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| Sofonea M. T. & 10 others (2022) Analyzing and modeling the spread of SARS-CoV-2 Omicron lineages BA.1 and BA.2 in France (September 1, 2021, to February 28, 2022). Emerg Infect Dis. 28(7): 1355-1365.
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| Reyné B., Richard Q., Selinger C., Sofonea M. T., Djidjou-Demasse R. & Alizon S. (2022) Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Math. Model. Nat. Phenom.. 17(7): 1-24.
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| Elie B., Lecorche E., Sofonea M. T., Trombert-Paolantoni S., Verdurme L., Guedj J., Foulongne V., Haim-Boukobza S., Roquebert B. & Alizon S. (2022) Variant-specific SARS-CoV-2 within-host kinetics. J Med Virol. 94(8): 3625-3633.
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| Elie B., Selinger C. & Alizon S. (2022) The source of individual heterogeneity shapes infectious disease outbreaks. Proceedings B. 289(1974): 20220232.
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| Crépey P., Noël H. & Alizon S. (2022) Challenges for mathematical epidemiological modelling. Anaesth. Crit. Care Pain Med.. 41(2): 101053.
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| Alizon S. & 37 others (2022) Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values. Eurosurveillance. 27(6): 2100406.
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| Thomine O., Alizon S., Barthélemy M., Boennec C. & Sofonea M. T. (2021) Emerging dynamics from high-resolution spatial numerical epidemics. eLife. 10: e71417.
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| Sofonea M. T., Boennec C., Michalakis Y. & Alizon S. (2021) Two waves and a high tide: the COVID-19 epidemic in France. Anaesth. Crit. Care Pain Med.. 40(3): 100881.
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| Sofonea M. T., Reyné B., Elie B., Djidjou-Demasse R., Selinger C., Michalakis Y. & Alizon S. (2021) Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics. 100459.
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| Sofonea M. T. & Alizon S. (2021) Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesth. Crit. Care Pain Med.. 40(4): 100943.
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| Selinger C. & 12 others (2021) Cytokine response following perturbation of the cervicovaginal milieu during HPV genital infection. Immunol Res. 69(3): 255--263.
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| Selinger C., Choisy M. & Alizon S. (2021) Predicting COVID-19 incidence in French hospitals using human contact network analytics. Int J Infect Dis. 111: 100--107.
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| Selinger C. & Alizon S. (2021) Reconstructing contact network structure and cross-immunity patterns from multiple infection histories. PLOS Comput Biol. 17(9): e1009375.
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| Roquebert B., Haim-Boukobza S., Trombert-Paolantoni S., Lecorche E., Verdurme L., Foulongne V., Burrel S., Alizon S. & Sofonea M. T. (2021) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. Int J Infect Dis. 113: 12-14.
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| Roquebert B., Trombert-Paolantoni S., Haim-Boukobza S., Lecorche E., Verdurme L., Foulongne V., Sofonea M. T. & Alizon S. (2021) 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. 26(23): 2100447.
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| Richard Q., Alizon S., Choisy M., Sofonea M. T. & Djidjou-Demasse R. (2021) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLoS Comput Biol. 17(3): e1008776.
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| Reyné B., Selinger C., Sofonea M. T., Miot S., Pisoni A., Tuaillon E., Bousquet J., Blain H. & Alizon S. (2021) Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities. Int J Epidemiol. 2020.11.27.20239913.
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| Michalakis Y., Sofonea M. T., Alizon S. & Bravo I. G. (2021) SARS-CoV-2 viral RNA levels are not 'viral load'. Trends Microbiol. 29(11): 970--972.
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| Haim-Boukobza S., Roquebert B., Trombert-Paolantoni S., Lecorche E., Verdurme L., Foulongne V., Selinger C., Michalakis Y., Sofonea M. T. & Alizon S. (2021) Detecting rapid spread of SARS-CoV-2 variants, France, January 26–February 16. Emerg Infect Dis. 27(5): 1496-1499.
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| Djidjou-Demasse R., Alizon S. & Sofonea M. T. (2021) Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. J Math Biol. 82(3): 16.
