Publications

The role of spatial epidemiology to support public health policies : case studies applied to health promotion, noncommunicable and infectious diseases in the canton of Vaud, Switzerland

A. L. Ladoy / S. Joost; I. Guessous (Dir.)

Lausanne, EPFL, 2024.

2023

Privacy-preserving contact tracing curbed COVID

M. Salathe

Nature. 2023-07-06. Vol. 619, num. 7968, p. 31-33. DOI : 10.1038/d41586-023-02130-6.

Hits and Misses: Digital Contact Tracing in a Pandemic

M. Garry; R. Zajac; L. Hope; M. Salathe; L. Levine et al.

Perspectives On Psychological Science. 2023-06-30. DOI : 10.1177/17456916231179365.

COVID-Twitter-BERT: A natural language processing model to analyse COVID-19 content on Twitter

M. Muller; M. Salathe; P. E. Kummervold

Frontiers In Artificial Intelligence. 2023-03-14. Vol. 6, p. 1023281. DOI : 10.3389/frai.2023.1023281.

Dynamics of social media behavior before and after SARS-CoV-2 infection

F. Durazzi; F. Pichard; D. Remondini; M. Salathe

Frontiers In Public Health. 2023-02-23. Vol. 10, p. 1069931. DOI : 10.3389/fpubh.2022.1069931.

Timeliness of online COVID-19 reports from official sources

L. Espinosa; O. Altunina; M. Salathe

Frontiers In Public Health. 2023-01-24. Vol. 10, p. 1027812. DOI : 10.3389/fpubh.2022.1027812.

2022

Deploying Decentralized, Privacy-Preserving Proximity Tracing

C. Troncoso; D. Bogdanov; E. Bugnion; S. Chatel; C. Cremers et al.

Communications Of The Acm. 2022-09-01. Vol. 65, num. 9, p. 48-57. DOI : 10.1145/3524107.

The Food Recognition Benchmark: Using Deep Learning to Recognize Food in Images

S. P. Mohanty; G. Singhal; E. A. Scuccimarra; D. Kebaili; H. Heritier et al.

Frontiers In Nutrition. 2022-05-06. Vol. 9, p. 875143. DOI : 10.3389/fnut.2022.875143.

Associations Between Device-Measured Physical Activity and Glycemic Control and Variability Indices Under Free-Living Conditions

D. El Fatouhi; H. Heritier; C. Allemann; L. Malisoux; N. Laouali et al.

Diabetes Technology & Therapeutics. 2022. Vol. 24, num. 3, p. 167-177. DOI : 10.1089/dia.2021.0294.

2021

Clusters of science and health related Twitter users become more isolated during the COVID-19 pandemic

F. Durazzi; M. Muller; M. Salathe; D. Remondini

Scientific Reports. 2021-10-04. Vol. 11, num. 1, p. 19655. DOI : 10.1038/s41598-021-99301-0.

Digital proximity tracing on empirical contact networks for pandemic control

G. Cencetti; G. Santin; A. Longa; E. Pigani; A. Barrat et al.

Nature Communications. 2021-03-12. Vol. 12, num. 1, p. 1655. DOI : 10.1038/s41467-021-21809-w.

CrowdNotifier: Decentralized Privacy-Preserving Presence Tracing

W. Lueks; S. Gürses; M. Veale; E. Bugnion; M. Salathé et al.

2021. p. 350-368. DOI : 10.2478/popets-2021-0074.

Toward a Common Performance and Effectiveness Terminology for Digital Proximity Tracing Applications

W. Lueks; J. Benzler; D. Bogdanov; G. Kirchner; R. Lucas et al.

Frontiers in Digital Health. 2021. Vol. 3. DOI : 10.3389/fdgth.2021.677929.

Supervised Learning Computer Vision Benchmark for Snake Species Identification From Photographs: Implications for Herpetology and Global Health

A. M. Durso; G. K. Moorthy; S. P. Mohanty; I. Bolon; M. Salathe et al.

Frontiers In Artificial Intelligence. 2021-01-01. Vol. 4, p. 582110. DOI : 10.3389/frai.2021.582110.

