Surname : ALIZON
Name : Samuel
Team :
SEE
Grade : DR2
Email address : This email address is being protected from spambots. You need JavaScript enabled to view it.
Telephone : (+33) 4 48 19 18 67
Fax : (+33) 4 48 19 18 79
Office : 315
Locality : CNRS/IRD La Valette
Employer : CNRS
Other : Personal home page
Publications :
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Alizon S, Bravo IG, Farrell PJ, Roberts S (2019) Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence. Philosophical Transactions of the Royal Society B: Biological Sciences 374: 20190041 doi |
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Alizon S, Murall CL, Saulnier E, Sofonea MT (2019) Detecting within-host interactions from genotype combination prevalence data. Epidemics 29: 100349 doi |
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Bourret J, Alizon S, Bravo IG (2019) COUSIN (COdon Usage Similarity INdex): A normalized measure of codon usage preferences. Genome Biology and Evolution 11: 3523-3528 doi |
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Murall CL, Alizon S (2019) Modelling the evolution of viral oncogenesis. Philosophical Transactions of the Royal Society B: Biological Sciences 374: 20180302 doi |
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Murall CL, Jackson R, Zehbe I, Boulle N, Segondy M, Alizon S (2019) Epithelial stratification shapes infection dynamics. PLoS Computational Biology 15: e1006646 doi |
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Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boue V, Buisson M, Christophe G, D'Auria G, De Taroni F, Foulongne V, Froissart R, Graf C, Grasset S, Groc S, Hirtz C, Jaussent A, Lajoie J, Lorcy F, Picot E, Picot MC, Ravel J, Reynes J, Rousset T, Seddiki A, Teirlinck M, Tribout V, Tuaillon E, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open 9: e025129 doi |
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Alizon S (2018) Inexpensive research in the golden open-access era. Trends in Ecology & Evolution 33: 301-303 doi |
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Alizon S, Methot PO (2018) Reconciling pasteur and darwin to control infectious diseases. PLoS Biology 16: e2003815 doi |
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Kamiya T, Mideo N, Alizon S (2018) Coevolution of virulence and immunosuppression in multiple infections. Journal of Evolutionary Biology 31: 995-1005 doi |
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Sofonea MT, Aldakak L, Boullosa LFVV, Alizon S (2018) Can ebola virus evolve to be less virulent in humans? Journal of Evolutionary Biology 31: 382-392 doi |
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Alizon S, Murall CL, Bravo IG (2017) Why human papillomavirus acute infections matter. Viruses 9: 293 doi |
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Alizon S, Saulnier E (2017) Phylodynamics of viral infections. Virologie 21: 119-129 doi |
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Murall CL, Abbate JL, Touzel MP, Allen-Vercoe E, Alizon S, Froissart R, McCann K (2017) Invasions of host-associated microbiome networks. In, Networks of Invasion: Empirical Evidence and Case Studies. Advances in Ecological Research. 57: 201-281 doi |
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Saulnier E, Gascuel O, Alizon S (2017) Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study. PLoS Computational Biology 13: e1005416 doi |
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Sofonea MT, Alizon S, Michalakis Y (2017) Exposing the diversity of multiple infection patterns. Journal of Theoretical Biology 419: 278-289 doi |
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Alizon S (2016) C'est grave Dr Darwin ? pp 240. Seuil |
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Alizon S (2016) A visionary pioneer of parasite ecology and evolution. American Naturalist 187: doi |
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Alizon S, Michalakis Y (2015) Adaptive virulence evolution: the good old fitness-based approach. Trends in Ecology & Evolution. 30: 248-254 doi
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Hartfield M, Alizon S (2015) Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Computational Biology. 11 doi
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Sofonea MT, Alizon S, Michalakis Y (2015) From within-host interactions to epidemiological competition: a general model for multiple infections. Philosophical Transactions of the Royal Society B: Biological Sciences 370: 20140303 doi |
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Alizon S (2014) Evolution of Disease Virulence. In Oxford Bibliographies in Evolutionary biology. Ed. Losos, J. Oxford University Press, New-York. doi
