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Samuel Alizon

CNRS Research Director and head of the Ecology & Evolution of Health team
134
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Current affiliations
  • 139750
Researcher identifiers
Web site
  • https://www.college-de-france.fr/personne/samuel-alizon

Presentation

Je suis Directeur de recherche au CNRS, affecté au [Centre Interdisciplinaire de Recherches en Biologie (CIRB)](https://www.college-de-france.fr/site/en-cirb/center-for-interdisciplinary-research-in-biology.htm) au Collège de France à Paris. Mes travaux portent sur l'écologie et l'évolution de la santé, notamment les virus humains tels que les papillomavirus humains (HPV), le VIH ou le SARS-CoV-2. Je développe en particulier des modèles mathématiques et des simulations numériques. Je suis l'auteur d'un livre grand public intitulé [Évolution, écologie et pandémies](https://www.editionspoints.com/ouvrage/evolution-ecologie-et-pandemies-samuel-alizon/9782757887233), publié en 2020 au Points Seuil. Pour plus de détails, voir mon [site internet personnel](https://alizon.ouvaton.org/index_fr.html).
CNRS research director, based at the [Centre for Interdisciplinary Research in Biology (CIRB)](https://www.college-de-france.fr/site/en-cirb/center-for-interdisciplinary-research-in-biology.htm) in Paris. Theoretical evolutionary ecologist specialised in the study of infectious diseases, with a particular interest in human viruses such as HIV, HCV, SARS-CoV-2, or HPV. For further details, see my [personal](https://alizon.ouvaton.org/) website.

Publications

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Does exposure to different menstrual products affect the vaginal environment?

Nicolas Tessandier , Ilkay Başak Uysal , Baptiste Elie , Christian Selinger , Sophie Grasset
Molecular Ecology, 2023, EVOLUTIONARY ECOLOGY OF HUMAN‐ASSOCIATED MICROBES, 32 (10), pp.2592-2601. ⟨10.1111/mec.16678⟩
Journal articles hal-03847887v1
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Predicting the virulence of future emerging zoonotic viruses

Samuel Alizon
PLoS Biology, 2023, 21 (9), pp.e3002286. ⟨10.1371/journal.pbio.3002286⟩
Journal articles hal-04201651v1
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Multiple infection theory rather than ‘socio‐virology’? A commentary on Leeks et al. 2023

Samuel Alizon
Journal of Evolutionary Biology, 2023, 36 (11), pp.1571-1576. ⟨10.1111/jeb.14245⟩
Journal articles hal-04293988v1
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COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences

Gonché Danesh , Corentin Boennec , Laura Verdurme , Mathilde Roussel , Sabine Trombert-Paolantoni
Peer Community Journal, 2023, 3, pp.e101. ⟨10.24072/pcjournal.333⟩
Journal articles hal-04246696v1
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Within-host evolutionary dynamics of antimicrobial quantitative resistance

Ramsès Djidjou-Demasse , Mircea T Sofonea , Marc Choisy , Samuel Alizon
Mathematical Modelling of Natural Phenomena, 2023, 18, pp.24. ⟨10.1051/mmnp/2023019⟩
Journal articles hal-03194023v4

Corrigendum to: Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities

Bastien Reyné , Christian Selinger , Mircea Sofonea , Stéphanie Miot , Amandine Pisoni
International Journal of Epidemiology, 2022, 51 (2), pp.689-689. ⟨10.1093/ije/dyab269⟩
Journal articles hal-04056156v1
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Les lois de la contagion. Fake news, virus, tendances…

Samuel Alizon
Natures Sciences Sociétés, 2022, 30 (1), pp.109-111. ⟨10.1051/nss/2022021⟩
Journal articles hal-03664004v1
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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020

Samuel Alizon , Christian Selinger , Mircea T Sofonea , Stéphanie Haim-Boukobza , Jean-Marc Giannoli
Eurosurveillance, 2022, 27 (6), pp.2100406. ⟨10.2807/1560-7917.ES.2022.27.6.2100406⟩
Journal articles hal-03175551v3
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Variant‐specific SARS‐CoV‐2 within‐host kinetics

Baptiste Elie , Bénédicte Roquebert , Mircea T Sofonea , Sabine Trombert-Paolantoni , Vincent Foulongne
Journal of Medical Virology, 2022, 94 (8), pp.3625-3633. ⟨10.1002/jmv.27757⟩
Journal articles hal-03651890v1
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Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022

