epidemics, (28)
Kraemer MUG, Reiner RC Jr., Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Davis Weaver N, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding N. (2019). Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nature microbiology, 4(5)
Ihantamalala FA, Rakotoarimanana FMJ, Ramiadantsoa T, Rakotondramanga JM, Pennober G, Rakotomanana F, Cauchemez S, Metcalf CJE, Herbreteau V, Wesolowski A. (2018). Spatial and temporal dynamics of malaria in Madagascar. Malaria journal, 17(1)
Salje H, Cummings DAT, Rodriguez-Barraquer I, Katzelnick LC, Lessler J, Klungthong C, Thaisomboonsuk B, Nisalak A, Weg A, Ellison D, Macareo L, Yoon IK, Jarman R, Thomas S, Rothman AL, Endy T, Cauchemez S. (2018). Reconstruction of antibody dynamics and infection histories to evaluate dengue risk. Nature, 557(7707)
Mitchell PK, Mier-Y-Teran-Romero L, Biggerstaff BJ, Delorey MJ, Aubry M, Cao-Lormeau VM, Lozier MJ, Cauchemez S, Johansson MA. (2018). Reassessing Serosurvey-Based Estimates of the Symptomatic Proportion of Zika Virus Infections. American journal of epidemiology, 188(1)
Courtejoie N, Salje H, Durand B, Zanella G, Cauchemez S. (2018). Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns. Epidemics, (25)
Paireau J, Pelat C, Caserio-Schönemann C, Pontais I, Le Strat Y, Lévy-Bruhl D, Cauchemez S. (2018). Mapping influenza activity in emergency departments in France using Bayesian model-based geostatistics. Influenza and other respiratory viruses, 12(6)
Cauchemez S, Bourhy H. (2018). Improving the provision of rabies post-exposure prophylaxis. The Lancet. Infectious diseases, 19(1)
Ihantamalala FA, Herbreteau V, Rakotoarimanana FMJ, Rakotondramanga JM, Cauchemez S, Rahoilijaona B, Pennober G, Buckee CO, Rogier C, Metcalf CJE, Wesolowski A. (2018). Estimating sources and sinks of malaria parasites in Madagascar. Nature communications, 9(1)
Nikolay B, Cauchemez S. (2018). Enterovirus outbreak dynamics. Science (New York, N.Y.), 361(6404)
Ali ST, Wu P, Cauchemez S, He D, Fang VJ, Cowling BJ, Tian L. (2018). Ambient ozone and influenza transmissibility in Hong Kong. The European respiratory journal, 51(5)
O'Reilly KM, Lowe R, Edmunds WJ, Mayaud P, Kucharski A, Eggo RM, Funk S, Bhatia D, Khan K, Kraemer MUG, Wilder-Smith A, Rodrigues LC, Brasil P, Massad E, Jaenisch T, Cauchemez S, Brady OJ, Yakob L. (2018). Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis. BMC medicine, 16(1)
Andronico A, Dorléans F, Fergé JL, Salje H, Ghawché F, Signate A, Daudens-Vaysse E, Baudouin L, Dub T, Aubry M, Cao-Lormeau VM, Ledrans M, Noel H, Mallet HP, Fontanet A, Cabié A, Cauchemez S. (2017). Real-Time Assessment of Health-Care Requirements During the Zika Virus Epidemic in Martinique. American journal of epidemiology, 186(10)
Nikolay B, Salje H, Sturm-Ramirez K, Azziz-Baumgartner E, Homaira N, Ahmed M, Iuliano AD, Paul RC, Rahman M, Hossain MJ, Luby SP, Cauchemez S, Gurley ES. (2016). Evaluating Hospital-Based Surveillance for Outbreak Detection in Bangladesh: Analysis of Healthcare Utilization Data. PLoS medicine, 14(1)
Imai N, Dorigatti I, Cauchemez S, Ferguson NM. (2016). Estimating Dengue Transmission Intensity from Case-Notification Data from Multiple Countries. PLoS neglected tropical diseases, 10(7)
Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Mills HL, Salje H, Collins C, Rodriquez-Barraquer I, Riley S, Truelove S, Algarni H, Alhakeem R, AlHarbi K, Turkistani A, Aguas RJ, Cummings DA, Van Kerkhove MD, Donnelly CA, Lessler J, Fraser C, Al-Barrak A, Ferguson NM. (2016). Unraveling the drivers of MERS-CoV transmission. Proceedings of the National Academy of Sciences of the United States of America, 113(32)
Kraemer MUG, Faria NR, Reiner RC Jr., Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S. (2017). Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. The Lancet. Infectious diseases, 17(3)
