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'MiVEGEC' publications by members of the group since 2005:

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Bedhomme S, Pantoja DP, Bravo IG (2017) Plasmid and clonal interference during post horizontal gene transfer evolution. Molecular Ecology 26: 1832-1847 doi

Gallet R, Froissart R, Ravigné V (2017) Things softly attained are long retained: dissecting the impacts of selection regimes on polymorphism maintenance in experimental spatially heterogeneous environments. bioRxiv doi   PCI recommendation

Happel AU, Jaumdally SZ, Pidwell T, Cornelius T, Jaspan HB, Froissart R, Barnabas SL, Passmore JAS (2017) Probiotics for vaginal health in south africa: what is on retailers' shelves?. BMC Womens Health 17: 7 doi

Nicolás-Párraga S, Alemany L, de Sanjosé S, Bosch FX, Bravo IG, RIS HPV TT and HPV VVAP study groups (2017) Differential HPV16 variant distribution in squamous cell carcinoma, adenocarcinoma and adenosquamous cell carcinoma. International Journal of Cancer 140: 2092-2100 doi

Pimenoff VN, de Oliveira CM, Bravo IG (2017) Transmission between archaic and modern human ancestors during the evolution of the oncogenic human papillomavirus 16. Molecular Biology and Evolution 34: 4-19 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

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

Willemsen A, Zwart MP, Ambros S, Carrasco JL, Elena SF (2017) 2b or not 2b: Experimental evolution of functional exogenous sequences in a plant RNA virus. Genome Biology and Evolution 9: 297-310 doi

Willemsen A, Zwart MP, Elena SF (2017) High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus. BMC Evolutionary Biology 17: 25 doi


Abbate JL, Murall CL, Richner H, Althaus CL (2016) Potential impact of sexual transmission on Ebola virus epidemiology: Sierra Leone as a case study. PLoS Neglected Tropical Diseases 10: e0004676 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

Blanc S, Michalakis Y (2016) Manipulation of hosts and vectors by plant viruses and impact of the environment. Current Opinion in Insect Science 16: 36-43 doi

Boithias L, Choisy M, Souliyaseng N, Jourdren M, Quet F, Buisson Y, Thammahacksa C, Silvera N, Latsachack K, Sengtaheuanghoung O, Pierret A, Rochelle-Newall E, Becerra S, Ribolzi O (2016) Hydrological regime and water shortage as drivers of the seasonal incidence of diarrheal diseases in a tropical montane environment. PLoS Neglected Tropical Diseases 10: e0005195 doi

Chazel M, Marchandin H, Keck N, Terru D, Carriere C, Ponsoda M, Jacomo V, Panteix G, Bouzinbi N, Bañuls AL, Choisy M, Solassol J, Aubry A, Godreuil S (2016) Evaluation of the SLOMYCO sensititre (R) panel for testing the antimicrobial susceptibility of Mycobacterium marinum isolates. Annals of Clinical Microbiology and Antimicrobials 15: 30 doi

Félez-Sánchez M, Vergara M, de Sanjosé S, Castellsague X, Alemany L, Bravo IG, Grp Vvapo Ris Hpv Tt Study (2016) Searching beyond the usual papillomavirus suspects in squamous carcinomas of the vulva, penis and head and neck. Infection, Genetics and Evolution 45: 198-204 doi

François S, Filloux D, Roumagnac P, Bigot D, Gayral P, Martin DP, Froissart R, Ogliastro M (2016) Discovery of parvovirus-related sequences in an unexpected broad range of animals. Scientific Reports 6: 30880 doi

Lievens EJP, Henriques GJB, Michalakis Y, Lenormand T (2016) Maladaptive sex ratio adjustment in the invasive brine shrimp Artemia franciscana. Current Biology 26: 1463-1467 doi

Mengual-Chulá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG (2016) Assessing parallel gene histories in viral genomes. BMC Evolutionary Biology 16: 32 doi

Nguyen VAT, Bañuls AL, Tran THT, Pham KLT, Nguyen TS, Nguyen HV, Nguyen NLT, Dang DA, Marks GB, Choisy M (2016) Mycobacterium tuberculosis lineages and anti-tuberculosis drug resistance in reference hospitals across Viet Nam. BMC Microbiology 16: 167 doi