Modeling infectious disease dynamics towards informed public health interventions, with applications on COVID-19 and cholera

J. C. B. Lemaitre / A. Rinaldo; D. Pasetto (Dir.)

Lausanne, EPFL, 2021.

Learning Self-Exciting Temporal Point Processes Under Noisy Observations

W. Trouleau / M. Grossglauser; P. Thiran (Dir.)

Lausanne, EPFL, 2021.

On the use of applied machine learning and digital infrastructure to leverage social media data in health and epidemiology

M. M. Müller / M. Salathé (Dir.)

Lausanne, EPFL, 2021.

2020

Early evidence of effectiveness of digital contact tracing for SARS-CoV-2 in Switzerland

M. Salathe; C. L. Althaus; N. Anderegg; D. Antonioli; T. Ballouz et al.

Swiss Medical Weekly. 2020-12-16. Vol. 150, p. w20457. DOI : 10.4414/smw.20457.

A digital reconstruction of the 1630–1631 large plague outbreak in Venice

G. Lazzari; G. Colavizza; F. Bortoluzzi; D. Drago; A. Erboso et al.

Scientific Reports. 2020-10-20. Vol. 10, num. 1, p. 17849. DOI : 10.1038/s41598-020-74775-6.

Assessing Public Opinion on CRISPR-Cas9: Combining Crowdsourcing and Deep Learning

M. Muller; M. Schneider; M. Salathe; E. Vayena

Journal Of Medical Internet Research. 2020-08-31. Vol. 22, num. 8, p. e17830. DOI : 10.2196/17830.

A research agenda for digital proximity tracing apps

V. W. Viktor; B. Sebastian; B. Edouard; P. M. Alan; S. Marcel et al.

Swiss Medical Weekly. 2020-07-16. Vol. 150, p. w20324. DOI : 10.4414/smw.2020.20234.

Keep calm and carry on vaccinating: Is anti-vaccination sentiment contributing to declining vaccine coverage in England?

M. Edelstein; M. Muller; S. Ladhani; J. Yarwood; M. Salathe et al.

Vaccine. 2020-07-14. Vol. 38, num. 33, p. 5297-5304. DOI : 10.1016/j.vaccine.2020.05.082.

COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation

S. Marcel; A. L. Christian; N. Richard; S. Silvia; H. Emma et al.

Swiss Medical Weekly. 2020-03-19. Vol. 150, p. w202205. DOI : 10.4414/smw.2020.20225.

Contact networks across ages: computational analysis of epidemiological dynamics

G. Lazzari / M. Salathé (Dir.)

Lausanne, EPFL, 2020.

2019

Snakebite and snake identification: empowering neglected communities and health-care providers with AI

R. R. de Castaneda; A. M. Durso; N. Ray; J. L. Fernandez; D. J. Williams et al.

Lancet Digital Health. 2019-09-01. Vol. 1, num. 5, p. E202-E203. DOI : 10.1016/S2589-7500(19)30086-X.

Assessment of menstrual health status and evolution through mobile apps for fertility awareness

L. Symul; K. Wac; P. Hillard; M. Salathe

npj Digital Medicine. 2019-07-16. Vol. 2, p. 64. DOI : 10.1038/s41746-019-0139-4.

WHO and ITU establish benchmarking process for artificial intelligence in health

T. Wiegand; R. Krishnamurthy; M. Kuglitsch; N. Lee; S. Pujari et al.

Lancet. 2019-07-06. Vol. 394, num. 10192, p. 9-11. DOI : 10.1016/S0140-6736(19)30762-7.

M. M. Mueller; M. Salathe

Crowdbreaks: Tracking Health Trends Using Public Social Media Data and Crowdsourcing

Frontiers In Public Health. 2019-04-12. Vol. 7, p. 81. DOI : 10.3389/fpubh.2019.00081.

Assessing the Dynamics and Control of Droplet- and Aerosol-Transmitted Influenza Using an Indoor Positioning System

T. Smieszek; G. Lazzari; M. Salathé

Scientific Reports. 2019. Vol. 9, num. 1, p. 2185. DOI : 10.1038/s41598-019-38825-y.