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| Debernardi A., Jarassier W., Soret C., Mougin C., Alizon S., Bravo I. G., Guenat D., Prétet J. L. & Lepiller Q. (2021) Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses. Arch Virol. 166: 3421–3425.
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| Danesh G. & 17 others (2021) Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal. 1: e45.
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| Danesh G., Virlogeux V., Ramière C., Charre C., Cotte L. & Alizon S. (2021) Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data. PLoS Pathog. 17(9): e1009916.
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| Beneteau T., Selinger C., Sofonea M. T. & Alizon S. (2021) Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections. PLOS Comput Biol. 17(9): e1009352.
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| Beneteau T., Elie B., Sofonea M. T. & Alizon S. (2021) Estimating dates of origin and end of COVID-19 epidemics. Peer Community Journal. 1: e70.
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| Alizon S. & Turner P. E. (2021) Can we eradicate viral pathogens? J Evol Biol. 34(12): 1851-1854.
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| Alizon S. & Sofonea M. T. (2021) SARS-CoV-2 virulence evolution: avirulence theory, immunity, and trade-offs. J Evol Biol. 34(12): 1867-1877.
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| Alizon S., Haim-Boukobza S., Foulongne V., Verdurme L., Trombert-Paolantoni S., Lecorche E., Roquebert B. & Sofonea M. T. (2021) Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021. Eurosurveillance. 26(28): 2100573.
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| Alizon S. (2021) Treating symptomatic infections and the co-evolution of virulence and drug resistance. Peer Community Journal. 1: e47.
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| Alizon S. (2021) Superspreading genomes. Science. 371(6529): 574--575.
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| Elie B. & Alizon S. (2020) Analyses génomiques et phylodynamiques du Sars-CoV-2. Revue Francophone des Laboratoires. 2020(526): 57--62.
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| Murall C. L. & 20 others (2020) HPV cervical infections and serological status in vaccinated and unvaccinated women. Vaccine. 38(51): 8167--8174.
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| Murall C. L. & 42 others (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open. 9(6): e025129.
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| Murall C. L., Jackson R., Zehbe I., Boulle N., Segondy M. & Alizon S. (2019) Epithelial stratification shapes infection dynamics. PLoS Comput Biol. 15(1): e1006646.
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| Murall C. L. & Alizon S. (2019) Modelling the evolution of viral oncogenesis. Phil Trans R Soc Lond B. 374(1773): 20180302.
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| Bourret J., Alizon S. & Bravo I. G. (2019) COUSIN (COdon Usage Similarity INdex): a normalized measure of Codon Usage Preferences. Genome Biol. Evol.. 11(12): evz262.
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| Alizon S., Murall C. L., Saulnier E. & Sofonea M. (2019) Detecting within-host interactions from genotype combination prevalence data. Epidemics. 29: 100349.
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| Alizon S., Bravo I. G., Farrell P. J. & Roberts S. (2019) Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence. Phil Trans R Soc Lond B. 374(1773): 20190041.
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| Sofonea M. T., Aldakak L., Boullosa L. F. & Alizon S. (2018) Can Ebola Virus evolve to be less virulent in humans? J Evol Biol. 31: 382-392.
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| Kamiya T., Mideo N. & Alizon S. (2018) Coevolution of virulence and immunosuppression in multiple infections. J Evol Biol. 31(7): 995-1005.
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| Alizon S. & Méthot P. (2018) Reconciling Pasteur and Darwin to control infectious diseases. PLoS Biol. 16(1): e2003815.
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| Alizon S. (2018) Inexpensive research in the golden open access era. Trends Ecol Evol. 33(5): 301-303.
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| Sofonea M., Alizon S. & Michalakis Y. (2017) Exposing the diversity of multiple infection patterns. J theor Biol. 419: 278 - 289.
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| Saulnier E., Gascuel O. & Alizon S. (2017) Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study. PLoS Comput Biol. 13(3): e1005416.
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| Alizon S., Murall C. L. & Bravo I. G. (2017) Why Human Papillomavirus Acute Infections Matter. Viruses. 9(10): 293.