Mircea Sofonea , Bénédicte Roquebert , Vincent Foulongne , David Morquin , Laura Verdurme
Emerging Infectious Diseases, 2022, 28 (7), pp.1355-1365. ⟨10.3201/eid2807.220033⟩
Journal articles hal-03714983v1
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The source of individual heterogeneity shapes infectious disease outbreaks

Baptiste Elie , Christian Selinger , Samuel Alizon
Proceedings of the Royal Society B: Biological Sciences, 2022, 289 (1974), pp.20220232. ⟨10.1098/rspb.2022.0232⟩
Journal articles hal-03175555v2
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TiPS : Rapidly simulating trajectories and phylogenies from compartmental models

Gonché Danesh , Emma Saulnier , Olivier Gascuel , Marc Choisy , Samuel Alizon
Methods in Ecology and Evolution, 2022, 14 (2), pp.487-495. ⟨10.1111/2041-210X.14038⟩
Journal articles hal-03903561v1
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Concomitant and productive genital infections by HSV-2 and HPV in two young women: A case report

Ilkay Başak Uysal , Vanina Boué , Carmen Lia Murall , Christelle Graf , Christian Selinger
IDCases, 2022, 30, pp.e01604. ⟨10.1016/j.idcr.2022.e01604⟩
Journal articles hal-03795483v1
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Challenges for mathematical epidemiological modelling

Pascal Crepey , Harold Noël , Samuel Alizon
Anaesthesia Critical Care & Pain Medicine, 2022, 41 (2), pp.101053. ⟨10.1016/j.accpm.2022.101053⟩
Journal articles hal-03607991v1
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Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics

Bastien Reyné , Quentin Richard , Christian Selinger , Mircea T Sofonea , Ramsès Djidjou-Demasse
Mathematical Modelling of Natural Phenomena, 2022, 17, pp.7. ⟨10.1051/mmnp/2022008⟩
Journal articles hal-03629334v1
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Predicting COVID-19 incidence in French hospitals using human contact network analytics

Christian Selinger , Marc Choisy , Samuel Alizon
International Journal of Infectious Diseases, 2021, 111, pp.100 - 107. ⟨10.1016/j.ijid.2021.08.029⟩
Journal articles hal-03267059v2
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Treating symptomatic infections and the co-evolution of virulence and drug resistance

Samuel Alizon
Peer Community Journal, 2021, 1, pp.e47. ⟨10.24072/pcjournal.38⟩
Journal articles hal-03001103v2
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Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021

Stéphanie Haim-Boukobza , Bénédicte Roquebert , Sabine Trombert-Paolantoni , Emmanuel Lecorche , Laura Verdurme
Emerging Infectious Diseases, 2021, 27 (5), pp.1496-1499. ⟨10.3201/eid2705.210397⟩
Journal articles hal-03150819v3
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Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities

Bastien Reyné , Christian Selinger , Mircea T Sofonea , Stéphanie Miot , Amandine Pisoni
International Journal of Epidemiology, 2021, 50 (6), pp.1788-1794. ⟨10.1093/ije/dyab121⟩
Journal articles hal-03289625v1
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Estimating dates of origin and end of COVID-19 epidemics

Thomas Bénéteau , Elie ` Baptiste , Mircea T Sofonea , Samuel Alizon
Peer Community Journal, 2021, 1, pp.e70. ⟨10.24072/pcjournal.63⟩
Journal articles hal-03120811v2
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SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

Benedicte Roquebert , Stéphanie Haim-Boukobza , Sabine Trombert-Paolantoni , Emmanuel Lecorche , Laura Verdurme
International Journal of Infectious Diseases, 2021, ⟨10.1016/j.ijid.2021.09.076⟩
Journal articles hal-03366559v1
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Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

Christian Selinger , Samuel Alizon
PLoS Computational Biology, 2021, 17 (9), pp.e1009375. ⟨10.1371/journal.pcbi.1009375⟩
Journal articles hal-03357549v1
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Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

Samuel Alizon , Stéphanie Haim-Boukobza , Vincent Foulongne , Laura Verdurme , Sabine Trombert-Paolantoni
Eurosurveillance, 2021, 26 (28), ⟨10.2807/1560-7917.ES.2021.26.28.2100573⟩
Journal articles hal-03289622v1
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The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

Bénédicte Roquebert , Sabine Trombert-Paolantoni , Stéphanie Haim-Boukobza , Emmanuel Lecorche , Laura Verdurme
Eurosurveillance, 2021, 26 (23), ⟨10.2807/1560-7917.es.2021.26.23.2100447⟩
Journal articles hal-03289627v1
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SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs

Samuel Alizon , Mircea T Sofonea
Journal of Evolutionary Biology, 2021, 34 (12), pp.1867 - 1877. ⟨10.1111/jeb.13896⟩
Journal articles hal-03289628v1
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Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections

Thomas Beneteau , Christian Selinger , Mircea T Sofonea , Samuel Alizon
PLoS Computational Biology, 2021, 17 (9), pp.e1009352. ⟨10.1371/journal.pcbi.1009352⟩
Journal articles hal-03357550v1
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Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

Gonché Danesh , Victor Virlogeux , Christophe Ramière , Caroline Charre , Laurent Cotte
PLoS Pathogens, 2021, 17 (9), pp.e1009916. ⟨10.1371/journal.ppat.1009916⟩
Journal articles hal-03357552v1
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Cytokine response following perturbation of the cervicovaginal milieu during HPV genital infection

Christian Selinger , Massilva Rahmoun , Carmen Lia Murall , Claire Bernat , Vanina Boué
Immunologic Research, 2021, 69 (3), pp.255-263. ⟨10.1007/s12026-021-09196-2⟩
Journal articles hal-03354891v1
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Superspreading genomes

Samuel Alizon
Science, 2021, 371 (6529), pp.574-575. ⟨10.1126/science.abg0100⟩
Journal articles hal-03133445v1
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Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses

A. Debernardi , W. Jarassier , C. Soret , C. Mougin , Samuel Alizon
Archives of Virology, 2021, 166 (12), pp.3421-3425. ⟨10.1007/s00705-021-05259-9⟩
Journal articles hal-03425708v1
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Within-host bacterial growth dynamics with both mutation and horizontal gene transfer

Ramsès Djidjou-Demasse , Samuel Alizon , Mircea T Sofonea
Journal of Mathematical Biology, 2021, ⟨10.1007/s00285-021-01571-9⟩
Journal articles hal-02500420v1
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Two waves and a high tide: the COVID-19 epidemic in France

Mircea T Sofonea , Corentin Boennec , Yannis Michalakis , Samuel Alizon
Anaesthesia Critical Care & Pain Medicine, 2021, 40 (3), pp.100881. ⟨10.1016/j.accpm.2021.100881⟩
Journal articles hal-03289626v2
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Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic

Quentin Richard , Samuel Alizon , Marc Choisy , Mircea T Sofonea , Ramsès Djidjou-Demasse
PLoS Computational Biology, 2021, ⟨10.1371/journal.pcbi.1008776⟩
Journal articles hal-02879512v3
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Emerging dynamics from high-resolution spatial numerical epidemics

Olivier Thomine , Samuel Alizon , Corentin Boennec , Marc Barthelemy , Mircea T Sofonea
eLife, 2021, 10, ⟨10.7554/elife.71417⟩
Journal articles hal-03415297v1
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Early phylodynamics analysis of the COVID-19 epidemic in France

Gonché Danesh , Baptiste Elie , Yannis Michalakis , Mircea T Sofonea , Antonin Bal
Peer Community Journal, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩
Journal articles hal-03001114v2
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Can we eradicate viral pathogens?

Samuel Alizon , Paul E Turner
Journal of Evolutionary Biology, 2021, 34 (12), pp.1851-1854. ⟨10.1111/jeb.13958⟩
Journal articles hal-03500287v1
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SARS-CoV-2 viral RNA levels are not 'viral load'

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon , Ignacio G. Bravo
Trends in Microbiology, 2021, 29 (11), pp.970-972. ⟨10.1016/j.tim.2021.08.008⟩
Journal articles hal-03419147v1
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Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France

Mircea T Sofonea , Samuel Alizon
Anaesthesia Critical Care & Pain Medicine, 2021, ⟨10.1016/j.accpm.2021.100943⟩
Journal articles hal-03366541v1
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Memory is key in capturing COVID-19 epidemiological dynamics

Mircea T Sofonea , Bastien Reyné , Baptiste Elie , Ramsès Djidjou-Demasse , Christian Selinger
Epidemics, 2021, 35, pp.100459. ⟨10.1016/j.epidem.2021.100459⟩
Journal articles hal-03289624v1
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10 Questions and 4 experts on Corona

Akiko Iwasaki , Gérard Krause , Samuel Alizon , Rino Rappuoli
EMBO Molecular Medicine, 2020, 12 (5), ⟨10.15252/emmm.202012317⟩
Journal articles hal-04053451v1
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HPV cervical infections and serological status in vaccinated and unvaccinated women

