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Samuel Alizon


CNRS research director, based in the MIVEGEC departement in Montpellier and CIRB department 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 website.


Journal articles92 documents

  • Baptiste Elie, Bénédicte Roquebert, Mircea T Sofonea, Sabine Trombert-Paolantoni, Vincent Foulongne, et al.. Variant‐specific SARS‐CoV‐2 within‐host kinetics. Journal of Medical Virology, Wiley-Blackwell, In press, ⟨10.1002/jmv.27757⟩. ⟨hal-03651890⟩
  • Bastien Reyné, Quentin Richard, Christian Selinger, Mircea T Sofonea, Ramsès Djidjou-Demasse, et al.. Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Mathematical Modelling of Natural Phenomena, EDP Sciences, 2022, 17, pp.7. ⟨10.1051/mmnp/2022008⟩. ⟨hal-03629334⟩
  • Pascal Crepey, Harold Noël, Samuel Alizon. Challenges for mathematical epidemiological modelling. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2022, 41 (2), pp.101053. ⟨10.1016/j.accpm.2022.101053⟩. ⟨hal-03607991⟩
  • Samuel Alizon, Christian Selinger, Mircea T Sofonea, Stéphanie Haim-Boukobza, Jean-Marc Giannoli, et al.. Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020. Eurosurveillance, European Centre for Disease Prevention and Control, 2022, 27 (6), pp.2100406. ⟨10.2807/1560-7917.ES.2022.27.6.2100406⟩. ⟨hal-03175551v3⟩
  • Samuel Alizon. Les lois de la contagion. Fake news, virus, tendances…. Natures Sciences Sociétés, EDP Sciences, A paraître, 30 (1). ⟨hal-03664004⟩
  • Bastien Reyné, Christian Selinger, Mircea T Sofonea, Stéphanie Miot, Amandine Pisoni, et al.. Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities. International Journal of Epidemiology, Oxford University Press (OUP), 2021, 50 (6), pp.1788-1794. ⟨10.1093/ije/dyab121⟩. ⟨hal-03289625⟩
  • Benedicte Roquebert, Stéphanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. International Journal of Infectious Diseases, Elsevier, 2021, ⟨10.1016/j.ijid.2021.09.076⟩. ⟨hal-03366559⟩
  • Bénédicte Roquebert, Sabine Trombert-Paolantoni, Stéphanie Haim-Boukobza, Emmanuel Lecorche, Laura Verdurme, et al.. 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. Eurosurveillance, European Centre for Disease Prevention and Control, 2021, 26 (23), ⟨10.2807/1560-7917.es.2021.26.23.2100447⟩. ⟨hal-03289627⟩
  • Thomas Bénéteau, Elie ` Baptiste, Mircea T Sofonea, Samuel Alizon. Estimating dates of origin and end of COVID-19 epidemics. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e70. ⟨10.1101/2021.01.19.21250080⟩. ⟨hal-03120811v2⟩
  • Christian Selinger, Samuel Alizon. Reconstructing contact network structure and cross-immunity patterns from multiple infection histories. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), pp.e1009375. ⟨10.1371/journal.pcbi.1009375⟩. ⟨hal-03357549⟩
  • Samuel Alizon, Stéphanie Haim-Boukobza, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, et al.. Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021. Eurosurveillance, European Centre for Disease Prevention and Control, 2021, 26 (28), ⟨10.2807/1560-⟩. ⟨hal-03289622⟩
  • Samuel Alizon. Superspreading genomes. Science, American Association for the Advancement of Science (AAAS), 2021, 371 (6529), pp.574-575. ⟨10.1126/science.abg0100⟩. ⟨hal-03133445⟩
  • Mircea T Sofonea, Samuel Alizon. Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, ⟨10.1016/j.accpm.2021.100943⟩. ⟨hal-03366541⟩
  • Mircea T Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics, Elsevier, 2021, 35, pp.100459. ⟨10.1016/j.epidem.2021.100459⟩. ⟨hal-03289624⟩