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| Alizon S. (2016) A Visionary Pioneer of Parasite Ecology and Evolution. Am Nat. 187: ii-iii.
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| Sofonea M., Alizon S. & Michalakis Y. (2015) From within-host interactions to epidemiological competition: a general model for multiple infections. Philos Trans R Soc Lond B. 370: 20140303.
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| Hartfield M. & Alizon S. (2015) Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Comput Biol. 11(3): e1004149.
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| Alizon S. & Michalakis Y. (2015) Adaptive virulence evolution: the good old fitness-based approach. Trends Ecol Evol. 30(5): 248-254.
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| Methot P. & Alizon S. (2014) What is a pathogen? Toward a process view of host-parasite interactions. Virulence. 5(8): 775-85.
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| Hartfield M., Murall C. L. & Alizon S. (2014) Clinical applications of pathogen phylogenies. Trends Mol Med. 20(7): 394-404.
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| Hartfield M., Bull R., White P. A., Lloyd A., Luciani F. & Alizon S. (2014) Evidence that hepatitis C virus genome partly controls infection outcome. Evol Appl. 7(5): 533-47.
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| Hartfield M. & Alizon S. (2014) Epidemiological feedbacks affect evolutionary emergence of pathogens. Am Nat. 183(4): E105-17.
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| Fraser C., Lythgoe K., Leventhal G. E., Shirreff G., Hollingsworth T. D., Alizon S. & Bonhoeffer S. (2014) Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science. 343(6177): 1243727.
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| Cousineau S. V. & Alizon S. (2014) Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance. J Evol Biol. 27(12): 2753-66.
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| Alizon S., Lion S., Murall C. L. & Abbate J. L. (2014) Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics. Virulence. 5(8): 825-827.
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| Shirreff G., Alizon S., Cori A., Guenthard H. F., Laeyendecker O., van Sighem A., Bezemer D. & Fraser C. (2013) How effectively can HIV phylogenies be used to measure heritability? Evol Med Public Health. 2013(1): 209-24.
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| Kamp C., Moslonka-Lefebvre M. & Alizon S. (2013) Epidemic spread on weighted networks. PLoS Comput Biol. 9(12): e1003352.
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| Hartfield M. & Alizon S. (2013) Introducing the outbreak threshold in epidemiology. PLoS Pathog. 6: e1003277.
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| Alizon S. & Fraser C. (2013) Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology. 10: 49.
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| Alizon S., de Roode J. C. & Michalakis Y. (2013) Multiple infections and the evolution of virulence. Ecol Lett. 16(4): 556-567.
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| Alizon S. (2013) On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison. J Evol Biol. 26(9): 2051-6.
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| Alizon S. (2013) Co-infection and super-infection models in evolutionary epidemiology. Interface Focus. 3: 20130031.
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| Alizon S. (2013) Parasite co-transmission and the evolutionary epidemiology of virulence. Evolution. 67(4): 921-933.
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| Moslonka-Lefebvre M., Bonhoeffer S. & Alizon S. (2012) Weighting for sex acts to understand the spread of STI on networks. J theor Biol. 311: 46-53.
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| Alizon S. & Magnus C. (2012) Modelling the course of an HIV infection: Insights from ecology and evolution. Viruses. 4(10): 1984-2013.
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| de Roode J. C., de Castillejo C. L. F., Faits T. & Alizon S. (2011) Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies. J Evol Biol. 24(4): 712-22.
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| Day T., Alizon S. & Mideo N. (2011) Bridging scales in the evolution of infectious disease life histories: theory. Evolution. 65(12): 3448-61.
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| Alizon S. & Michalakis Y. (2011) The transmission-virulence trade-off and superinfection: comments to smith. Evolution. 65(12): 3633-8.
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| Alizon S. & Lion S. (2011) Within-host parasite cooperation and the evolution of virulence. Proc R Soc Lond B. 278(1725): 3738-3747.
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| Alizon S., Luciani F. & Regoes R. R. (2011) Epidemiological and clinical consequences of within-host evolution. Trends Microbiol. 19(1): 24-32.