Carmen Lia Murall , Bastien Reyné , Christian Selinger , Claire Bernat , Vanina Boué
Vaccine, 2020, 38 (51), pp.8167-8174. ⟨10.1016/j.vaccine.2020.10.078⟩
Journal articles hal-03001077v2
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Analyses génomiques et phylodynamiques du SARS-Cov-2

Baptiste Elie , Samuel Alizon
Revue Francophone des Laboratoires, 2020, 2020 (526), pp.57-62. ⟨10.1016/S1773-035X(20)30314-2⟩
Journal articles hal-02893568v2
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COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences

Jérôme Bourret , Samuel Alizon , Ignacio Bravo
Genome Biology and Evolution, 2019, 11 (12), pp.3523-3528. ⟨10.1093/gbe/evz262⟩
Journal articles hal-02957623v1
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Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study

Carmen Murall , Massilva Rahmoun , Christian Selinger , Monique Baldellou , Claire Bernat
BMJ Open, 2019, 9 (6), pp.e025129. ⟨10.1136/bmjopen-2018-025129⟩
Journal articles hal-02157154v1
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Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence

Samuel Alizon , Ignacio G Bravo , Paul Farrell , Sally Roberts
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1773), pp.20190041. ⟨10.1098/rstb.2019.0041⟩
Journal articles hal-02108649v3
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Epithelial stratification shapes infection dynamics

Carmen Lia Murall , Robert Jackson , Ingeborg Zehbe , Nathalie Boulle , Michel Segondy
PLoS Computational Biology, 2019, 15 (1), pp.e1006646. ⟨10.1371/journal.pcbi.1006646⟩
Journal articles hal-02069914v1
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Modelling the evolution of viral oncogenesis

Carmen Lia Murall , Samuel Alizon
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses, 374 (1773), pp.20180302. ⟨10.1098/rstb.2018.0302⟩
Journal articles hal-02124893v1
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Detecting within-host interactions from genotype combination prevalence data

Samuel Alizon , Carmen Lia Murall , Emma Saulnier , Mircea T Sofonea
Epidemics, 2019, 29, pp.100349. ⟨10.1016/j.epidem.2019.100349⟩
Journal articles hal-02387765v1
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Can Ebola Virus evolve to be less virulent in humans?

Mircea T Sofonea , L. Aldakak , Luis F. V. V. Boullosa , Samuel Alizon
Journal of Evolutionary Biology, 2018, 31 (3), pp.382 - 392. ⟨10.1111/jeb.13229⟩
Journal articles hal-01897077v1
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Reconciling Pasteur and Darwin to control infectious diseases

Samuel Alizon , Pierre-Olivier Méthot
PLoS Biology, 2018, 16 (1), pp.e2003815. ⟨10.1371/journal.pbio.2003815⟩
Journal articles hal-01737461v1
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Coevolution of virulence and immunosuppression in multiple infections

Tsukushi Kamiya , Nicole Mideo , Samuel Alizon
Journal of Evolutionary Biology, 2018, 31 (7), pp.995 - 1005. ⟨10.1111/jeb.13280⟩
Journal articles hal-01898496v1
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Inexpensive Research in the Golden Open-Access Era

Samuel Alizon
Trends in Ecology and Evolution, 2018, 33 (5), pp.301 - 303. ⟨10.1016/j.tree.2018.02.005⟩
Journal articles hal-01788084v1
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Simulating the effect of public health interventions using dated virus sequences and geographical data

Samuel Alizon
Peer Community in Evolutionary Biology, 2018, pp.100046. ⟨10.24072/pci.evolbiol.100046⟩
Journal articles hal-01705816v1
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Predicting HIV virulence evolution in response to widespread treatment

Samuel Alizon , Roger Kouyos
Peer Community in Evolutionary Biology, 2017, ⟨10.24072/pci.evolbiol.100013⟩
Journal articles hal-01467624v1
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Exposing the diversity of multiple infection patterns

Mircea T Sofonea , Samuel Alizon , Yannis Michalakis
Journal of Theoretical Biology, 2017, 419, pp.278 - 289. ⟨10.1016/j.jtbi.2017.02.011⟩
Journal articles hal-01567902v1
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Why Human Papillomavirus Acute Infections Matter