  • Christian Selinger, Massilva Rahmoun, Carmen Lia Murall, Claire Bernat, Vanina Boué, et al.. Cytokine response following perturbation of the cervicovaginal milieu during HPV genital infection. Immunologic Research, Humana Press, 2021, 69 (3), pp.255-263. ⟨10.1007/s12026-021-09196-2⟩. ⟨hal-03354891⟩
  • Samuel Alizon, Paul E Turner. Can we eradicate viral pathogens?. Journal of Evolutionary Biology, Wiley, 2021, 34 (12), pp.1851-1854. ⟨10.1111/jeb.13958⟩. ⟨hal-03500287⟩
  • Gonché Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, et al.. Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data. PLoS Pathogens, Public Library of Science, 2021, 17 (9), pp.e1009916. ⟨10.1371/journal.ppat.1009916⟩. ⟨hal-03357552⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon, Ignacio G. Bravo. SARS-CoV-2 viral RNA levels are not 'viral load'. Trends in Microbiology, Elsevier, 2021, 29 (11), pp.970-972. ⟨10.1016/j.tim.2021.08.008⟩. ⟨hal-03419147⟩
  • Ramsès Djidjou-Demasse, Samuel Alizon, Mircea T Sofonea. Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. Journal of Mathematical Biology, Springer Verlag (Germany), 2021, ⟨10.1007/s00285-021-01571-9⟩. ⟨hal-02500420⟩
  • Samuel Alizon, Mircea T Sofonea. SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs. Journal of Evolutionary Biology, Wiley, 2021, 34 (12), pp.1867 - 1877. ⟨10.1111/jeb.13896⟩. ⟨hal-03289628⟩
  • Mircea T Sofonea, Corentin Boennec, yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, 40 (3), pp.100881. ⟨10.1016/j.accpm.2021.100881⟩. ⟨hal-03289626⟩
  • Thomas Beneteau, Christian Selinger, Mircea T Sofonea, Samuel Alizon. Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), pp.e1009352. ⟨10.1371/journal.pcbi.1009352⟩. ⟨hal-03357550⟩
  • A. Debernardi, W. Jarassier, C. Soret, C. Mougin, Samuel Alizon, et al.. Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses. Archives of Virology, Springer Verlag, 2021, ⟨10.1007/s00705-021-05259-9⟩. ⟨hal-03425708⟩
  • Gonché Danesh, Baptiste Elie, yannis Michalakis, Mircea T Sofonea, Antonin Bal, et al.. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩. ⟨hal-03001114v2⟩
  • Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T Sofonea, Ramsès Djidjou-Demasse. Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLoS Computational Biology, Public Library of Science, 2021, ⟨10.1371/journal.pcbi.1008776⟩. ⟨hal-02879512v3⟩
  • Olivier Thomine, Samuel Alizon, Corentin Boennec, Marc Barthelemy, Mircea T Sofonea. Emerging dynamics from high-resolution spatial numerical epidemics. eLife, eLife Sciences Publication, 2021, 10, ⟨10.7554/elife.71417⟩. ⟨hal-03415297⟩
  • Samuel Alizon. Treating symptomatic infections and the co-evolution of virulence and drug resistance. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e47. ⟨10.24072/pcjournal.38⟩. ⟨hal-03001103v2⟩
  • Stéphanie Haim-Boukobza, Bénédicte Roquebert, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021. Emerging Infectious Diseases, Centers for Disease Control and Prevention, 2021, 27 (5), pp.1496-1499. ⟨10.3201/eid2705.210397⟩. ⟨hal-03150819v3⟩
  • Christian Selinger, Marc Choisy, Samuel Alizon. Predicting COVID-19 incidence in French hospitals using human contact network analytics. International Journal of Infectious Diseases, Elsevier, 2021, 111, pp.100 - 107. ⟨10.1016/j.ijid.2021.08.029⟩. ⟨hal-03267059v2⟩
  • Baptiste Elie, Samuel Alizon. Analyses génomiques et phylodynamiques du SARS-Cov-2. Revue Francophone des Laboratoires, Elsevier, 2020, 2020 (526), pp.57-62. ⟨10.1016/S1773-035X(20)30314-2⟩. ⟨hal-02893568v2⟩