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| Abbot P. & 141 others (2011) Inclusive fitness theory and eusociality. Nature. 471(7339): E1-4.
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| Froissart R., Doumayrou J., Vuillaume F., Alizon S. & Michalakis Y. (2010) The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies. Philos. Trans. R. Soc. B. 365(1548): 1907-18.
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| Alizon S. & 18 others (2010) Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathog. 6(9): e1001123.
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| Alizon S. & Boldin B. (2010) Within-host viral evolution in a heterogeneous environment. Insights into the HIV co-receptor switch. J Evol Biol. 23: 2625-2635.
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| Luciani F. & Alizon S. (2009) The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus. PLoS Comput Biol. 5(11): e1000565.
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| Alizon S., Hurford A., Mideo N. & van Baalen M. (2009) Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. J Evol Biol. 22: 245-259.
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| Alizon S. (2009) The Price equation framework to study disease within-host evolution. J Evol Biol. 22: 1123-1132.
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| Mideo N., Alizon S. & Day T. (2008) Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases. Trends Ecol Evol. 23(9): 511-517.
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| Day T., Mideo N. & Alizon S. (2008) Why is HIV not vector-borne? Evol App. 1: 17-27.
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| Alizon S. & van Baalen M. (2008) Transmission–virulence trade-offs in vector-borne diseases. Theor Popul Biol. 74(1): 6-15.
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| Alizon S. & van Baalen M. (2008) Acute or Chronic? Within-host models with immune dynamics, infection outcome and parasite evolution. Am Nat. 172(6): E244-E256.
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| Alizon S. & van Baalen M. (2008) Multiple infections, immune dynamics and virulence evolution. Am Nat. 172(4): E150-E158.
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| Alizon S. & Taylor P. (2008) Empty sites can promote altruistic behaviour. Evolution. 62(6): 1335-1344.
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| Alizon S., Kucera M. & Jansen V. A. A. (2008) Competition between cryptic species explains variations in rates of lineage evolution. Proc Natl Acad Sci USA. 105(34): 12382-12386.
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| Alizon S. (2008) Decreased overall virulence in co-infected hosts leads to the persistence of virulent parasites. Am Nat. 172(2): E67-E79.
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| Alizon S. (2008) Transmission-recovery trade-offs to study parasite evolution. Am Nat. 172(3): E113-E121.
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| Gallet R., Alizon S., Comte P., Gutierrez A., Depaulis F., Van Baalen M., Michel E., Mü . &ller-Graf C. D. M. (2007) Predation and disturbance interact to shape prey species diversity. Am Nat. 170: 143-154.
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| Alizon S. & van Baalen M. (2005) Emergence of a convex trade-off between transmission and virulence. Am Nat. 165(6): E155-E167.
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| Alizon S. (2022) Phylogénies d'infections et phylodynamique. In: Étude de l'évolution par l'approche mathématique et informatique. (Didier, Gilles; Guindon, Stéphane, eds.) ISTE, London, UK
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| Alizon S. (2015) Pourquoi les parasites nuisent-ils à leurs hôtes ? In: Les maladies infectieuses. (Vittecoq, M; Roche, B; Prugnolle, F; Renaud, F; Thomas, F, eds.) De Boeck, Paris, France, p. 139-158.
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| Alizon S. (2010) Application de la biologie évolutive au contrôle des maladies infectieuses. In: Biologie évolutive. (Thomas, F; Lefèvre, T; Raymond, M, eds.) De Boeck, Bruxelles, Belgium, p. 778.
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| Alizon S. (2010) Diversité des maladies infectieuses. In: BiodiversitéS. (Alain, K; Aumeeruddy-Thomas, Y; Devictor, V; Langlais, A; Maris, V; Not, F; Prévot-Julliard, A C; Puijalon, S; Pujol, B, eds.) Cherche Midi, Paris, France, p. 45.
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| Alizon S. (2010) En biologie, le libre accès au quotidien. In: Hermès, La Revue. (Farchy, J; Froissart, Pascal; Méadel, C, eds.) CNRS Editions, Paris, France 57(2):, p. 47-49.
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