Nicolás-Párraga S, Gandini C, Pimenoff VN, Alemany L, de Sanjose S, Bosch FX, Bravo IG, Ris Hpv TT, Grp Hpv Vvap Study (2016) HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus. Cancer Medicine 5: 2909-2919 doi

Peyre M, Choisy M, Sobhy H, Kilany WH, Gely M, Tripodi A, Dauphin G, Saad M, Roger F, Lubroth J, Jobre Y (2016) Added value of avian influenza (H5) day-old chick vaccination for disease control in Egypt. Avian Diseases 60: 245-252

Sicard A, Michalakis Y, Gutiérrez S, Blanc S (2016) The strange lifestyle of multipartite viruses. PLoS Pathogens 12: e1005819 doi

Thebaud G, Michalakis Y (2016) Comment on "Large bottleneck size in cauliflower mosaic virus populations during host plant colonization" by Monsion et al. (2008). PLoS Pathogens 12: e1005512 doi

Thuy DM, Peacock TP, Bich VTN, Fabrizio T, Hoang DN, Tho ND, Diep NT, Nguyen M, Hoa LNM, Trang HTT, Choisy M, Inui K, Newman S, Trung NV, van Doorn R, To TL, Iqbal M, Bryant JE (2016) Prevalence and diversity of H9N2 avian influenza in chickens of northern Vietnam, 2014. Infection, Genetics and Evolution 44: 530-540 doi

Willemsen A, Zwart MP, Higueras P, Sardanyes J, Elena SF (2016) Predicting the stability of homologous gene duplications in a plant RNA virus. Genome Biology and Evolution 8: 3065-3082 doi

Zhang ZL, Gu QY, Vasudevan AAJ, Hain A, Kloke BP, Hasheminasab S, Mulnaes D, Sato K, Cichutek K, Haussinger D, Bravo IG, Smits SHJ, Gohlke H, Münk C (2016) Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors. Retrovirology 13: 46 doi


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

Duncan AB, Agnew P, Noel V & Michalakis Y (2015) The consequences of co-infections for parasite transmission in the mosquito Aedes aegypti. Journal of Animal Ecology. 84: 498-508 doi

Gutiérrez S, Pirolles E, Yvon M, Baecker V, Michalakis Y, Blanc S (2015) The multiplicity of cellular infection changes depending on the route of cell infection in a plant virus. Journal of Virology 89: 9665-9675 doi

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

Hoa LNM, Bryant JE, Choisy M, Nguyet LA, Bao NT, Trang NH, Chuc NTK, Toan TK, Saito T, Takemae N, Horby P, Wertheim H, Fox A (2015) Population susceptibility to a variant swine-origin influenza virus A(H3N2) in Vietnam, 2011-2012. Epidemiology and Infection 143: 2959-2964 doi

Murall CL, Bauch CT & Day T (2015) Could the human papillomavirus vaccines drive virulence evolution? Proceedings of the Royal Society of London, Series B. 282: 1069 doi

Sicard A, Zeddam JL, Yvon M, Michalakis Y, Gutiérrez S, Blanc S (2015) Circulative nonpropagative aphid transmission of nanoviruses: an oversimplified view. Journal of Virology 89: 9719-9726 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

Thai PQ, Choisy M, Duong TN, Thiem VD, Yen NT, Hien NT, Weiss DJ, Boni MF, Horby P (2015) Seasonality of absolute humidity explains seasonality of influenza-like illness in Vietnam. Epidemics 13: 65-73 doi

Trang NV, Choisy M, Nakagomi T, Chinh NTM, Doan YH, Yamashiro T, Bryant JE, Nakagomi O, Anh DD (2015) Determination of cut-off cycle threshold values in routine RT-PCR assays to assist differential diagnosis of norovirus in children hospitalized for acute gastroenteritis. Epidemiology and Infection 143: 3292-3299 doi

Viet TL, Choisy M, Bryant JE, Trong DV, Quang TP, Horby P, Tran HN, Kieu HTT, Vu TN, Van KN, Quynh ML, Wertheim HFL (2015) A dengue outbreak on a floating village at Cat Ba island in Vietnam. BMC Public Health 15: 940 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

Choisy M & de Roode JC (2014) The ecology and evolution of animal medication: genetically fixed response versus phenotypic plasticity. American Naturalist. 184: S31-S46 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

