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How modelling can help steer the course set by the World Health Organization 2021-2030 roadmap on neglected tropical diseases

Gates Open Research, 2021; : . 10.12688/gatesopenres.13327.1
Henrik Salje , Maria Theresa Alera, Mary Noreen Chua, Taweewun Hunsawong, Damon Ellison, Anon Srikiatkhachorn, Richard G. Jarman , Gregory D. Gromowski, Isabel Rodriguez-Barraquer, Simon Cauchemez , Derek A. T. Cummings, Louis Macareo, In-Kyu Yoon, Stefan Fernandez and Alan L. Rothman.

Evaluation of the extended efficacy of the Dengvaxia vaccine against symptomatic and subclinical dengue infection

Nature Medicine, 2021; : . 10.1038/s41591-021-01392-9
Birgit Nikolay, Gabriel Ribeiro dos Santos, Marc Lipsitch, Mahmudur Rahman, Stephen P.Luby, Henrik Salje, Emily S.Gurley and Simon Cauchemeza.

Assessing the feasibility of Nipah vaccine efficacy trials based on previous outbreaks in Bangladesh

Vaccine, 2021; : . 10.1016/j.vaccine.2021.08.027
Belman, S., Saha, S. and Beale, M. A.

SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs

Nature Reviews Microbiology, 2021; : . 10.1038/s41579-021-00664-y
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Seroprevalence of anti-SARS-CoV-2 IgG at the first epidemic peak in French Guiana, July 2020

PLOS Neglected Tropical Diseases, 2021; : . https://doi.org/10.1371/journal.pntd.0009945
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Antigenic evolution of dengue viruses over 20 years

Science, 2021; : . https://doi.org/10.1126/science.abk0058
O'Driscoll M, Salje H, Chang AY, Watson H

Arthralgia resolution rate following chikungunya virus infection.

Int J Infect Dis, 2021; 112: 1-7. 10.1016/j.ijid.2021.08.066
Juliette Paireau, Sophie Guillot, Fatima Aït El Belghiti, Soraya Matczak, Sabine Trombert-Paolantoni, Véronique Jacomo, Muhamed-Kheir Taha, Henrik Salje, Sylvain Brisse, Daniel Lévy-Bruhl, Simon Cauchemez, Julie Toubiana

Effect of change in vaccine schedule on pertussis epidemiology in France: a modelling and serological study

The Lancet Infectious Diseases, 2021; : . https://doi.org/10.1016/S1473-3099(21)00267-X
Cécile Tran Kiem , Pascal Crépey , Paolo Bosetti, Daniel Levy Bruhl, Yazdan Yazdanpanah, Henrik Salje, Pierre-Yves Boëlle, Simon Cauchemez

Lockdown as a last resort option in case of COVID-19 epidemic rebound: a modelling study

Euro Surveillance, 2021; 26 (22): pii=200153. https://doi.org/10.2807/1560-7917.ES.2021.26.22.2001536
Nathanaël Hozé, Juliette Paireau, Nathanaël Lapidus, Cécile Tran Kiem, Henrik Salje, Gianluca Severi, Mathilde Touvier, Marie Zins, Xavier de Lamballerie, Daniel Lévy-Bruhl, Fabrice Carratm Simon Cauchemez

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, 2021; 6 (6): e408-e415. https://doi.org/10.1016/S2468-2667(21)00064-5
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Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study

The Lancet Microbe, 2021; : . https://doi.org/10.1016/S2666-5247(21)00094-X
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Psoriasis characteristics for the early detection of psoriatic arthritis

The Journal of Rheumatology, 2021; 48 (5): . https://doi.org/10.3899/jrheum.201123
Xiao-Ke Xu, Lin Wang, Sen Pei

Multiscale mobility explains differential associations between the gross domestic product and COVID-19 transmission in Chinese cities

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Zhanwei Du, Lin Wang, Bingyi Yang, Sheikh Taslim Ali, Tim K. Tsang, Songwei Shan, Peng Wu, Eric H.Y. Lau, Benjamin J. Cowling, and Lauren Ancel Meyers

Risk for International Importations of Variant SARS-CoV-2 Originating in the United Kingdom

Emerging Infectious Diseases, 2021; 27(5): 1527–1529. https://dx.doi.org/10.3201%2Feid2705.210050
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Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

