David J Haw, Derek A T Cummings, Justin Lessler, Henrik Salje, Jonathan M Read, Steven Riley

Differential mobility and local variation in infection attack rate

PLoS Computational Biology, 2019; 15(1): e1006600. 10.1371/journal.pcbi.1006600
John R. Giles, Henrik Salje, and Justin Lessler

The IDSpatialStats R Package: Quantifying Spatial Dependence of Infectious Disease Spread

The R Journal, 2019; 11/2: 308-327.
K. Ruchusatsawat, P. Wongjaroen, A. Posanacharoen, I. Rodriguez-Barraquer, S. Sangkitporn, D. A.T. Cummings and H. Salje

Observational study into the long-term circulation of Zika in Thailand

Lancet Infectious Diseases, 2019; 19(4): 439-446. 10.1016/S1473-3099(18)30718-7
A. Cousien, S. Abel, A. Monthieux, A. Andronico, I. Calmont, M. Cervantes, R. Césaire, P. Gallian, X. de Lamballerie, C. Laouénan, F. Najioullah, S. Pierre-François, M. Pircher, H. Salje, Q. ten Bosch, A. Cabié, and S. Cauchemez

Assessing Zika virus transmission within households during an outbreak in Martinique, 2015-2016

American Journal of Epidemiology, 2019; 188(7): 1389-1396. 10.1093/aje/kwz091
Birgit Nikolay, Henrik Salje, M Jahangir Hossain, AKM Dawlat Khan, Hossain MS Sazzad, Mahmudur Rahman, Peter Daszak, Ute Ströher, Juliet RC Pulliam, A Marm Kilpatrick, Stuart T Nichol, John D Klena, Sharmin Sultana, Sayma Afroj, Stephen P Luby, Simon Cauchemez, Emily S Gurley

Transmission of Nipah virus: 14 years of investigations in Bangladesh

New England Journal of Medicine, 2019; 380(19): 1804-1814. 10.1056/NEJMoa1805376
S. Hegde, H. Salje, H. Sazzad, M. J. Hossain, M. Rahman, P. Daszak, S. Luby, E. S. Gurley

Using Healthcare Seeking Behaviors to Estimate the Number of Nipah Outbreaks Missed by Hospital-Based Surveillance in Bangladesh

Internation Journal of Epidemiology, 2019; 48(4): 1219-1227. 10.1093/ije/dyz057
Mikhail Churakov, Christian J. Villabona-Arenas, Moritz U. G. Kraemer, Henrik Salje, Simon Cauchemez

Spatio-temporal dynamics of dengue in Brazil: seasonal travelling waves and determinants of regional synchrony

PLoS Neglected Tropical Diseases, 2019; 13(4): e0007012. 10.1371/journal.pntd.0007012
A. M. Weaver, E. S. Gurley, C. Crabtree-Ide, H. Salje, E.-H. Yoo, L. Mu, N. Akter and P. K. Ram

Air pollution dispersion from biomass stoves to neighboring homes in Mirpur, Dhaka, Bangladesh

BMC Public Health, 2019; 19(1): 425. 10.1186/s12889-019-6751-z
I. Rodriguez-Barraquer, H. Salje and DAT Cummings

Opportunities for improved surveillance and control of dengue from age-specific case data

eLife, 2019; 8: e45474. 10.7554/eLife.45474
H. Salje, K. Paul, R. Paul, I. Rodriguez-Barraquer, Z. Rahman, M. S. Alam, M. Rahman, H. M. Al-Amin, J. Heffelfinger and E. Gurley

Nationally-representative serostudy of dengue in Bangladesh allows generalizable disease burden estimates

eLife, 2019; 8: e42869. 10.7554/eLife.42869
C. Flamand, S. Bailly, C. Fritzell, L. Berthelot, J. Vanhomwegen, H. Salje, J. Paireau, S. Matheus, A. Enfissi, S. Fernandes-Pellerin, F. Djossou, S. Linares, J.-F. Carod, M. Kazanji, J.-C. Manuguerra, S. Cauchemez and D. Rousset

Impact of Zika virus emergence in French Guiana: A large general population seroprevalence survey

Journal of Infectious Diseases , 2019; 220(12): 1915-1925. 10.1093/infdis/jiz396
I. Rodriguez-Barraquer, H. Salje and D. A. T. Cummings

Dengue pre-vaccination screening and positive predictive values

Lancet Infectious Diseases , 2019; 19(2): 132-134. 10.1016/S1473-3099(18)30799-0
T. Succo, H. Noël, B. Nikolay, M. Maquart, A. Cochet, I. Leparc-Goffart, O. Catelinois, H. Salje, C. Pelat, P. de Crouy-Chanel, H. de Valk, S. Cauchemez, and C. Rousseau

Dengue serosurvey after a 2-month long outbreak in Nîmes, France, 2015: was there more than met the eye?