2018

Digital epidemiology: what is it, and where is it going?

M. Salathe

Life Sciences Society And Policy. 2018-01-04. Vol. 14, p. 1. DOI : 10.1186/s40504-017-0065-7.

Likelihood-free Inference of Population Genetic Parameters from Time-Sampled Genetic Data

H. Shim / F. G. van der Goot Grunberg (Dir.)

Lausanne, EPFL, 2018.

Localizing the Source of an Epidemic Using Few Observations

B. M. Spinelli / P. Thiran; L. E. Celis (Dir.)

Lausanne, EPFL, 2018.

A field-based modelling framework of the ecohydrology of schistosomiasis

F. J. Perez Saez / A. Rinaldo (Dir.)

Lausanne, EPFL, 2018.

2017

Critical dynamics in population vaccinating behavior

A. D. Pananos; T. M. Bury; C. Wang; J. Schonfeld; S. P. Mohanty et al.

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2017. Vol. 114, num. 52, p. 13762-13767. DOI : 10.1073/pnas.1704093114.

An ecological and digital epidemiology analysis on the role of human behavior on the 2014 Chikungunya outbreak in Martinique

B. Roche; B. Gaillard; L. Leger; R. Pelagie-Moutenda; T. Sochacki et al.

Scientific Reports. 2017. Vol. 7, p. 5967. DOI : 10.1038/s41598-017-05957-y.

Precision global health in the digital age

A. Flahault; A. Geissbuhler; I. Guessous; P. J. Guerin; I. Bolon et al.

Swiss Medical Weekly. 2017. Vol. 147, p. w14423. DOI : 10.4414/smw.2017.14423.

Spatially explicit modeling of cholera epidemics

F. Finger / A. Rinaldo; E. Bertuzzo (Dir.)

Lausanne, EPFL, 2017.

2016

Digital Pharmacovigilance and Disease Surveillance: Combining Traditional and Big-Data Systems for Better Public Health

M. Salathe

Journal of Infectious Diseases. 2016-11-14. Vol. 214, p. S399-S403. DOI : 10.1093/infdis/jiw281.

Statistical physics of vaccination

Z. Wang; C. T. Bauch; S. Bhattacharyya; A. D’Onofrio; P. Manfredi et al.

Physics Reports-Review Section Of Physics Letters. 2016. Vol. 664, p. 1-113. DOI : 10.1016/j.physrep.2016.10.006.

Using Deep Learning for Image-Based Plant Disease Detection

S. P. Mohanty; D. P. Hughes; M. Salathe

Frontiers In Plant Science. 2016. Vol. 7, p. 1419. DOI : 10.3389/fpls.2016.01419.

Infectious Disease Containment Based on a Wireless Sensor System

X. Sun; Z. Lu; X. Zhang; M. Salathe; G. Cao

Ieee Access. 2016. Vol. 4, p. 1558-1569. DOI : 10.1109/Access.2016.2551199.

2015

Ethical challenges of big data in public health

E. Vayena; M. Salathé; L. C. Madoff; J. S. Brownstein

PLoS computational biology. 2015. Vol. 11, num. 2, p. e1003904. DOI : 10.1371/journal.pcbi.1003904.

C. L. Althaus; M. Salathé

Measles Vaccination Coverage and Cases among Vaccinated Persons

Emerging infectious diseases. 2015. Vol. 21, num. 8, p. 1480-1. DOI : 10.3201/eid2108.150284.

Targeted vaccination based on a wireless sensor system

S. Xiao; L. Zongqing; Z. Xiaomei; M. Salathé; C. Guohong

2015. Thirteenth IEEE International Conference on Pervasive Computing and Communications, St. Louis, Missouri, USA, March 23-27, 2015. p. 215-220. DOI : 10.1109/PERCOM.2015.7146531.

Modeling Individual-Level Infection Dynamics Using Social Network Information

S. Tuarob; C. Tucker; M. Salathé; N. Ram

2015. The 24th ACM International Conference on Information and Knowledge Management, Melbourne, Australia, October 19-23, 2015. p. 1501-1510. DOI : 10.1145/2806416.2806575.