Cauchemez S, Besnard M, Garel C, Fontanet A, Mallet HP. (2016). Could clinical symptoms be a predictor of complications in Zika virus infection? - Authors' reply. Lancet, 388(10042)
Cauchemez S, Besnard M, Bompard P, Dub T, Guillemette-Artur P, Eyrolle-Guignot D, Salje H, Van Kerkhove MD, Abadie V, Garel C, Fontanet A, Mallet HP. (2016). Association between Zika virus and microcephaly in French Polynesia, 2013-15: a retrospective study. Lancet, 387(10033)
Salje H, Lessler J, Paul KK, Azman AS, Rahman MW, Rahman M, Cummings D, Gurley ES, Cauchemez S. (2016). How social structures, space, and behaviors shape the spread of infectious diseases using chikungunya as a case study. Proceedings of the National Academy of Sciences of the United States of America, 113(47)
Lessler J, Salje H, Van Kerkhove MD, Ferguson NM, Cauchemez S, Rodriquez-Barraquer I, Hakeem R, Jombart T, Aguas R, Al-Barrak A, Cummings DA, . (2016). Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia. American journal of epidemiology, 183(7)
Tsang TK, Fang VJ, Chan KH, Ip DK, Leung GM, Peiris JS, Cowling BJ, Cauchemez S. (2016). Individual Correlates of Infectivity of Influenza A Virus Infections in Households. PLoS One, 11(5)
Fumanelli L, Ajelli M, Merler S, Ferguson NM, Cauchemez S. (2015). Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics. PLoS computational biology, 12(1)
Imai N, Dorigatti I, Cauchemez S, Ferguson NM. (2015). Estimating dengue transmission intensity from sero-prevalence surveys in multiple countries. PLoS neglected tropical diseases, 9(4)
Gambhir M, Clark TA, Cauchemez S, Tartof SY, Swerdlow DL, Ferguson NM. (2015). A change in vaccine efficacy and duration of protection explains recent rises in pertussis incidence in the United States. PLoS computational biology, 11(4)
Faye O, Andronico A, Faye O, Salje H, Boëlle PY, Magassouba N, Bah EI, Koivogui L, Diallo B, Diallo AA, Keita S, Konde MK, Fowler R, Fall G, Cauchemez S, Sall AA. (2015). Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study. PLoS medicine, 12(12)
Salje H, Cauchemez S, Alera MT, Rodriguez-Barraquer I, Thaisomboonsuk B, Srikiatkhachorn A, Lago CB, Villa D, Klungthong C, Tac-An IA, Fernandez S, Velasco JM, Roque VG Jr., Nisalak A, Macareo LR, Levy JW, Cummings D, Yoon IK. (2016). Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission. The Journal of infectious diseases, 213(4)
Tsang TK, Lau LLH, Cauchemez S, Cowling BJ. (2016). Household Transmission of Influenza Virus. Trends in microbiology, 24(2)
Faye O, Boëlle PY, Heleze E, Faye O, Loucoubar C, Magassouba N, Soropogui B, Keita S, Gakou T, Bah el HI, Koivogui L, Sall AA, Cauchemez S. (2015). Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study. The Lancet. Infectious diseases, 15(3)
Xu C, Chan KH, Tsang TK, Fang VJ, Fung RO, Ip DK, Cauchemez S, Leung GM, Peiris JS, Cowling BJ. (2015). Comparative Epidemiology of Influenza B Yamagata- and Victoria-Lineage Viruses in Households. American journal of epidemiology, 182(8)
Tsang TK, Cowling BJ, Fang VJ, Chan KH, Ip DK, Leung GM, Peiris JS, Cauchemez S. (2015). Influenza A Virus Shedding and Infectivity in Households. The Journal of infectious diseases, 212(9)
Iyengar P, von Mollendorf C, Tempia S, Moerdyk A, Valley-Omar Z, Hellferscee O, Martinson N, Chhagan M, McMorrow M, Gambhir M, Cauchemez S, Variava E, Masonoke K, Cohen AL, Cohen C. (2015). Case-ascertained study of household transmission of seasonal influenza - South Africa, 2013. The Journal of infection, 71(5)
Tsang TK, Fang VJ, Perera RA, Ip DK, Leung GM, Peiris JS, Cauchemez S, Cowling BJ. (2015). Interpreting Seroepidemiologic Studies of Influenza in a Context of Nonbracketing Sera. Epidemiology (Cambridge, Mass.), 27(1)
Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N. (2014). OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, (7)