Eurosurveillance, 2018; 23: 23. 10.2807/1560-7917.ES.2018.23.23.1700482
M. C. Cortes, S. Cauchemez, N. Lefrancq, S. Luby, M. Hossain, H. Sazzad, M. Rahman, P. Daszak, and H. Salje*, E. Gurley*

Characterization of the spatial and temporal distribution of Nipah virus spillover events in Bangladesh 2007 – 2013

Journal of Infectious Diseases, 2018; 217(9): 1390-1394. 10.1093/infdis/jiy015
A. Azman, F. Luquero, H. Salje, N. Mbaïbardoum, N. Adalbert, M. Ali, E. Bertuzzo, F. Finger, B. Toure, L. Massing, R. Ramazani, B. Saga, M. Allan, D. Olson, J. Leglise, K. Porten and J. Lessler

Micro-hotspots of Risk in Urban Cholera Epidemics

Journal of Infectious Diseases, 2018; 218(7): 1164-1168. 10.1093/infdis/jiy283
N. Courtejoie, H. Salje, B. Durand, G. Zanella, and S. Cauchemez

Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns

Epidemics, 2018; 25: 54-60. 10.1016/j.epidem.2018.05.005
L. C. Katzelnick, A. Escoto, B. McElvany, C. Chávez, H. Salje, W. Luo, I. Rodriguez-Barraquer, R. Jarman, A. P. Durbin, S. Diehl, D. J. Smith, S. Whitehead, and D. A. T. Cummings

Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus

PLoS Neglected Tropical Diseases, 2018; 12(10): e0006862. 10.1371/journal.pntd.0006862
H. Salje, D. A. T. Cummings, I. Rodriguez-Barraquer, L. C. Katzelnick, J. Lessler, C. Klungthong, B. Thaisomboonsuk, A. Nisalak, A. Weg, D. Ellison, L. Macareo, I-K Yoon, R. Jarman, S. Thomas, A. L. Rothman, T. Endy and S. Cauchemez

Reconstruction of antibody dynamics and infection histories to evaluate dengue risk

Nature, 2018; 557(7707): 719-723. 10.1038/s41586-018-0157-4
S. Pollett, M. Melendrez, I. Maljkovic-Berry, S. Duchêne, H. Salje, D. A. T. Cummings, R. G. Jarman

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

Infection, Genetics and Evolution, 2018; 62: 279-295. 10.1016/j.meegid.2018.04.032
Moritz U G Kraemer, Nuno R Faria, Robert C Reiner Jr, Nick Golding, Birgit Nikolay, Stephanie Stasse, Michael A Johansson, Henrik Salje, Ousmane Faye, G R William Wint, Matthias Niedrig, Freya M Shearer, Sarah C Hill, Robin N Thompson, Donal Bisanzio, Nuno Taveira, Heinrich H Nax, Bary S R Pradelski, Elaine O Nsoesie, Nicholas R Murphy, Isaac I Bogoch, Kamran Khan, John S Brownstein, Andrew J Tatem, Tulio de Oliveira, David L Smith, Amadou A Sall, Oliver G Pybus, Simon I Hay, Simon Cauchemez

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study

The Lancet Infectious Diseases, 2017; 17(3): P330-338,. 10.1016/S1473-3099(16)30513-8
Alessio Andronico, Frédérique Dorléans, Jean-Louis Fergé, Henrik Salje, Frédéric Ghawché, Aissatou Signate, Elise Daudens-Vaysse, Laure Baudouin, Timothée Dub, Maite Aubry, Van-Mai Cao-Lormeau, Martine Ledrans, Harold Noel, Henri-Pierre Mallet, Arnaud Fontanet, André Cabié, Simon Cauchemez

Real-time assessment of healthcare requirements during the Zika virus epidemic in Martinique

American Journal of Epidemiology, 2017; 186(10): 1194-1203. 10.1093/aje/kwx008
B. Nikolay, H. Salje, K. Sturm-Ramirez, E. Azziz-Baumgartner, N. Homaira, M. Ahmed, A. D. Iuliano, R. C. Paul, M. Rahman, M. J. Hossain, S. P. Luby, S. Cauchemez and E. S. Gurley