Identifying Adverse Effects of HIV Drug Treatment and Associated Sentiments Using Twitter

C. Adrover; T. Bodnar; Z. Huang; A. Telenti; M. Salathé

JMIR Public Health and Surveillance. 2015. Vol. 1, num. 2, p. e7. DOI : 10.2196/publichealth.4488.

2014

An ensemble heterogeneous classification methodology for discovering health-related knowledge in social media messages

S. Tuarob; C. S. Tucker; M. Salathe; N. Ram

Journal of biomedical informatics. 2014. Vol. 49, p. 255-68. DOI : 10.1016/j.jbi.2014.03.005.

Positive network assortativity of influenza vaccination at a high school: implications for outbreak risk and herd immunity

V. C. Barclay; T. Smieszek; J. He; G. Cao; J. J. Rainey et al.

PloS One. 2014. Vol. 9, num. 2, p. e87042. DOI : 10.1371/journal.pone.0087042.

How should social mixing be measured: comparing web-based survey and sensor-based methods

T. Smieszek; V. C. Barclay; I. Seeni; J. J. Rainey; H. Gao et al.

BMC infectious diseases. 2014. Vol. 14, p. 136. DOI : 10.1186/1471-2334-14-136.

Two Sides of a Coin: Separating Personal Communication and Public Dissemination Accounts in Twitter

P. Yin; N. Ram; W-C. Lee; C. Tucker; S. Khandelwal et al.

2014. 18th Pacific-Asia Conference, PAKDD 2014, Tainan, Taiwan, May 13-16, 2014. p. 163-175. DOI : 10.1007/978-3-319-06608-0_14.

On the ground validation of online diagnosis with Twitter and medical records

T. Bodnar; V. Barclay; N. Ram; C. Tucker; M. Salathé

2014. 23rd International World Wide Web Conference, Seoul, Korea, April 7-11, 2014. p. 651-656. DOI : 10.1145/2567948.2579272.

Targeting HIV-related Medication Side Effects and Sentiment Using Twitter Data

C. Adrover; T. Bodnar; M. Salathé

arXiv. 2014. Vol. 1404.3610.

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2013

Influenza A (H7N9) and the importance of digital epidemiology

M. Salathé; C. C. Freifeld; S. R. Mekaru; A. F. Tomasulo; J. S. Brownstein

The New England journal of medicine. 2013. Vol. 369, num. 5, p. 401-4. DOI : 10.1056/NEJMp1307752.

The dynamics of health behavior sentiments on a large online social network

M. Salathé; D. Vu; S. Khandelwal; D. Hunter

EPJ Data Science. 2013. Vol. 2, num. 1, p. 4. DOI : 10.1140/epjds16.

Validating models for disease detection using twitter

T. Bodnar; M. Salathé

2013. 22nd International World Wide Web Conference (WWW 2013), Rio de Janeiro, Brazil, May 13 – 17, 2013. p. 699-702. DOI : 10.1145/2487788.2488027.

Complex social contagion makes networks more vulnerable to disease outbreaks

E. Campbell; M. Salathé

Scientific Reports. 2013. Vol. 3, p. 1905. DOI : 10.1038/srep01905.

A low-cost method to assess the epidemiological importance of individuals in controlling infectious disease outbreaks

T. Smieszek; M. Salathé

BMC medicine. 2013. Vol. 11, p. 35. DOI : 10.1186/1741-7015-11-35.

Discovering health-related knowledge in social media using ensembles of heterogeneous features

S. Tuarob; C. Tucker; M. Salathé; N. Ram

2013. 22nd ACM international conference on Information & Knowledge Management (CIKM 2013), San Francisco, CA, USA, October 27 – November 01, 2013. p. 1685-1690. DOI : 10.1145/2505515.2505629.

Understanding population displacements on location-based call records using road data

Z. Huang; U. Kumar; T. Bodnar; M. Salathé

2013. 21st ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM SIGSPATIAL GIS 2013), Orlando, Florida, USA, November 5-8, 2013. p. 17-21. DOI : 10.1145/2534190.2534199.