Samuel Alizon , Carmen Murall , Ignacio G Bravo
Viruses, 2017, 9 (10), pp.293. ⟨10.3390/v9100293⟩
Journal articles hal-01638068v1
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Modelling the evolution of how vector-borne parasites manipulate the vector's host choice

Samuel Alizon
Peer Community in Evolutionary Biology, 2017, pp.100023. ⟨10.24072/pci.evolbiol.100023⟩
Journal articles hal-01560018v1
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Phylodynamique des infections virales

Samuel Alizon , Emma Saulnier
Virologie, 2017, 21 (3), pp.119-129. ⟨10.1684/vir.2017.0696⟩
Journal articles hal-01638067v1
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Utilisation des phylogénies d'infections en épidémiologie

Samuel Alizon , Emma Saulnier
Bulletin de veille scientifique , 2017, 31, pp.42-43
Journal articles anses-01533229v1
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Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study

Emma Saulnier , Olivier Gascuel , Samuel Alizon
PLoS Computational Biology, 2017, 13 (3), pp.e1005416. ⟨10.1371/journal.pcbi.1005416⟩
Journal articles hal-01567904v1
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A Visionary Pioneer of Parasite Ecology and Evolution

Samuel Alizon
The American Naturalist, 2016, 187 (6), pp.ii-iii. ⟨10.1086/686526⟩
Journal articles hal-01567905v1
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Adaptive virulence evolution: the good old fitness-based approach

Samuel Alizon , Yannis Michalakis
Trends in Ecology and Evolution, 2015, 30 (5), pp.248-254. ⟨10.1016/j.tree.2015.02.009⟩
Journal articles hal-01567907v1

From within-host interactions to epidemiological competition: a general model for multiple infections

Mircea T Sofonea , Samuel Alizon , Yannis Michalakis
Philosophical Transactions of the Royal Society B: Biological Sciences, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩
Journal articles hal-01571806v1
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Within-host stochastic emergence dynamics of immune-escape mutants

Matthew Hartfield , Samuel Alizon
PLoS Computational Biology, 2015, 11 (3), pp.e1004149. ⟨10.1371/journal.pcbi.1004149⟩
Journal articles hal-01567908v1
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What is a pathogen? Toward a process view of host-parasite interactions

Pierre-Olivier Methot , Samuel Alizon
Virulence, 2014, 5 (8), pp.775-85. ⟨10.4161/21505594.2014.960726⟩
Journal articles hal-01567912v1
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Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance

Susan V Cousineau , Samuel Alizon
Journal of Evolutionary Biology, 2014, 27 (12), pp.2753-66. ⟨10.1111/jeb.12541⟩
Journal articles hal-01567915v1
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Evidence that hepatitis C virus genome partly controls infection outcome

Matthew Hartfield , Rowena Bull , Peter A White , Andrew Lloyd , Fabio Luciani
Evolutionary Applications, 2014, 7 (5), pp.533-47. ⟨10.1111/eva.12151⟩
Journal articles hal-01567913v1
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Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics

Samuel Alizon , Sébastien Lion , Carmen Lia Murall , Jessica Lee Abbate
Virulence, 2014, 5 (8), pp.825-827. ⟨10.4161/21505594.2014.976514⟩
Journal articles hal-01567909v1
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Epidemiological feedbacks affect evolutionary emergence of pathogens

Matthew Hartfield , Samuel Alizon
The American Naturalist, 2014, 183 (4), pp.E105-17. ⟨10.1086/674795⟩
Journal articles hal-01567911v1

Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective

Christophe Fraser , Katrina Lythgoe , Gabriel E Leventhal , George Shirreff , T Deirdre Hollingsworth
Science, 2014, 343 (6177), pp.1243727. ⟨10.1126/science.1243727⟩
Journal articles hal-01567910v1

Clinical applications of pathogen phylogenies

Matthew Hartfield , Carmen Lia Murall , Samuel Alizon
Trends in Molecular Medicine, 2014, 20 (7), pp.394-404. ⟨10.1016/j.molmed.2014.04.002⟩
Journal articles hal-01567914v1
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How effectively can HIV phylogenies be used to measure heritability?