  • Carmen Lia Murall, Bastien Reyné, Christian Selinger, Claire Bernat, Vanina Boué, et al.. HPV cervical infections and serological status in vaccinated and unvaccinated women. Vaccine, Elsevier, 2020, 38 (51), pp.8167-8174. ⟨10.1016/j.vaccine.2020.10.078⟩. ⟨hal-03001077v2⟩
  • Samuel Alizon, Ignacio G Bravo, Paul Farrell, Sally Roberts. Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2019, 374 (1773), pp.20190041. ⟨10.1098/rstb.2019.0041⟩. ⟨hal-02108649v3⟩
  • Samuel Alizon, Carmen Lia Murall, Emma Saulnier, Mircea T Sofonea. Detecting within-host interactions from genotype combination prevalence data. Epidemics, Elsevier, 2019, 29, pp.100349. ⟨10.1016/j.epidem.2019.100349⟩. ⟨hal-02387765⟩
  • Carmen Murall, Massilva Rahmoun, Christian Selinger, Monique Baldellou, Claire Bernat, et al.. Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open, BMJ Publishing Group, 2019, 9 (6), pp.e025129. ⟨10.1136/bmjopen-2018-025129⟩. ⟨hal-02157154⟩
  • Jérôme Bourret, Samuel Alizon, Ignacio Bravo. COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2019, 11 (12), pp.3523-3528. ⟨10.1093/gbe/evz262⟩. ⟨hal-02957623⟩
  • Carmen Lia Murall, Robert Jackson, Ingeborg Zehbe, Nathalie Boulle, Michel Segondy, et al.. Epithelial stratification shapes infection dynamics. PLoS Computational Biology, Public Library of Science, 2019, 15 (1), pp.e1006646. ⟨10.1371/journal.pcbi.1006646⟩. ⟨hal-02069914⟩
  • Carmen Lia Murall, Samuel Alizon. Modelling the evolution of viral oncogenesis. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2019, Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses, 374 (1773), pp.20180302. ⟨10.1098/rstb.2018.0302⟩. ⟨hal-02124893⟩
  • Samuel Alizon, Pierre-Olivier Méthot. Reconciling Pasteur and Darwin to control infectious diseases. PLoS Biology, Public Library of Science, 2018, 16 (1), pp.e2003815. ⟨10.1371/journal.pbio.2003815⟩. ⟨hal-01737461⟩
  • Samuel Alizon. Inexpensive Research in the Golden Open-Access Era. Trends in Ecology and Evolution, Elsevier, 2018, 33 (5), pp.301 - 303. ⟨10.1016/j.tree.2018.02.005⟩. ⟨hal-01788084⟩
  • Tsukushi Kamiya, Nicole Mideo, Samuel Alizon. Coevolution of virulence and immunosuppression in multiple infections. Journal of Evolutionary Biology, Wiley, 2018, 31 (7), pp.995 - 1005. ⟨10.1111/jeb.13280⟩. ⟨hal-01898496⟩
  • Mircea T Sofonea, L. Aldakak, Luis F. V. V. Boullosa, Samuel Alizon. Can Ebola Virus evolve to be less virulent in humans?. Journal of Evolutionary Biology, Wiley, 2018, 31 (3), pp.382 - 392. ⟨10.1111/jeb.13229⟩. ⟨hal-01897077⟩
  • Mircea T Sofonea, Samuel Alizon, yannis Michalakis. Exposing the diversity of multiple infection patterns. Journal of Theoretical Biology, Elsevier, 2017, 419, pp.278 - 289. ⟨10.1016/j.jtbi.2017.02.011⟩. ⟨hal-01567902⟩
  • Emma Saulnier, Olivier Gascuel, Samuel Alizon. Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study. PLoS Computational Biology, Public Library of Science, 2017, 13 (3), pp.e1005416. ⟨10.1371/journal.pcbi.1005416⟩. ⟨hal-01567904⟩
  • Samuel Alizon, Carmen Murall, Ignacio G Bravo. Why Human Papillomavirus Acute Infections Matter. Viruses, MDPI, 2017, 9 (10), pp.293. ⟨10.3390/v9100293⟩. ⟨hal-01638068⟩
  • Samuel Alizon. Modelling the evolution of how vector-borne parasites manipulate the vector's host choice. Peer Community in Evolutionary Biology, Peer Community in, 2017, pp.100023. ⟨10.24072/pci.evolbiol.100023⟩. ⟨hal-01560018⟩