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Alizon S, Lion S, Murall CL & Abbate JL (2014) Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics. Virulence. 5: 825-827 doi |
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Cousineau SV & Alizon S (2014) Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance. Journal of Evolutionary Biology. 27: 2753-2766 doi |
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Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S & Bonhoeffer S (2014) Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science. 343: 6117 doi |
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Hartfield M & Alizon S (2014) Epidemiological feedbacks affect evolutionary emergence of pathogens. American Naturalist. 183: E105-E117 doi pdf
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Hartfield M, Bull R, White PA, Lloyd A, Luciani F, Alizon S & the HITS investigators(2014) Evidence that hepatitis C virus genome partly controls infection outcome. Evolutionary Applications. 7: 533-547 doi
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Hartfield M, Murall CL & Alizon S (2014) Clinical applications of pathogen phylogenies. Trends in Molecular Medicine. 20: 394-404 doi |
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Methot PO & Alizon S (2014) What is a pathogen? Toward a process view of host-parasite interactions. Virulence. 5: 775-785 doi |
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Alizon S & Fraser C (2013) Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology. 10: 49 doi |
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Alizon S (2013) Co-infection and super-infection models in evolutionary epidemiology. Interface Focus. 3: 31 doi
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Alizon S (2013) On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison. Journal of Evolutionary Biology. 26: 2051-2056 doi |
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Alizon S (2013) Parasite co-transmission and the evolutionary epidemiology of virulence. Evolution. 67: 921-933 doi |
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Alizon S, de Roode JC & Michalakis Y (2013) Multiple infections and the evolution of virulence. Ecology Letters. 16: 556-567 doi |
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Hartfield M & Alizon S (2013) Introducing the outbreak threshold in epidemiology. PLoS Pathogens. 9: e1003277 doi pdf
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Kamp C, Moslonka-Lefebvre M & Alizon S (2013) Epidemic spread on weighted networks. PLoS Computational Biology. 9: e1003352 doi |
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Shirreff G, Alizon S, Cori A, Günthard H, Laeyendecker O, van Sighem A, Bezemer D & Fraser C (2013) How effectively can HIV phylogenies be used to measure heritability? Evolution, Medicine, and Public Health. 2013: 209-224 doi |
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Alizon S & Magnus C (2012) Modelling the course of an HIV Infection: Insights from ecology and evolution. Viruses. 4: 1984-2013 doi |
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Moslonka-Lefebvre M, Bonhoeffer S & Alizon S (2012) Weighting for sex acts to understand the spread of STI on networks. Journal of Theoretical Biology. 311: 46-53 doi [- correction -] pdf
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Abbot P, Abe J, Alcock J, Alizon S, Alpedrinha JA, Andersson M, Andre JB, van Baalen M, Balloux F, Balshine S, Barton N, Beukeboom LW, Biernaskie JM, Bilde T, Borgia G, Breed M, Brown S, Bshary R, Buckling A, Burley NT, Burton-Chellew MN, Cant MA, Chapuisat M, Charnov EL, Clutton-Brock T, Cockburn A, Cole BJ, Colegrave N, Cosmides L, Couzin ID, Coyne JA, Creel S, Crespi B, Curry RL, Dall SR, Day T, Dickinson JL, Dugatkin LA, El Mouden C, Emlen ST, Evans J, Ferriere R, Field J, Foitzik S, Foster K, Foster WA, Fox CW, Gadau J, Gandon S, Gardner A, Gardner MG, Getty T, Goodisman MA, Grafen A, Grosberg R, Grozinger CM, Gouyon PH, Gwynne D, Harvey PH, Hatchwell BJ, Heinze J, Helantera H, Helms KR, Hill K, Jiricny N, Johnstone RA, Kacelnik A, Kiers ET, Kokko H, Komdeur J, Korb J, Kronauer D, Kummerli R, Lehmann L, Linksvayer TA, Lion S, Lyon B, Marshall JA, McElreath R, Michalakis Y, Michod RE, Mock D, Monnin T, Montgomerie R, Moore AJ, Mueller UG, Noe R, Okasha S, Pamilo P, Parker GA, Pedersen JS, Pen I, Pfennig D, Queller DC, Rankin DJ, Reece SE, Reeve HK, Reuter M, Roberts G, Robson SK, Roze D, Rousset F, Rueppell O, Sachs JL, Santorelli L, Schmid-Hempel P, Schwarz MP, Scott-Phillips T, Shellmann-Sherman J, Sherman PW, Shuker DM, Smith J, Spagna JC, Strassmann B, Suarez AV, Sundstrom L, Taborsky M, Taylor P, Thompson G, Tooby J, Tsutsui ND, Tsuji K, Turillazzi S, Ubeda F, Vargo EL, Voelkl B, Wenseleers T, West SA, West-Eberhard MJ, Westneat DF, Wiernasz DC, Wild G, Wrangham R, Young AJ, Zeh DW, Zeh JA & Zink A (2011) Inclusive fitness theory and eusociality. Nature. 471: E1-4; author reply E9-10 doi