Do TTT, Martens P, Luu NH, Wright P & Choisy M (2014) Climatic-driven seasonality of emerging dengue fever in Hanoi, Vietnam. BMC Public Health. 14: 1078 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

Park AW, Vandekerkhove J & Michalakis Y (2014) Sex in an uncertain world: environmental stochasticity helps restore competitive balance between sexually and asexually reproducing populations. Journal of Evolutionary Biology. 27: 1650-1661 doi pdf

Roche B, Broutin H, Choisy M, Godreuil S, Constantin de Magny G, Chevaleyre Y, Zucker JD, Breban R, Cazelles B & Simard F (2014) The niche reduction approach: an opportunity for optimal control of infectious diseases in low-income countries? BMC Public Health. 14: 753 doi

Sangare I, Dabire R, Yameogo B, Da DF, Michalakis Y & Cohuet A (2014) Stress dependent infection cost of the human malaria agent Plasmodium falciparum on its natural vector Anopheles coluzzii. Infection, Genetics and Evolution. 25: 57-65 doi

Sy VE, Agnew P, Sidobre C & Michalakis Y (2014) Reduced survival and reproductive success generates selection pressure for the dengue mosquito Aedes aegypti to evolve resistance against infection by the microsporidian parasite Vavraia culicis. Evolutionary Applications. 7: 468-479 doi pdf


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

Berngruber TW, Froissart R, Choisy M & Gandon S (2013) Evolution of virulence in emerging epidemics. PLoS Pathogens. 9: e1003209 doi

Decaestecker E, De Gersem H, Michalakis Y & Raeymaekers JAM (2013) Damped long-term host-parasite Red Queen coevolutionary dynamics: a reflection of dilution effects? Ecology Letters. 16: 1455-1462 doi

Doumayrou J, Avellan A, Froissart R & Michalakis Y (2013) An experimental test of the transmission-virulence trade-off in a plant virus. Evolution. 67: 477-486 doi

Doumayrou J, Leblaye S, Froissart R & Michalakis Y (2013) Reduction of leaf area and symptom severity as proxies of disease-induced plant mortality: The example of the Cauliflower mosaic virus infecting two Brassicaceae hosts. Virus Research. 176: 91-100 doi

Gascuel F, Choisy M, Duplantier JM, Debarre F & Brouat C (2013) Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus. PLoS Computational Biology. 9: 1003039 doi

Gutiérrez S, Michalakis Y, Van Munster M & Blanc S (2013) Plant feeding by insect vectors can affect life cycle, population genetics and evolution of plant viruses. Functional Ecology. 27: 610-622 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

Rode NO, Landes J, Lievens EJP, Flaven E, Segard A, Jabbour-Zahab R, Michalakis Y, Agnew P, Vivares CP & Lenormand T (2013) Cytological, molecular and life cycle characterization of Anostracospora rigaudi n. g., n. sp and Enterocytospora artemiae n. g., n. sp., two new microsporidian parasites infecting gut tissues of the brine shrimp Artemia. Parasitology. 140: 1168-1185 doi pdf

Sangare I, Michalakis Y, Yameogo B, Dabire R, Morlais I & Cohuet A (2013) Studying fitness cost of Plasmodium falciparum infection in malaria vectors: validation of an appropriate negative control. Malaria Journal. 12: 2 doi

Schmit O, Adolfsson S, Vandekerkhove J, Rueda J, Bode SNS, Rossetti G, Michalakis Y, Jokela J, Martens K & Mesquita-Joanes F (2013) The distribution of sexual reproduction of the geographic parthenogen Eucypris virens (Crustacea: Ostracoda) matches environmental gradients in a temporary lake. Canadian Journal of Zoology. 91: 660-671 doi

Schmit O, Fukova I, Vandekerkhove J, Michalakis Y, Matzke-Karasz R, Rossetti G, Martens K & Mesquita-Joanes F (2013) Mate recognition as a reproductive barrier in sexual and parthenogenetic Eucypris virens (Crustacea, Ostracoda). Animal Behaviour. 85: 977-985 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

Sicard A, Yvon M, Timchenko T, Gronenborn B, Michalakis Y, Gutierrez S & Blanc S (2013) Gene copy number is differentially regulated in a multipartite virus. Nature Communications. 4: 2248 doi