  • Samuel Alizon, Emma Saulnier. Utilisation des phylogénies d'infections en épidémiologie. Bulletin de veille scientifique , ANSES, 2017, pp.42-43. ⟨anses-01533229⟩
  • Samuel Alizon, Emma Saulnier. Phylodynamique des infections virales. Virologie, John Libbey Eurotext 2017, 21 (3), pp.119-129. ⟨10.1684/vir.2017.0696⟩. ⟨hal-01638067⟩
  • Samuel Alizon, Roger Kouyos. Predicting HIV virulence evolution in response to widespread treatment. Peer Community in Evolutionary Biology, Peer Community in, 2017, ⟨10.24072/pci.evolbiol.100013⟩. ⟨hal-01467624⟩
  • Samuel Alizon. A Visionary Pioneer of Parasite Ecology and Evolution. American Naturalist, University of Chicago Press, 2016, 187 (6), pp.ii-iii. ⟨10.1086/686526⟩. ⟨hal-01567905⟩
  • Mircea T Sofonea, Samuel Alizon, yannis Michalakis. From within-host interactions to epidemiological competition: a general model for multiple infections. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩. ⟨hal-01571806⟩
  • Matthew Hartfield, Samuel Alizon. Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Computational Biology, Public Library of Science, 2015, 11 (3), pp.e1004149. ⟨10.1371/journal.pcbi.1004149⟩. ⟨hal-01567908⟩
  • Samuel Alizon, yannis Michalakis. Adaptive virulence evolution: the good old fitness-based approach. Trends in Ecology and Evolution, Elsevier, 2015, 30 (5), pp.248-254. ⟨10.1016/j.tree.2015.02.009⟩. ⟨hal-01567907⟩
  • Susan V Cousineau, Samuel Alizon. Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance. Journal of Evolutionary Biology, Wiley, 2014, 27 (12), pp.2753-66. ⟨10.1111/jeb.12541⟩. ⟨hal-01567915⟩
  • Matthew Hartfield, Samuel Alizon. Epidemiological feedbacks affect evolutionary emergence of pathogens. American Naturalist, University of Chicago Press, 2014, 183 (4), pp.E105-17. ⟨10.1086/674795⟩. ⟨hal-01567911⟩
  • Matthew Hartfield, Carmen Lia Murall, Samuel Alizon. Clinical applications of pathogen phylogenies. Trends in Molecular Medicine, Elsevier, 2014, 20 (7), pp.394-404. ⟨10.1016/j.molmed.2014.04.002⟩. ⟨hal-01567914⟩
  • Samuel Alizon, Sébastien Lion, Carmen Lia Murall, Jessica Lee Abbate. Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics. Virulence, Taylor & Francis, 2014, 5 (8), pp.825-827. ⟨10.4161/21505594.2014.976514⟩. ⟨hal-01567909⟩
  • Matthew Hartfield, Rowena Bull, Peter A White, Andrew Lloyd, Fabio Luciani, et al.. Evidence that hepatitis C virus genome partly controls infection outcome. Evolutionary Applications, Blackwell, 2014, 7 (5), pp.533-47. ⟨10.1111/eva.12151⟩. ⟨hal-01567913⟩
  • Christophe Fraser, Katrina Lythgoe, Gabriel E Leventhal, George Shirreff, T Deirdre Hollingsworth, et al.. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science, American Association for the Advancement of Science (AAAS), 2014, 343 (6177), pp.1243727. ⟨10.1126/science.1243727⟩. ⟨hal-01567910⟩
  • Pierre-Olivier Methot, Samuel Alizon. What is a pathogen? Toward a process view of host-parasite interactions. Virulence, Taylor & Francis, 2014, 5 (8), pp.775-85. ⟨10.4161/21505594.2014.960726⟩. ⟨hal-01567912⟩
  • Christel Kamp, Mathieu Moslonka-Lefebvre, Samuel Alizon. Epidemic spread on weighted networks. PLoS Computational Biology, Public Library of Science, 2013, 9 (12), pp.e1003352. ⟨10.1371/journal.pcbi.1003352⟩. ⟨hal-01567923⟩
  • Matthew Hartfield, Samuel Alizon. Introducing the outbreak threshold in epidemiology. PLoS Pathogens, Public Library of Science, 2013, 6, pp.e1003277. ⟨10.1371/journal.ppat.1003277⟩. ⟨hal-01567921⟩