George Shirreff , Samuel Alizon , Anne Cori , Huldrych F Guenthard , Oliver Laeyendecker
Evolution, Medicine, and Public Health, 2013, 2013 (1), pp.209-24. ⟨10.1093/emph/eot019⟩
Journal articles hal-01567924v1

On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison

Samuel Alizon
Journal of Evolutionary Biology, 2013, 26 (9), pp.2051-6. ⟨10.1111/jeb.12199⟩
Journal articles hal-01567920v1
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Epidemic spread on weighted networks

Christel Kamp , Mathieu Moslonka-Lefebvre , Samuel Alizon
PLoS Computational Biology, 2013, 9 (12), pp.e1003352. ⟨10.1371/journal.pcbi.1003352⟩
Journal articles hal-01567923v1
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Multiple infections and the evolution of virulence

Samuel Alizon , Jacobus C De Roode , Yannis Michalakis
Ecology Letters, 2013, 16 (4), pp.556-567. ⟨10.1111/ele.12076⟩
Journal articles hal-01567918v1
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Introducing the outbreak threshold in epidemiology

Matthew Hartfield , Samuel Alizon
PLoS Pathogens, 2013, 6, pp.e1003277. ⟨10.1371/journal.ppat.1003277⟩
Journal articles hal-01567921v1

Co-infection and super-infection models in evolutionary epidemiology

Samuel Alizon
Interface Focus, 2013, 3, pp.20130031. ⟨10.1098/rsfs.2013.0031⟩
Journal articles hal-01567919v1

Parasite co-transmission and the evolutionary epidemiology of virulence

Samuel Alizon
Evolution - International Journal of Organic Evolution, 2013, 67 (4), pp.921-933. ⟨10.1111/j.1558-5646.2012.01827.x⟩
Journal articles hal-01567917v1
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Within-host and between-host evolutionary rates across the HIV-1 genome

Samuel Alizon , Christophe Fraser
Retrovirology, 2013, 10, pp.49. ⟨10.1186/1742-4690-10-49⟩
Journal articles hal-01567922v1
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Weighting for sex acts to understand the spread of STI on networks

Mathieu Moslonka-Lefebvre , Sebastian Bonhoeffer , Samuel Alizon
Journal of Theoretical Biology, 2012, 311 (octobre2012 et janvier 2013), pp.46-53. ⟨10.1016/j.jtbi.2012.06.031⟩
Journal articles hal-01567925v1
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Modelling the course of an HIV infection: Insights from ecology and evolution

Samuel Alizon , Carsten Magnus
Viruses, 2012, 4 (10), pp.1984-2013. ⟨10.3390/v4101984⟩
Journal articles hal-01567926v1

Epidemiological and clinical consequences of within-host evolution

Samuel Alizon , Fabio Luciani , Roland R. Regoes
Trends in Microbiology, 2011, 19 (1), pp.24-32. ⟨10.1016/j.tim.2010.09.005⟩
Journal articles hal-01567931v1

The transmission-virulence trade-off and superinfection: comments to smith

Samuel Alizon , Yannis Michalakis
Evolution - International Journal of Organic Evolution, 2011, 65 (12), pp.3633-8. ⟨10.1111/j.1558-5646.2011.01432.x⟩
Journal articles hal-01567930v1

Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies

Jacobus C De Roode , C Lopez Fernandez De Castillejo , T Faits , Samuel Alizon
Journal of Evolutionary Biology, 2011, 24 (4), pp.712-22. ⟨10.1111/j.1420-9101.2010.02213.x⟩
Journal articles hal-01567929v1

Inclusive fitness theory and eusociality

Patrick Abbot , Jun Abe , John Alcock , Samuel Alizon , Joao a C Alpedrinha
Nature, 2011, 471 (7339), pp.E1-4. ⟨10.1038/nature09831⟩
Journal articles hal-01567932v1

Bridging scales in the evolution of infectious disease life histories: theory

Troy Day , Samuel Alizon , Nicole Mideo
Evolution - International Journal of Organic Evolution, 2011, 65 (12), pp.3448-61. ⟨10.1111/j.1558-5646.2011.01394.x⟩
Journal articles hal-01567927v1

Within-host parasite cooperation and the evolution of virulence

Samuel Alizon , Sébastien Lion
Proceedings of the Royal Society B: Biological Sciences, 2011, 278 (1725), pp.3738-3747. ⟨10.1098/rspb.2011.0471⟩
Journal articles hal-01567928v1

The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies

R Froissart , J Doumayrou , F Vuillaume , Samuel Alizon , Y Michalakis
Philosophical Transactions of the Royal Society B: Biological Sciences, 2010, 365 (1548), pp.1907-18. ⟨10.1098/rstb.2010.0068⟩
Journal articles hal-01567933v1

Within-host viral evolution in a heterogeneous environment. Insights into the HIV co-receptor switch