Evaluating hospital-based surveillance for outbreak detection: a healthcare utilization study from Bangladesh

PLoS Medicine, 2017; 14(1): e1002218. 10.1371/journal.pmed.1002218
E. Gurley, S. Hegde, K. Hossain, H. Sazzad, M. Hossain, M. Rahman, M. Sharker, H. Salje, M. Islam, J. Epstein, S. Khan, A. Kilpatrick, P. Daszak, and S. Luby

Convergence of Humans, Bats, Trees, and Culture in Nipah Virus Transmission, Bangladesh

Emerging Infectious Diseases, 2017; 23(9): 1446-1453. 10.3201/eid2309.161922
H. Salje, J. Lessler, I. Berry, M. Melendrez, T. Endy, S. Kalanarooj, A. A-Nuegoonpipat, S. Chanama, S. Sangkijporn, C. Klungthong, B. Thaisomboonsuk, A. Nisalak, R. V. Gibbons, S. Iamsirithaworn, L. Macareo, I.-K. Yoon, A. Sangarsang, R. Jarman and D. A. T. Cummings

Dengue diversity across spatial and temporal scales: local structure and the impact of host population size

Science, 2017; 355(6331): 1302-1306. 10.1126/science.aaj9384
François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Cheryl Tarr, Jean Rauzier, Nizar Fawal, Karen H Keddy, Henrik Salje, Sandra Moore, Asish K Mukhopadhyay, Raymond Bercion, Francisco J Luquero, Antoinette Ngandjio, Mireille Dosso, Elena Monakhova, Benoit Garin1, Christiane Bouchier, Carlo Pazzani, Ankur Mutreja, Roland Grunow, Fati Sidikou, Laurence Bonte2, Sébastien Breurec, Maria Damian, Berthe-Marie Njanpop-Lafourcade, Guillaume Sapriel, Anne-Laure Page, Monzer Hamze, Myriam Henkens, Goutam Chowdhury, Martin Mengel, Jean-Louis Koeck, Jean-Michel Fournier, Gordon Dougan, Patrick A D Grimont, Julian Parkhill, Kathryn E Holt, Renaud Piarroux, Thandavarayan Ramamurthy, Marie-Laure Quilici, Nicholas R Thomson

Genomic history of the seventh pandemic of cholera in Africa

Science, 2017; 358(3634): 785-789. 10.1126/science.aad5901
R. F. Arthur, E. S. Gurley, H. Salje, L. S.P. Bloomfield, W. O. Bagge and J. H. Jones

Contact structure, geography and human behavior: the importance of social forces to infectious disease dynamics

Philosophical Transactions of the Royal Society B, 2017; 372: 1719. 10.1098/rstb.2016.0454
Kyra H Grantz, Madhura S Rane, Henrik Salje, Gregory E Glass, Stephen E Schachterle, Derek A T Cummings

Reply to Shanks and Brundage: Many plausible mechanisms of pandemic mortality disparities

Proceedings of the National Academy of Sciences of the United States of America, 2017; 114(18): E3588-E358. 10.1073/pnas.1703851114
Cuong Hoang Quoc, Salje Henrik, Rodriguez-Barraquer Isabel, Yoon In-Kyu, Nguyen Van Vinh Chau, Nguyen Thanh Hung, Ha Manh Tuan, Phan Trong Lan, Bridget Willis, Ananda Nisalak, Siripen Kalayanarooj, Derek A T Cummings, Cameron P Simmons

Synchrony of Dengue Incidence in Ho Chi Minh City and Bangkok

PLoS Neglected Tropical Diseases, 2016; 10(12): e0005188. 10.1371/journal.pntd.0005188
Paul F Horwood, Alessio Andronico, Arnaud Tarantola, Henrik Salje, Veasna Duong, Channa Mey, Sovann Ly, Philippe Dussart, Simon Cauchemez, Philippe Buchy

Seroepidemiology of Human Enterovirus 71 Infection among Children, Cambodia

Emerging Infectious Diseases, 2016; 22(1): 92-5. 10.3201/eid2201.151323
Henrik Salje, Simon Cauchemez, Maria Theresa Alera, Isabel Rodriguez-Barraquer, Butsaya Thaisomboonsuk, Anon Srikiatkhachorn, Catherine B Lago, Daisy Villa, Chonticha Klungthong, Ilya A Tac-An, Stefan Fernandez, John Mark Velasco, Vito G Roque Jr, Ananda Nisalak, Louis R Macareo, Jens W Levy, Derek Cummings, In-Kyu Yoon

Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission

Journal of Infectious Diseases, 2016; 213(4): 604-10. 10.1093/infdis/jiv470
Justin Lessler, Henrik Salje, Maria D Van Kerkhove, Neil M Ferguson, Simon Cauchemez, Isabel Rodriquez-Barraquer, Rafat Hakeem, Thibaut Jombart, Ricardo Aguas, Ali Al-Barrak, Derek A T Cummings, MERS-CoV Scenario and Modeling Working Group

Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia

American Journal of Epidemiology, 2016; 183(7): 657-63. 10.1093/aje/kwv452
Isabel Rodriguez-Barraquer, Henrik Salje, Derek A T Cummings

Dengue Vaccine in Regions of Endemic Disease

The New England Journal of Medicine, 2016; 374(14): 1388. 10.1056/NEJMc1514451
Hannah E Clapham, Isabel Rodriguez-Barraquer, Andrew S Azman, Benjamin M Althouse, Henrik Salje, Robert V Gibbons, Alan L Rothman, Richard G Jarman, Ananda Nisalak, Butsaya Thaisomboonsuk, Siripen Kalayanarooj, Suchitra Nimmannitya, David W Vaughn, Sharone Green, In-Kyu Yoon, Derek A T Cummings

Dengue Virus (DENV) Neutralizing Antibody Kinetics in Children After Symptomatic Primary and Postprimary DENV Infection

Journal of Infectious Dissease, 2016; 213(9): 1428-35. 10.1093/infdis/jiv759
Nicholas G Reich, Stephen A Lauer, Krzysztof Sakrejda, Sopon Iamsirithaworn, Soawapak Hinjoy, Paphanij Suangtho, Suthanun Suthachana, Hannah E Clapham, Henrik Salje, Derek A T Cummings, Justin Lessler

Challenges in Real-Time Prediction of Infectious Disease: A Case Study of Dengue in Thailand

PLoS Neglected Tropical Diseases, 2016; 10(6): e0004761. 10.1371/journal.pntd.0004761
I. Morales, H. Salje, S. Saha, and E. S. Gurley

Seasonal Distribution and Climatic Correlates of Dengue Disease in Dhaka, Bangladesh

The American Journal of Tropical Medicine and Hygiene, 2016; 94(6): 1359-61. 10.4269/ajtmh.15-0846
J. Lessler, H. Salje, M. K. Grabowski, and D. A. T. Cummings

Measuring Spatial Dependence for Infectious Disease Epidemiology

PLoS ONE, 2016; 11(5): e0155249. 10.1371/journal.pone.0155249
S. Cauchemez, P. Nouvellet, A. Cori, T. Jombart, T. Garske, H. Clapham, S. Moore, H. L. Mills, H. Salje, C. Collins, I. Rodriquez-Barraquer, S. Riley, S. Truelove, H. Algarni, R. Alhakeem, K. AlHarbi, A. Turkistani, R. J. Aguas, D. A. T. Cummings, M. D. Van Kerkhove, C. A. Donnelly, J. Lessler, C. Fraser, A. Al-Barrak, N. M. Ferguson

Unraveling the drivers of MERS-CoV transmission

Proceedings of the National Academy of Sciences of the United States of America, 2016; 113(32): 9081-6. 10.1073/pnas.1519235113
S. Cauchemez, M. Besnard, P. Bompard, T. Dub, P. Guillemette-Artur, D. Eyrolle-Guignot, H. Salje, M. D. Van Kerkhove, V. Abadie, C. Garel, A. Fontanet, and H.-P. Mallet,

Association between Zika virus and microcephaly in French Polynesia, 2013-15: a retrospective study

The Lancet, 2016; 387(10033): 2125-2132. 10.1016/S0140-6736(16)00651-6
H. Salje, D.A.T. Cummings and J. Lessler

Estimating infectious disease transmission distances using the overall distribution of cases

Epidemics, 2016; 17: 10-18. 10.1016/j.epidem.2016.10.001
H. Salje, J. Lessler, K. Paul, A. Azman, M.W. Rahman, M. Rahman, D.A.T Cummings, E.S. Gurley, and S. Cauchemez

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, 2016; 113(47): 13420-1342. 10.1073/pnas.1611391113

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