  • Samuel Alizon, Christophe Fraser. Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology, BioMed Central, 2013, 10, pp.49. ⟨10.1186/1742-4690-10-49⟩. ⟨hal-01567922⟩
  • Samuel Alizon, Jacobus C De Roode, yannis Michalakis. Multiple infections and the evolution of virulence. Ecology Letters, Wiley, 2013, 16 (4), pp.556-567. ⟨10.1111/ele.12076⟩. ⟨hal-01567918⟩
  • Samuel Alizon. Co-infection and super-infection models in evolutionary epidemiology. Interface Focus, Royal Society publishing, 2013, 3, pp.20130031. ⟨10.1098/rsfs.2013.0031⟩. ⟨hal-01567919⟩
  • Samuel Alizon. Parasite co-transmission and the evolutionary epidemiology of virulence. Evolution - International Journal of Organic Evolution, Wiley, 2013, 67 (4), pp.921-933. ⟨10.1111/j.1558-5646.2012.01827.x⟩. ⟨hal-01567917⟩
  • George Shirreff, Samuel Alizon, Anne Cori, Huldrych F Guenthard, Oliver Laeyendecker, et al.. How effectively can HIV phylogenies be used to measure heritability?. Evolution, Medicine, and Public Health, Oxford : Oxford University Press, 2013, 2013 (1), pp.209-24. ⟨10.1093/emph/eot019⟩. ⟨hal-01567924⟩
  • Samuel Alizon. On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison. Journal of Evolutionary Biology, Wiley, 2013, 26 (9), pp.2051-6. ⟨10.1111/jeb.12199⟩. ⟨hal-01567920⟩
  • Samuel Alizon, Carsten Magnus. Modelling the course of an HIV infection: Insights from ecology and evolution. Viruses, MDPI, 2012, 4 (10), pp.1984-2013. ⟨10.3390/v4101984⟩. ⟨hal-01567926⟩
  • Mathieu Moslonka-Lefebvre, Sebastian Bonhoeffer, Samuel Alizon. Weighting for sex acts to understand the spread of STI on networks. Journal of Theoretical Biology, Elsevier, 2012, 311 (octobre2012 et janvier 2013), pp.46-53. ⟨10.1016/j.jtbi.2012.06.031⟩. ⟨hal-01567925⟩
  • Samuel Alizon, yannis Michalakis. The transmission-virulence trade-off and superinfection: comments to smith. Evolution - International Journal of Organic Evolution, Wiley, 2011, 65 (12), pp.3633-8. ⟨10.1111/j.1558-5646.2011.01432.x⟩. ⟨hal-01567930⟩
  • Samuel Alizon, Fabio Luciani, Roland R. Regoes. Epidemiological and clinical consequences of within-host evolution. Trends in Microbiology, Elsevier, 2011, 19 (1), pp.24-32. ⟨10.1016/j.tim.2010.09.005⟩. ⟨hal-01567931⟩
  • Samuel Alizon, Sébastien Lion. Within-host parasite cooperation and the evolution of virulence. Proceedings of the Royal Society B: Biological Sciences, Royal Society, The, 2011, 278 (1725), pp.3738-3747. ⟨10.1098/rspb.2011.0471⟩. ⟨hal-01567928⟩
  • Jacobus C De Roode, C Lopez Fernandez De Castillejo, T Faits, Samuel Alizon. Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies. Journal of Evolutionary Biology, Wiley, 2011, 24 (4), pp.712-22. ⟨10.1111/j.1420-9101.2010.02213.x⟩. ⟨hal-01567929⟩
  • Troy Day, Samuel Alizon, Nicole Mideo. Bridging scales in the evolution of infectious disease life histories: theory. Evolution - International Journal of Organic Evolution, Wiley, 2011, 65 (12), pp.3448-61. ⟨10.1111/j.1558-5646.2011.01394.x⟩. ⟨hal-01567927⟩
  • Patrick Abbot, Jun Abe, John Alcock, Samuel Alizon, Joao a C Alpedrinha, et al.. Inclusive fitness theory and eusociality. Nature, Nature Publishing Group, 2011, 471 (7339), pp.E1-4. ⟨10.1038/nature09831⟩. ⟨hal-01567932⟩
  • R Froissart, J Doumayrou, F Vuillaume, Samuel Alizon, y Michalakis. The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2010, 365 (1548), pp.1907-18. ⟨10.1098/rstb.2010.0068⟩. ⟨hal-01567933⟩