Cauchemez S, Ferguson NM, Fox A, Mai le Q, Thanh le T, Thai PQ, Thoang DD, Duong TN, Minh Hoa le N, Tran Hien N, Horby P. (2014). Determinants of influenza transmission in South East Asia: insights from a household cohort study in Vietnam. PLoS pathogens, 10(8)
Tsang TK, Cauchemez S, Perera RA, Freeman G, Fang VJ, Ip DK, Leung GM, Malik Peiris JS, Cowling BJ. (2014). Association between antibody titers and protection against influenza virus infection within households. The Journal of infectious diseases, 210(5)
Pelat C, Ferguson NM, White PJ, Reed C, Finelli L, Cauchemez S, Fraser C. (2014). Optimizing the precision of case fatality ratio estimates under the surveillance pyramid approach. American journal of epidemiology, 180(10)
Cauchemez S, Van Kerkhove MD, Archer BN, Cetron M, Cowling BJ, Grove P, Hunt D, Kojouharova M, Kon P, Ungchusak K, Oshitani H, Pugliese A, Rizzo C, Saour G, Sunagawa T, Uzicanin A, Wachtel C, Weisfuse I, Yu H, Nicoll A. (2014). School closures during the 2009 influenza pandemic: national and local experiences. BMC infectious diseases, (14)
Churcher TS, Cohen JM, Novotny J, Ntshalintshali N, Kunene S, Cauchemez S. (2014). Public health. Measuring the path toward malaria elimination. Science (New York, N.Y.), 344(6189)
Biggerstaff M, Cauchemez S, Reed C, Gambhir M, Finelli L. (2014). Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature. BMC infectious diseases, (14)
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N. (2013). Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS computational biology, 10(1)
Gambhir M, Swerdlow DL, Finelli L, Van Kerkhove MD, Biggerstaff M, Cauchemez S, Ferguson NM. (2013). Multiple contributory factors to the age distribution of disease cases: a modeling study in the context of influenza A(H3N2v). Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, (57 Suppl 1)
Dorigatti I, Cauchemez S, Ferguson NM. (2013). Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England. Proceedings of the National Academy of Sciences of the United States of America, 110(33)
Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf S, Ferguson NM. (2013). Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. The Lancet. Infectious diseases, 14(1)
Cori A, Ferguson NM, Fraser C, Cauchemez S. (2013). A new framework and software to estimate time-varying reproduction numbers during epidemics. American journal of epidemiology, 178(9)
Cauchemez S, Epperson S, Biggerstaff M, Swerdlow D, Finelli L, Ferguson NM. (2013). Using routine surveillance data to estimate the epidemic potential of emerging zoonoses: application to the emergence of US swine origin influenza A H3N2v virus. PLoS medicine, 10(3)
Dorigatti I, Cauchemez S, Pugliese A, Ferguson NM. (2012). A new approach to characterising infectious disease transmission dynamics from sentinel surveillance: application to the Italian 2009-2010 A/H1N1 influenza pandemic. Epidemics, 4(1)
Cauchemez S, Horby P, Fox A, Mai le Q, Thanh le T, Thai PQ, Hoa le NM, Hien NT, Ferguson NM. (2012). Influenza infection rates, measurement errors and the interpretation of paired serology. PLoS pathogens, 8(12)
Opatowski L, Fraser C, Griffin J, de Silva E, Van Kerkhove MD, Lyons EJ, Cauchemez S, Ferguson NM. (2011). Transmission characteristics of the 2009 H1N1 influenza pandemic: comparison of 8 Southern hemisphere countries. PLoS pathogens, 7(9)
Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly CA, Ghani A, Ferguson N. (2012). Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. Journal of the Royal Society, Interface, 9(67)
Cauchemez S, Ferguson NM. (2012). Methods to infer transmission risk factors in complex outbreak data. Journal of the Royal Society, Interface, 9(68)
