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Surname : ALIZON
Name : Samuel
Team : SEE
Grade : CR1
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 :

Alizon S, Saulnier E (2017) Phylodynamics of viral infections. Virologie 21: 119-129 doi

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

Saulnier E, Gascuel O, Alizon S (2017) Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study. PLoS Computational Biology 13: e1005416 doi

Sofonea MT, Alizon S, Michalakis Y (2017) Exposing the diversity of multiple infection patterns. Journal of Theoretical Biology 419: 278-289 doi

Alizon S (2016) C'est grave Dr Darwin ? pp 240. Seuil

Alizon S (2016) A visionary pioneer of parasite ecology and evolution. American Naturalist 187: doi

Alizon S, Michalakis Y (2015) Adaptive virulence evolution: the good old fitness-based approach. Trends in Ecology & Evolution. 30: 248-254 doi

Hartfield M & Alizon S (2015) Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Computational Biology. 11 doi

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

Alizon S (2014) Evolution of Disease Virulence. In Oxford Bibliographies in Evolutionary biology. Ed. Losos, J. Oxford University Press, New-York. doi

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

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

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

Hartfield M & Alizon S (2014) Epidemiological feedbacks affect evolutionary emergence of pathogens. American Naturalist. 183: E105-E117 doi pdf

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

Hartfield M, Murall CL & Alizon S (2014) Clinical applications of pathogen phylogenies. Trends in Molecular Medicine. 20: 394-404 doi

Methot PO & Alizon S (2014) What is a pathogen? Toward a process view of host-parasite interactions. Virulence. 5: 775-785 doi

Alizon S & Fraser C (2013) Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology. 10: 49 doi

Alizon S (2013) Co-infection and super-infection models in evolutionary epidemiology. Interface Focus. 3: 31 doi

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

Alizon S (2013) Parasite co-transmission and the evolutionary epidemiology of virulence. Evolution. 67: 921-933 doi

Alizon S, de Roode JC & Michalakis Y (2013) Multiple infections and the evolution of virulence. Ecology Letters. 16: 556-567 doi

Hartfield M & Alizon S (2013) Introducing the outbreak threshold in epidemiology. PLoS Pathogens. 9: e1003277 doi pdf

Kamp C, Moslonka-Lefebvre M & Alizon S (2013) Epidemic spread on weighted networks. PLoS Computational Biology. 9: e1003352 doi

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

Alizon S & Magnus C (2012) Modelling the course of an HIV Infection: Insights from ecology and evolution. Viruses. 4: 1984-2013 doi

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

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

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

Alizon S & Michalakis Y (2011) The transmission-virulence trade-off and superinfection: comments to Smith. Evolution. 65: 3633-3638 doi

Alizon S, Luciani F & Regoes RR (2011) Epidemiological and clinical consequences of within-host evolution. Trends in Microbiology. 19: 24-32 doi pdf

Day T, Alizon S & Mideo N (2011) Bridging scales in the evolution of infectious disease life histories: theory. Evolution. 65: 3448-3461 doi

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

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 pdf

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

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

Alizon S (2009) The Price equation framework to study disease within-host evolution. Journal of Evolutionary Biology. 22: 1123-1132 pdf

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

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

Alizon S (2008) Decreased overall virulence in coinfected hosts leads to the persistence of virulent parasites. American Naturalist. 172: E67-E79 pdf

Alizon S (2008) Transmission-recovery trade-offs to study parasite evolution. American Naturalist. 172: E113-E121 pdf

Alizon S & Taylor P (2008) Empty sites can promote altruistic behavior. Evolution. 62: 1335-1344 pdf

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

Alizon S & van Baalen M (2008) Multiple infections, immune dynamics, and the evolution of virulence. American Naturalist. 172: E150-E168 pdf

Alizon S & van Baalen M (2008) Transmission-virulence trade-offs in vector-borne diseases. Theoretical Population Biology. 74: 6-15

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

Day T, Mideo N & Alizon S (2008) Why is HIV not vector-borne? Evolutionary Applications. 1: 17-27 pdf

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

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

Alizon S & van Baalen M (2005) Emergence of a convex trade-off between transmission and virulence. American Naturalist. 165: E155-E167 pdf