  • Samuel Alizon, Viktor Von Wyl, Tanja Stadler, Roger D. Kouyos, Sabine yerly, et al.. Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathogens, Public Library of Science, 2010, 6 (9), pp.e1001123. ⟨10.1371/journal.ppat.1001123⟩. ⟨hal-01567934⟩
  • Samuel Alizon, Barbara Boldin. Within-host viral evolution in a heterogeneous environment. Insights into the HIV co-receptor switch. Journal of Evolutionary Biology, Wiley, 2010, 23, pp.2625-2635. ⟨10.1111/j.1420-9101.2010.02139.x⟩. ⟨hal-01567935⟩
  • Fabio Luciani, Samuel Alizon. The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus. PLoS Computational Biology, Public Library of Science, 2009, 5 (11), pp.e1000565. ⟨10.1371/journal.pcbi.1000565⟩. ⟨hal-01567937⟩
  • Samuel Alizon. The Price equation framework to study disease within-host evolution. Journal of Evolutionary Biology, Wiley, 2009, 22, pp.1123-1132. ⟨10.1111/j.1420-9101.2009.01726.x⟩. ⟨hal-01567936⟩
  • Samuel Alizon, Amy Hurford, Nicole Mideo, Minus van Baalen. Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. Journal of Evolutionary Biology, Wiley, 2009, 22, pp.245-259. ⟨10.1111/j.1420-9101.2008.01658.x⟩. ⟨hal-01567938⟩
  • Samuel Alizon. Decreased overall virulence in co-infected hosts leads to the persistence of virulent parasites. American Naturalist, University of Chicago Press, 2008, 172 (2), pp.E67-E79. ⟨10.1086/588077⟩. ⟨hal-01567946⟩
  • Samuel Alizon, Minus van Baalen. Acute or Chronic? Within-host models with immune dynamics, infection outcome and parasite evolution. American Naturalist, University of Chicago Press, 2008, 172 (6), pp.E244-E256. ⟨10.1086/592404⟩. ⟨hal-01567941⟩
  • Samuel Alizon, P Taylor. Empty sites can promote altruistic behaviour. Evolution - International Journal of Organic Evolution, Wiley, 2008, 62 (6), pp.1335-1344. ⟨10.1111/j.1558-5646.2008.00369.x⟩. ⟨hal-01567940⟩
  • Troy Day, Nicole Mideo, Samuel Alizon. Why is HIV not vector-borne?. Evol App, 2008, 1, pp.17-27. ⟨10.1111/j.1752-4571.2007.00014.x⟩. ⟨hal-01567945⟩
  • Samuel Alizon, Minus van Baalen. Transmission-virulence trade-offs in vector-borne diseases. Theoretical Population Biology, Elsevier, 2008, 74, pp.6 - 15. ⟨10.1016/j.tpb.2008.04.003⟩. ⟨hal-01396035⟩
  • Samuel Alizon, Minus van Baalen. Multiple infections, immune dynamics and virulence evolution. American Naturalist, University of Chicago Press, 2008, 172 (4), pp.E150-E158. ⟨10.1086/590958⟩. ⟨hal-01567942⟩
  • Samuel Alizon, Michal Kucera, Vincent A. A. Jansen. Competition between cryptic species explains variations in rates of lineage evolution. Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2008, 105 (34), pp.12382-12386. ⟨10.1073/pnas.0805039105⟩. ⟨hal-01567944⟩
  • Nicole Mideo, Samuel Alizon, Troy Day. Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases. Trends in Ecology and Evolution, Elsevier, 2008, 23 (9), pp.511-517. ⟨10.1016/j.tree.2008.05.009⟩. ⟨hal-01567939⟩
  • Samuel Alizon. Transmission-recovery trade-offs to study parasite evolution. American Naturalist, University of Chicago Press, 2008, 172 (3), pp.E113-E121. ⟨10.1086/589892⟩. ⟨hal-01567943⟩
  • Romain Gallet, Samuel Alizon, Pierre-Arnaud Comte, Arnaud Gutierrez, Frantz Depaulis, et al.. Predation and disturbance interact to shape prey species diversity. American Naturalist, University of Chicago Press, 2007, 170, pp.143-154. ⟨10.1086/518567⟩. ⟨hal-01567947⟩
  • Samuel Alizon, Minus van Baalen. Emergence of a convex trade-off between transmission and virulence. American Naturalist, University of Chicago Press, 2005, 165 (6), pp.E155-E167. ⟨10.1086/430053⟩. ⟨hal-01567948⟩