Samuel Alizon , Barbara Boldin
Journal of Evolutionary Biology, 2010, 23, pp.2625-2635. ⟨10.1111/j.1420-9101.2010.02139.x⟩
Journal articles hal-01567935v1
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Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

Samuel Alizon , Viktor Von Wyl , Tanja Stadler , Roger D. Kouyos , Sabine Yerly
PLoS Pathogens, 2010, 6 (9), pp.e1001123. ⟨10.1371/journal.ppat.1001123⟩
Journal articles hal-01567934v1

The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus

Fabio Luciani , Samuel Alizon
PLoS Computational Biology, 2009, 5 (11), pp.e1000565. ⟨10.1371/journal.pcbi.1000565⟩
Journal articles hal-01567937v1

The Price equation framework to study disease within-host evolution

Samuel Alizon
Journal of Evolutionary Biology, 2009, 22, pp.1123-1132. ⟨10.1111/j.1420-9101.2009.01726.x⟩
Journal articles hal-01567936v1

Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future

Samuel Alizon , Amy Hurford , Nicole Mideo , Minus van Baalen
Journal of Evolutionary Biology, 2009, 22, pp.245-259. ⟨10.1111/j.1420-9101.2008.01658.x⟩
Journal articles hal-01567938v1

Decreased overall virulence in co-infected hosts leads to the persistence of virulent parasites

Samuel Alizon
The American Naturalist, 2008, 172 (2), pp.E67-E79. ⟨10.1086/588077⟩
Journal articles hal-01567946v1
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Transmission-virulence trade-offs in vector-borne diseases

Samuel Alizon , Minus van Baalen
Theoretical Population Biology, 2008, 74, pp.6 - 15. ⟨10.1016/j.tpb.2008.04.003⟩
Journal articles hal-01396035v1

Empty sites can promote altruistic behaviour

Samuel Alizon , P Taylor
Evolution - International Journal of Organic Evolution, 2008, 62 (6), pp.1335-1344. ⟨10.1111/j.1558-5646.2008.00369.x⟩
Journal articles hal-01567940v1

Why is HIV not vector-borne?

Troy Day , Nicole Mideo , Samuel Alizon
Evol App, 2008, 1, pp.17-27. ⟨10.1111/j.1752-4571.2007.00014.x⟩
Journal articles hal-01567945v1

Competition between cryptic species explains variations in rates of lineage evolution

Samuel Alizon , Michal Kucera , Vincent A. A. Jansen
Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (34), pp.12382-12386. ⟨10.1073/pnas.0805039105⟩
Journal articles hal-01567944v1

Multiple infections, immune dynamics and virulence evolution

Samuel Alizon , Minus van Baalen
The American Naturalist, 2008, 172 (4), pp.E150-E158. ⟨10.1086/590958⟩
Journal articles hal-01567942v1

Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases

Nicole Mideo , Samuel Alizon , Troy Day
Trends in Ecology and Evolution, 2008, 23 (9), pp.511-517. ⟨10.1016/j.tree.2008.05.009⟩
Journal articles hal-01567939v1

Transmission-recovery trade-offs to study parasite evolution

Samuel Alizon
The American Naturalist, 2008, 172 (3), pp.E113-E121. ⟨10.1086/589892⟩
Journal articles hal-01567943v1

Acute or Chronic? Within-host models with immune dynamics, infection outcome and parasite evolution

Samuel Alizon , Minus van Baalen
The American Naturalist, 2008, 172 (6), pp.E244-E256. ⟨10.1086/592404⟩
Journal articles hal-01567941v1

Predation and disturbance interact to shape prey species diversity

Romain Gallet , Samuel Alizon , Pierre-Arnaud Comte , Arnaud Gutierrez , Frantz Depaulis
The American Naturalist, 2007, 170, pp.143-154. ⟨10.1086/518567⟩
Journal articles hal-01567947v1

Emergence of a convex trade-off between transmission and virulence

Samuel Alizon , Minus van Baalen
The American Naturalist, 2005, 165 (6), pp.E155-E167. ⟨10.1086/430053⟩
Journal articles hal-01567948v1
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Épidémiologie et évolution du SARS-CoV-2

Samuel Alizon , Mircea T Sofonea
Les années COVID : comment y survivre, , pp.65-74, 2023, 978-2-493270-69-6
Book sections hal-04184205v1
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Phylodynamique

Samuel Alizon
ISTE. Modèles et méthodes pour l’évolution biologique, , 2022, 9781789480696. ⟨10.51926/ISTE.9069.ch11⟩
Book sections hal-02884408v1
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Invasions of Host-Associated Microbiome Networks