MacIntyre CR, Wang Q, Cauchemez S, Seale H, Dwyer DE, Yang P, Shi W, Gao Z, Pang X, Zhang Y, Wang X, Duan W, Rahman B, Ferguson N. (2011). A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. Influenza and other respiratory viruses, 5(3)
Cauchemez S, Bhattarai A, Marchbanks TL, Fagan RP, Ostroff S, Ferguson NM, Swerdlow D, . (2011). Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza. Proceedings of the National Academy of Sciences of the United States of America, 108(7)
Donnelly CA, Finelli L, Cauchemez S, Olsen SJ, Doshi S, Jackson ML, Kennedy ED, Kamimoto L, Marchbanks TL, Morgan OW, Patel M, Swerdlow DL, Ferguson NM, . (2010). Serial intervals and the temporal distribution of secondary infections within households of 2009 pandemic influenza A (H1N1): implications for influenza control recommendations. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, (52 Suppl 1)
Eggo RM, Cauchemez S, Ferguson NM. (2011). Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States. Journal of the Royal Society, Interface, 8(55)
MacIntyre CR, Cauchemez S, Dwyer DE, Seale H, Cheung P, Browne G, Fasher M, Wood J, Gao Z, Booy R, Ferguson N. (2009). Face mask use and control of respiratory virus transmission in households. Emerging infectious diseases, 15(2)
Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, Finelli L, Ferguson NM. (2009). Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. The New England journal of medicine, 361(27)
Truscott J, Fraser C, Hinsley W, Cauchemez S, Donnelly C, Ghani A, Ferguson N, Meeyai A. (2009). Quantifying the transmissibility of human influenza and its seasonal variation in temperate regions. PLoS currents, (1)
Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM. (2009). Managing and reducing uncertainty in an emerging influenza pandemic. The New England journal of medicine, 361(2)
Cauchemez S, Ferguson NM, Wachtel C, Tegnell A, Saour G, Duncan B, Nicoll A. (2009). Closure of schools during an influenza pandemic. The Lancet. Infectious diseases, 9(8)
Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Alpuche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C, . (2009). Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, N.Y.), 324(5934)
Legrand J, Egan JR, Hall IM, Cauchemez S, Leach S, Ferguson NM. (2008). Estimating the location and spatial extent of a covert anthrax release. PLoS computational biology, 5(1)
Cauchemez S, Valleron AJ, Boëlle PY, Flahault A, Ferguson NM. (2008). Estimating the impact of school closure on influenza transmission from Sentinel data. Nature, 452(7188)
Cauchemez S, Ferguson NM. (2008). Likelihood-based estimation of continuous-time epidemic models from time-series data: application to measles transmission in London. Journal of the Royal Society, Interface, 5(25)
Cauchemez S, Temime L, Valleron AJ, Varon E, Thomas G, Guillemot D, Boëlle PY. (2006). S. pneumoniae transmission according to inclusion in conjugate vaccines: Bayesian analysis of a longitudinal follow-up in schools. BMC infectious diseases, (6)
Cauchemez S, Boëlle PY, Thomas G, Valleron AJ. (2006). Estimating in real time the efficacy of measures to control emerging communicable diseases. American journal of epidemiology, 164(6)
Cauchemez S, Boëlle PY, Donnelly CA, Ferguson NM, Thomas G, Leung GM, Hedley AJ, Anderson RM, Valleron AJ. (2005). Real-time estimates in early detection of SARS. Emerging infectious diseases, 12(1)
Ferguson NM, Cummings DA, Cauchemez S, Fraser C, Riley S, Meeyai A, Iamsirithaworn S, Burke DS. (2005). Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature, 437(7056)
Viboud C, Boëlle PY, Cauchemez S, Lavenu A, Valleron AJ, Flahault A, Carrat F. (2004). Risk factors of influenza transmission in households. The British journal of general practice : the journal of the Royal College of General Practitioners, 54(506)
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