Books3 documents

  • Samuel Alizon. Évolution, écologie et pandémies : Faire dialoguer Pasteur et Darwin. Points Sciences, 2020, 2757887238. ⟨hal-03045497⟩
  • Stéphane Blanc, - Gilles Boëtsch, Martine Hossaert-Mckey, François Renaud, Stephanie Thiebault, et al.. Ecologie de la santé : Pour une nouvelle lecture de nos maux. Edition du Cherche Midi CNRS, 176 p., 2017, Documents (Cherche Midi), ISBN: 9782749154251 9782749154251. ⟨hal-02785631⟩
  • Samuel Alizon. C'est grave Dr Darwin ? L'évolution, les microbes et nous. Le Seuil, 2016, 2021102920. ⟨hal-01638066⟩

Book sections5 documents

  • Samuel Alizon. Phylogénies d'infections et phylodynamique. Étude de l’évolution par l’approche mathématique et informatique, A paraître. ⟨hal-02884408⟩
  • C. L. Murall, J. L. Abbate, M. Puelma Touzel, E. Allen-Vercoe, Samuel Alizon, et al.. Invasions of Host-Associated Microbiome Networks. 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⟩. ⟨hal-01567903⟩
  • Samuel Alizon, F. Angelier, Guillaume Bécard, Laurent Bezin, F Courchamp, et al.. L’être vivant dans son environnement. CNRS Editions. Etonnant vivant. Découvertes et promesses du XXIème siècle (Livre blanc)., 2017. ⟨hal-01923240⟩
  • Pierre-Olivier Methot, Samuel Alizon. Emerging diseases and the evolution of virulence: the case of the Spanish influenza pandemic. 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⟩. ⟨hal-01567906⟩
  • Samuel Alizon. Evolution of Infectious Disease Virulence. Jonathan Losos. Evolutionary biology, Oxford Bibliographies, 2014, ⟨10.1093/OBO/9780199941728-0018⟩. ⟨hal-01567916⟩