Synthesizing Social Proximity Networks by Combining Subjective Surveys with Digital Traces

H. Xia; J. Chen; M. Marathe; H. Mortveit; M. Salathé

2013. IEEE 16th International Conference on Computational Science and Engineering (CSE), Sydney, Australia, December 03-05, 2013. p. 188-195. DOI : 10.1109/CSE.2013.38.

The Social Maintenance of Cooperation through Hypocrisy

T. Bodnar; M. Salathé

arXiv. 2013. Vol. 1304.3747.

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2012

Digital epidemiology

M. Salathé; L. Bengtsson; T. J. Bodnar; D. D. Brewer; J. S. Brownstein et al.

PLoS computational biology. 2012. Vol. 8, num. 7, p. e1002616. DOI : 10.1371/journal.pcbi.1002616.

R. Mostowy; J. Engelstädter; M. Salathé

Non-genetic inheritance and the patterns of antagonistic coevolution

BMC evolutionary biology. 2012. Vol. 12, p. 93. DOI : 10.1186/1471-2148-12-93.

Governing the global commons with local institutions

T. Bodnar; M. Salathé

PloS One. 2012. Vol. 7, num. 4, p. e34051. DOI : 10.1371/journal.pone.0034051.

M. Salathé; S. Khandelwal

2011

Assessing vaccination sentiments with online social media: implications for infectious disease dynamics and control

PLoS computational biology. 2011. Vol. 7, num. 10, p. e1002199. DOI : 10.1371/journal.pcbi.1002199.

Measuring school contact networks using wireless sensor technology

J. Jones; M. Salathé; M. Feldman; M. Kazandjieva; J. Lee et al.

2011. 36th Annual Meeting: Human Biology Association, Minneapolis, Minesota, USA, April 13-14, 2011. p. 263. DOI : 10.1002/ajhb.21153.

2010

Modelling the influence of human behaviour on the spread of infectious diseases: a review

S. Funk; M. Salathé; V. A. A. Jansen

Journal of the Royal Society, Interface / the Royal Society. 2010. Vol. 7, num. 50, p. 1247-56. DOI : 10.1098/rsif.2010.0142.

A high-resolution human contact network for infectious disease transmission

M. Salathé; M. Kazandjieva; J. W. Lee; P. Levis; M. W. Feldman et al.

Proceedings of the National Academy of Sciences of the United States of America. 2010. Vol. 107, num. 51, p. 22020-5. DOI : 10.1073/pnas.1009094108.

Dynamics and control of diseases in networks with community structure

M. Salathé; J. H. Jones

PLoS computational biology. 2010. Vol. 6, num. 4, p. e1000736. DOI : 10.1371/journal.pcbi.1000736.

Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance

D. J. Salkeld; M. Salathé; P. Stapp; J. H. Jones

Proceedings of the National Academy of Sciences of the United States of America. 2010. Vol. 107, num. 32, p. 14247-50. DOI : 10.1073/pnas.1002826107.

Experiences in measuring a human contact network for epidemiology research

M. Kazandjieva; J. Lee; M. Salathé; M. Feldman; J. Jones et al.

2010. 6th Workshop on Hot Topics in Embedded Networked Sensors (HotEMNETS’10), Killarney, Ireland, June 28-29, 2010. p. 7. DOI : 10.1145/1978642.1978651.

On the evolution of sexual reproduction in hosts coevolving with multiple parasites

R. Mostowy; M. Salathé; R. D. Kouyos; S. Bonhoeffer

Evolution; international journal of organic evolution. 2010. Vol. 64, num. 6, p. 1644-56. DOI : 10.1111/j.1558-5646.2010.00951.x.

2009

Early assessment of anxiety and behavioral response to novel swine-origin influenza A(H1N1)

J. H. Jones; M. Salathé

PloS One. 2009. Vol. 4, num. 12, p. e8032. DOI : 10.1371/journal.pone.0008032.