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Alizon S & Lion S (2011) Within-host parasite cooperation and the evolution of virulence. Proceedings of the Royal Society of London, Series B. 278: 3738-3747 doi
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Alizon S & Michalakis Y (2011) The transmission-virulence trade-off and superinfection: comments to Smith. Evolution. 65: 3633-3638 doi
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Alizon S, Luciani F & Regoes RR (2011) Epidemiological and clinical consequences of within-host evolution. Trends in Microbiology. 19: 24-32 doi
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Day T, Alizon S & Mideo N (2011) Bridging scales in the evolution of infectious disease life histories: theory. Evolution. 65: 3448-3461 doi
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de Roode JC, Fernandez de Castillejo CL, Faits T & Alizon S (2011) Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies. Journal of Evolutionary Biology. 24: 712-722 doi
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Alizon S & Boldin B (2010) Within-host viral evolution in a heterogeneous environment: insights into the HIV co-receptor switch. Journal of Evolutionary Biology. 23: 2625-2635 doi
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Alizon S, von Wyl V, Stadler T, Kouyos RD, Yerly S, Hirschel B, Böni J, Shah C, Klimkait T, Furrer H, Rauch A, Vernazza PL, Bernasconi E, Battegay M, Bürgisser P, Telenti A, Günthard HF, Bonhoeffer S & the Swiss HIV Cohort Study (2010) Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathogens. 6: e1001123 pdf
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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. Philosophical Transactions of the Royal Society B: Biological Sciences. 365: 1907-1918 pdf
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Alizon S (2009) The Price equation framework to study disease within-host evolution. Journal of Evolutionary Biology. 22: 1123-1132 pdf
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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. Journal of Evolutionary Biology. 22: 245-259 pdf
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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 Computational Biology. 5: e1000565 pdf
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Alizon S (2008) Decreased overall virulence in coinfected hosts leads to the persistence of virulent parasites. American Naturalist. 172: E67-E79 pdf
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Alizon S (2008) Transmission-recovery trade-offs to study parasite evolution. American Naturalist. 172: E113-E121 pdf
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Alizon S & Taylor P (2008) Empty sites can promote altruistic behavior. Evolution. 62: 1335-1344 pdf
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Alizon S & van Baalen M (2008) Acute or chronic? Within-host models with immune dynamics, infection outcome, and parasite evolution. American Naturalist. 172: E244-E256 pdf
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Alizon S & van Baalen M (2008) Multiple infections, immune dynamics, and the evolution of virulence. American Naturalist. 172: E150-E168 pdf
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Alizon S & van Baalen M (2008) Transmission-virulence trade-offs in vector-borne diseases. Theoretical Population Biology. 74: 6-15 |
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Alizon S, Kucera M & Jansen VAA (2008) Competition between cryptic species explains variations in rates of lineage evolution. Proceedings of the National Academy of Sciences USA. 105: 12382-12386 pdf
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Day T, Mideo N & Alizon S (2008) Why is HIV not vector-borne? Evolutionary Applications. 1: 17-27 pdf
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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 in Ecology & Evolution. 23: 511-517 doi pdf
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Gallet R, Alizon S, Comte PA, Gutierrez A, Depaulis F, van Baalen M, Michel E & Muller-Graf CDM (2007) Predation and disturbance interact to shape prey species diversity. American Naturalist. 170: 143-154 |
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Alizon S & van Baalen M (2005) Emergence of a convex trade-off between transmission and virulence. American Naturalist. 165: E155-E167 pdf
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