Nature Communications, 2021; 12: 1810. https://doi.org/10.1038/s41467-021-21888-9
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Modelling distributions of Aedes aegypti and Aedes albopictus using climate, host density and interspecies competition

PLOS Neglected Tropical Diseases, 2021; 15(3): e0009063. https://doi.org/10.1371/journal.pntd.0009063
Noemie Lefrancq, Juliette Paireau, Nathanael Hoze, Noemie Courtejoie, Yazdan Yazdanpanah, Lila Bouadma, Pierre-Yves Boelle, Fanny Chereau, Henrik Salje, Simon Cauchemez

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, 2021; 5: 100087. https://doi.org/10.1016/j.lanepe.2021.100087
Cécile Kiem, Paolo Bosetti, Juliette Paireau, Pascal Crepey, Henrik Salje, Noémie Lefrancq, Arnaud Fontanet, Daniel Benamouzig, Pierre-Yves Boëlle, Jean-Claude Desenclos, Lulla Opatowski, Simon Cauchemez

SARS-CoV-2 transmission across age groups in France and implications for control

Nature Communications, 2021; : . 10.1038/s41467-021-27163-1
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Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana

Nature Communications, 2021; 12: 1634 . https://doi.org/10.1038/s41467-021-21944-4
C. Jessica E. Metcalf, Juliette Paireau, Megan O’Driscoll, Mathilde Pivette, Bruno Hubert, Isabelle Pontais, Derek Cummings, Simon Cauchemez, Henrik Salje

Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms

MedRxiv, 2021; : . https://doi.org/10.1101/2021.01.07.21249381
Clifton D McKee, Ausraful Islam, Stephen P Luby, Henrik Salje, Peter J Hudson, Raina K Plowright, Emily Gurley

The Ecology of Nipah Virus in Bangladesh: A Nexus of Land-Use Change and Opportunistic Feeding Behavior in Bats

Viruses, 2021; 13: . https://doi.org/10.3390/v13020169
Sophie Belman, Michael T. Parsons, Amanda B. Spurdle, David E. Goldgar & Bing-Jian Feng

Considerations in assessing germline variant pathogenicity using cosegregation analysis

Genetics in Medicine, 2020; 22: 2052–2059. https://doi.org/10.1038/s41436-020-0920-4
Hui-Jia Li, Lin Wang, Yan Zhang, Matjaž Perc

Optimization of identifiability for efficient community detection

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Xiao-Ke Xu, Xiao Fan Liu, Ye Wu, Sheikh Taslim Ali, Zhanwei Du, Paolo Bosetti, Eric H Y Lau, Benjamin J Cowling, Lin Wang

Reconstruction of Transmission Pairs for Novel Coronavirus Disease 2019 (COVID-19) in Mainland China: Estimation of Superspreading Events, Serial Interval, and Hazard of Infection

Clinical Infectious Diseases, 2020; 71 (12): 3163–3167. https://doi.org/10.1093/cid/ciaa790
Sheikh Taslim Ali, Lin Wang, Eric HY Lau, Xiao-Ke Xu, Zhanwei Du, Ye Wu, Gabriel M Leung, Benjamin J Cowling

Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions

Science, 2020; 369 (6507): 1106-1109. 10.1126/science.abc9004
Zhanwei Du, Xiaoke Xu, Lin Wang, Spencer J. Fox, Benjamin J. Cowling, Alison P. Galvani, and Lauren Ancel Meyers

Effects of Proactive Social Distancing on COVID-19 Outbreaks in 58 Cities, China

Emerging Infectious Diseases, 2020; 26 (9): 2267-2269. https://dx.doi.org/10.3201%2Feid2609.201932
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Seroprevalence of anti-SARS-CoV-2 IgG at the epidemic peak in French Guiana

MedRxiv, 2020; : . https://doi.org/10.1101/2020.09.27.20202465
Paolo Bosetti, Bich-Tram Huynh, Armiya Youssouf Abdou, Marie Sanchez, Catherine Eisenhauer, Noémie Courtejoie, Jérôme Accardo, Henrik Salje, Didier Guillemot, Mathieu Moslonka-Lefebvre, Pierre-Yves Boëlle, Guillaume Béraud, Simon Cauchemez, Lulla Opatowski

Lockdown impact on age-specific contact patterns and behaviours in France

MedRxiv, 2020; : . https://doi.org/10.1101/2020.10.07.20205104
Juliette Paireau, Alexandra Mailles, Catherine Eisenauher, Franck de Laval, François Delon, Paolo Bosetti, Henrik Salje, Valérie Pontiès, Simon Cauchemez