M. Salathé; J. Van Cleve; M. W. Feldman

Evolution of stochastic switching rates in asymmetric fitness landscapes

Genetics. 2009. Vol. 182, num. 4, p. 1159-64. DOI : 10.1534/genetics.109.103333.

M. Salathé; R. D. Kouyos; S. Bonhoeffer

On the causes of selection for recombination underlying the red queen hypothesis

The American naturalist. 2009. Vol. 174, num. Suppl 1, p. S31-42. DOI : 10.1086/599085.

The role of epistasis on the evolution of recombination in host-parasite coevolution

R. D. Kouyos; M. Salathé; S. P. Otto; S. Bonhoeffer

Theoretical population biology. 2009. Vol. 75, num. 1, p. 1-13. DOI : 10.1016/j.tpb.2008.09.007.

M. Salathé; R. D. Kouyos; S. Bonhoeffer

2008

The state of affairs in the kingdom of the Red Queen

Trends in ecology & evolution. 2008. Vol. 23, num. 8, p. 439-45. DOI : 10.1016/j.tree.2008.04.010.

M. Salathé; S. Bonhoeffer

The effect of opinion clustering on disease outbreaks

Journal of the Royal Society, Interface / the Royal Society. 2008. Vol. 5, num. 29, p. 1505-8. DOI : 10.1098/rsif.2008.0271.

Rapid parasite adaptation drives selection for high recombination rates

M. Salathé; R. D. Kouyos; R. R. Regoes; S. Bonhoeffer

Evolution; international journal of organic evolution. 2008. Vol. 62, num. 2, p. 295-300. DOI : 10.1111/j.1558-5646.2007.00265.x.

Parasites lead to evolution of robustness against gene loss in host signaling networks

M. Salathé; O. S. Soyer

Molecular systems biology. 2008. Vol. 4, p. 202. DOI : 10.1038/msb.2008.44.

R. D. Kouyos; M. Salathé; S. Bonhoeffer

2007

The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations

BMC evolutionary biology. 2007. Vol. 7, p. 211. DOI : 10.1186/1471-2148-7-211.

The evolution of complexity on the level of genes, individuals and populations

M. Salathé / S. Bonhoeffer (Dir.)

Ecole Polytechnique Fédérale de Zürich (ETHZ), 2007.

2006

Signal transduction networks: topology, response and biochemical processes

O. S. Soyer; M. Salathé; S. Bonhoeffer

Journal of theoretical biology. 2006. Vol. 238, num. 2, p. 416-25. DOI : 10.1016/j.jtbi.2005.05.030.

M. Salathé; M. Ackermann; S. Bonhoeffer

The effect of multifunctionality on the rate of evolution in yeast

Molecular biology and evolution. 2006. Vol. 23, num. 4, p. 721-2. DOI : 10.1093/molbev/msj086.

Mutation accumulation in space and the maintenance of sexual reproduction

M. Salathé; R. Salathé; P. Schmid-Hempel; S. Bonhoeffer

Ecology letters. 2006. Vol. 9, num. 8, p. 941-6. DOI : 10.1111/j.1461-0248.2006.00942.x.

High epitope expression levels increase competition between T cells

A. Scherer; M. Salathé; S. Bonhoeffer

PLoS computational biology. 2006. Vol. 2, num. 8, p. e109. DOI : 10.1371/journal.pcbi.0020109.

Sexual selection and its effect on the fixation of an asexual clone

M. Salathé

Biology letters. 2006. Vol. 2, num. 4, p. 536-8. DOI : 10.1098/rsbl.2006.0529.

2005

Neutral drift and polymorphism in gene-for-gene systems

M. Salathe; A. Scherer; S. Bonhoeffer

Ecology Letters. 2005. Vol. 8, num. 9, p. 925-932. DOI : 10.1111/j.1461-0248.2005.00794.x.

The evolution of network topology by selective removal

M. Salathé; R. M. May; S. Bonhoeffer

Journal of the Royal Society, Interface / the Royal Society. 2005. Vol. 2, num. 5, p. 533-6. DOI : 10.1098/rsif.2005.0072.