C. L. Murall , J. L. Abbate , M. Puelma Touzel , E. Allen-Vercoe , Samuel Alizon
Research, BT - Advances in Ecological. Networks of Invasion: Empirical Evidence and Case Studies, 57, Academic Press, 2017, Advances in Ecological Research, ⟨10.1016/bs.aecr.2016.11.002⟩
Book sections hal-01567903v1

L’être vivant dans son environnement

Samuel Alizon , F. Angelier , Guillaume Bécard , Laurent Bezin , F Courchamp
CNRS Editions. Etonnant vivant. Découvertes et promesses du XXIème siècle (Livre blanc)., 2017
Book sections hal-01923240v1

Emerging diseases and the evolution of virulence: the case of the Spanish influenza pandemic

Pierre-Olivier Methot , Samuel Alizon
Marc Silberstein and Gérard Lambert and Philippe Huneman. Disease, Classification, and Evidence. New Essays in the Philosophy of Medicine, 7, Springer, pp.93-130, 2015, History, Philosophy and Theory of the Life Sciences, ⟨10.1007/978-94-017-8887-8_5⟩
Book sections hal-01567906v1

Evolution of Infectious Disease Virulence

Samuel Alizon
Jonathan Losos. Evolutionary biology, Oxford Bibliographies, 2014, ⟨10.1093/OBO/9780199941728-0018⟩
Book sections hal-01567916v1
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SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins

Samuel Alizon , Frédéric Cazals , Stéphane Guindon , Claire Lemaitre , Tristan Mary-Huard
[Research Report] CNRS. 2021, pp.1-35
Reports hal-03170023v1
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De Delta à Omicron, scénarios de tendances hospitalières pour l'hiver 2021-2022

Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 16, CNRS - Centre National de la Recherche Scientifique; IRD - Institut de recherche pour le developpement; Université de Montpellier. 2021
Reports hal-03502127v1
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Évolution de la virulence et COVID-19

Samuel Alizon , Yannis Michalakis , Mircea T Sofonea
[Rapport de recherche] 12, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950712v1
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Modéliser l'épidémie de COVID-19 (résumé)

Samuel Alizon , Mircea T Sofonea , Yannis Michalakis
[Rapport de recherche] 7, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950651v1
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Estimation du nombre de reproduction de l’épidémie de COVID-19 en France

Gonché Danesh , Samuel Alizon
[Rapport de recherche] 1, Centre national de la recherche scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882680v1
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Phylodynamique du COVID-19 en France

Gonché Danesh , Baptiste Elie , Samuel Alizon
[Rapport de recherche] 4, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882688v1
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Modélisation de l’épidémie de COVID-19 : modèle SEAIR

Samuel Alizon , Bastien Reyné , Christian Selinger
[Rapport de recherche] 3, Centre national de la recherche scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier. 2020
Reports hal-02882687v1
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Stochasticité et épidémie de COVID-19

Thomas Bénéteau , Baptiste Elie , Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 8, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950660v1
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Immunité de groupe et contrôle de l’épidémie de COVID-19

Mircea T Sofonea , Samuel Alizon
[Rapport Technique] 2, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882682v1
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Analyse de l’épidémie de COVID-19 en France et scénarios de contrôle

Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 9, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950665v1
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Les effets sexe spécifiques de COVID-19 en France et l’implication potentielle des déficits en G6PD

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon
[Rapport de recherche] 11, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950702v1
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Limites et délais dans l’estimation du nombre de reproduction

Samuel Alizon , Bastien Reyné , Mircea T Sofonea
[Rapport de recherche] 5, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882697v1
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Phylodynamique du COVID-19 en France : variations temporelles de la croissance épidémique

Gonché Danesh , Baptiste Elie , Samuel Alizon
[Rapport de recherche] 6, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882698v1
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Les effets sexe spécifiques de COVID-19 en France pourraient-ils être expliqués par des comorbidités ?

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon
[Rapport de recherche] 10, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950676v1
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Évolution de la virulence des parasites : apports des modèles emboîtés

Samuel Alizon
Evolution [q-bio.PE]. Université Pierre et Marie Curie (Paris VI), 2006. Français. ⟨NNT : ⟩
Theses tel-01638064v1
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Dynamics and evolution of infectious diseases

Samuel Alizon
Populations and Evolution [q-bio.PE]. Université Montpellier 2, 2013
Habilitation à diriger des recherches tel-01638065v1