Early chains of transmission of COVID-19 in France

MedRxiv, 2020; : . https://doi.org/10.1101/2020.11.17.20232264
Angkana T. Huang, Bernardo Garcia-Carreras, Matt D. T. Hitchings, Bingyi Yang, Leah C. Katzelnick, Susan M. Rattigan, Brooke A. Borgert, Carlos A. Moreno, Benjamin D. Solomon, Luke Trimmer-Smith, Veronique Etienne, Isabel Rodriguez-Barraquer, Justin Lessler, Henrik Salje, Donald S. Burke, Amy Wesolowski & Derek A. T. Cummings

A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity

Nature Communications, 2020; 11: 4704. 10.1038/s41467-020-18450-4
Hannah Clapham, James Hay, Isobel Routledge, Saki Takahashi, Marc Choisy, Derek Cummings, Bryan Grenfell, C. Jessica E. Metcalf, Michael Mina, Isabel Rodriguez Barraquer, Henrik Salje, and Clarence C. Tam

Seroepidemiologic Study Designs for Determining SARS-COV-2 Transmission and Immunity

Emerging Infectious Diseases, 2020; 26(9): 1978-1986. 10.3201/eid2609.201840
Megan O'Driscoll, Gabriel Ribeiro Dos Santos, Lin Wang, Derek A.T. Cummings, Andrew S Azman, Juliette Paireau, Arnaud Fontanet, Simon Cauchemez, Henrik Salje

Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries

Nature, 2020; : . https://doi.org/10.1038/s41586-020-2918-0
Nabeel Abdur Rehman, Henrik Salje, Moritz U G Kraemer, Lakshminarayanan Subramanian, Umar Saif, Rumi Chunara

Quantifying the localized relationship between vector containment activities and dengue incidence in a real-world setting: A spatial and time series modelling analysis based on geo-located data from Pakistan

PLoS Neglected Tropical Diseases, 2020; 14(5): e0008273. 10.1371/journal.pntd.0008273
In-Kyu Yoon, Anon Srikiatkhachorn, Maria Theresa Alera, Stefan Fernandez, Derek A T Cummings, Henrik Salje

Pre-existing chikungunya virus neutralizing antibodies correlate with risk of symptomatic infection and subclinical seroconversion in a Philippine cohort

International Journal of Infectious Diseases, 2020; 95: 167-173. 10.1016/j.ijid.2020.03.073
Birgit Nikolay, Henrik Salje, A K M Dawlat Khan, Hossain M S Sazzad, Syed M Satter, Mahmudur Rahman, Stephanie Doan, Barbara Knust, Meerjady Sabrina Flora, Stephen P Luby, Simon Cauchemez, Emily S Gurley

A Framework to Monitor Changes in Transmission and Epidemiology of Emerging Pathogens: Lessons From Nipah Virus

Journal of Infectious Diseases, 2020; 221(Supplement_4): S363-S369. 10.1093/infdis/jiaa074
Kishor Kumar Paul, Henrik Salje, Muhammad W Rahman, Mahmudur Rahman, Emily S Gurley

Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh

International Journal of Infectious Diseases, 2020; 97: 306-312. 10.1016/j.ijid.2020.05.111
Nathanaël Hozé, Henrik Salje, Dominique Rousset, Camille Fritzell, Jessica Vanhomwegen, Sarah Bailly, Matthieu Najm, Antoine Enfissi, Jean-Claude Manuguerra, Claude Flamand, Simon Cauchemez

Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers

Nature Communications, 2020; 11: 2842. 10.1038/s41467-020-16516-x
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, Levy-Bruhl D, Fontanet A, Opatowski L, Boelle PY, Cauchemez S

Estimating the burden of SARS-CoV-2 in France.

Science, 2020; 369: 208-211. 10.1126/science.abc3517
Teissier Y, Paul R, Aubry M, Rodo X, Dommar C, Salje H, Sakuntabhai A, Cazelles B, Cao-Lormeau VM

Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014.

PLoS Neglected Tropical Diseases, 2020; 14: e0008110. 10.1371/journal.pntd.0008110
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

Changing contact patterns over disease progression: Nipah virus as a case study.

Journal of Infectious Diseases, 2020; 222(3): 438-442. 10.1093/infdis/jiaa091

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