Preprints, Working Papers, ...5 documents

  • Ramsès Djidjou-Demasse, Mircea T Sofonea, Marc Choisy, Samuel Alizon. Within-host evolutionary dynamics of antimicrobial quantitative resistance. 2021. ⟨hal-03194023v4⟩
  • Mircea T Sofonea, Corentin Boennec, yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. 2021. ⟨hal-03322646⟩
  • Baptiste Elie˚, Christian Selinger, Samuel Alizon. The source of individual heterogeneity shapes infectious disease outbreaks. 2021. ⟨hal-03175555⟩
  • Mircea T Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France. 2020. ⟨hal-02619546⟩
  • Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea T Sofonea. Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. 2020. ⟨hal-03045490⟩

Reports14 documents

  • Samuel Alizon, Mircea T Sofonea. De Delta à Omicron, scénarios de tendances hospitalières pour l'hiver 2021-2022. [Rapport de recherche] 16, CNRS - Centre National de la Recherche Scientifique; IRD - Institut de recherche pour le developpement; Université de Montpellier. 2021. ⟨hal-03502127⟩
  • Samuel Alizon, Frédéric Cazals, Stéphane Guindon, Claire Lemaitre, Tristan Mary-Huard, et al.. 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. [Research Report] CNRS. 2021, pp.1-35. ⟨hal-03170023⟩
  • Samuel Alizon, Mircea T Sofonea, yannis Michalakis. Modéliser l'épidémie de COVID-19 (résumé). [Rapport de recherche] 7, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950651⟩
  • Gonché Danesh, Samuel Alizon. Estimation du nombre de reproduction de l’épidémie de COVID-19 en France. [Rapport de recherche] 1, Centre national de la recherche scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882680⟩
  • Gonché Danesh, Baptiste Elie, Samuel Alizon. Phylodynamique du COVID-19 en France. [Rapport de recherche] 4, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882688⟩
  • Mircea T Sofonea, Samuel Alizon. Immunité de groupe et contrôle de l’épidémie de COVID-19. [Rapport Technique] 2, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882682⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France pourraient-ils être expliqués par des comorbidités ?. [Rapport de recherche] 10, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950676⟩
  • Thomas Bénéteau, Baptiste Elie, Samuel Alizon, Mircea T Sofonea. Stochasticité et épidémie de COVID-19. [Rapport de recherche] 8, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950660⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France et l’implication potentielle des déficits en G6PD. [Rapport de recherche] 11, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950702⟩
  • Samuel Alizon, Mircea T Sofonea. Analyse de l’épidémie de COVID-19 en France et scénarios de contrôle. [Rapport de recherche] 9, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950665⟩
  • Samuel Alizon, Bastien Reyné, Christian Selinger. Modélisation de l’épidémie de COVID-19 : modèle SEAIR. [Rapport de recherche] 3, Centre national de la recherche scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier. 2020. ⟨hal-02882687⟩
  • Samuel Alizon, Bastien Reyné, Mircea T Sofonea. Limites et délais dans l’estimation du nombre de reproduction. [Rapport de recherche] 5, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882697⟩
  • Gonché Danesh, Baptiste Elie, Samuel Alizon. Phylodynamique du COVID-19 en France : variations temporelles de la croissance épidémique. [Rapport de recherche] 6, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882698⟩
  • Samuel Alizon, yannis Michalakis, Mircea T Sofonea. Évolution de la virulence et COVID-19. [Rapport de recherche] 12, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950712⟩

Theses1 document

  • Samuel Alizon. Évolution de la virulence des parasites : apports des modèles emboîtés. Evolution [q-bio.PE]. Université Pierre et Marie Curie (Paris VI), 2006. Français. ⟨tel-01638064⟩

Habilitation à diriger des recherches1 document

  • Samuel Alizon. Dynamics and evolution of infectious diseases. Populations and Evolution [q-bio.PE]. Université Montpellier 2, 2013. ⟨tel-01638065⟩

Other publications2 documents