Vale PF, Choisy M & Little TJ (2013) Host nutrition alters the variance in parasite transmission potential. Biology Letters. 9: 1145 doi


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

Broutin V, Bañuls AL, Aubry A, Keck N, Choisy M, Bernardet JF, Michel C, Raymond JC, Libert C, Barnaud A, Stragier P, Portaels F, Terru D, Belon C, Dereure O, Gutierrez C, Boschiroli ML, Van De Perre P, Cambau E & Godreuil S (2012) Genetic diversity and population structure of Mycobacterium marinum: new insights into host and environmental specificities. Journal of Clinical Microbiology. 50: 3627-3634 doi

Choisy M & Rohani P (2012) Changing spatial epidemiology of pertussis in continental USA. Proceedings of the Royal Society of London, Series B. 279: 4574-4581 doi

Duncan AB, Agnew P, Noel V, Demettre E, Seveno M, Brizard JP & Michalakis Y (2012) Proteome of Aedes aegypti in response to infection and coinfection with microsporidian parasites. Ecology and Evolution. 3: 199 doi pdf

Gimonneau G, Pombi M, Choisy M, Morand S, Dabire RK & Simard F (2012) Larval habitat segregation between the molecular forms of the mosquito Anopheles gambiae in a rice field area of Burkina Faso, West Africa. Medical and Veterinary Entomology. 26: 9-17 doi

Gutiérrez S, Michalakis Y & Blanc S (2012) Virus population bottlenecks during within-host progression and host-to-host transmission. Current Opinion in Virology. 2: 546–555 doi

Gutiérrez S, Yvon M, Pirolles E, Garzo E, Fereres A, Michalakis Y & Blanc S (2012) Circulating virus load determines the size of bottlenecks in viral populations progressing within a host. PLoS Pathogens. 8: e1003009 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

Mouline K, Mamai W, Agnew P, Tchonfienet M, Brengues C, Dabire R, Robert V & Simard F (2012) Physiology and development of the M and S molecular forms of Anopheles gambiae in Burkina Faso (West Africa). Medical and Veterinary Entomology. 26: 447-454 doi pdf

Multeau C, Froissart R, Perrin A, Castelli I, Casartelli M & Ogliastro M (2012) Four amino acids of an insect densovirus capsid determine midgut tropism and virulence. Journal of Virology. 86: 5937-5941 doi pdf

Nguyen TVA, Choisy M, Nguyen DH, Thanh HTT, Kim LTP, Phuong TTD, Philippe J, Nguyen TS, Ho ML, Tran SV, Bañuls AL & Dang DA (2012) High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in Northern Vietnam: sampling effect, rural and urban disparities. PLoS One. 7: e45553 doi

Vale PF, Choisy M, Froissart R, Sanjuan R & Gandon S (2012) The distribution of mutational fitness effects of phage phi X174 on different hosts. Evolution. 66: 3495-3507 doi


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

Marcombe S, Darriet F, Agnew P, Etienne M, Yp-Tcha MM, Yebakima A & Corbel V (2011) Field efficacy of new larvicide products for control of multi-resistant Aedes aegypti populations in Martinique (French West Indies). American Journal of Tropical Medicine and Hygiene. 84: 118-126 doi pdf

Marcombe S, Darriet F, Tolosa M, Agnew P, Duchon S, Etienne M, Yptcha M, Chandre F, Corbel V & Yébakima A (2011) Pyrethroid resistance reduces the efficacy of space sprays for dengue control on the island of Martinique (Caribbean). PLoS Neglected Tropical Diseases. 5: e1202 doi pdf

Vuillaume F, Thebaud G, Urbino C, Forfert N, Granier M, Froissart R, Blanc S & Peterschmitt M (2011) Distribution of the phenotypic effects of random homologous recombination between two virus species. PLoS Pathogens. 7: e1002028 doi pdf


Adolfsson S, Michalakis Y, Paczesniak D, Bode SN, Butlin RK, Lamatsch DK, Martins MJ, Schmit O, Vandekerkhove J & Jokela J (2010) Evaluation of elevated ploidy and asexual reproduction as alternative explanations for geographic parthenogenesis in Eucypris virens ostracods. Evolution. 64: 986-997 pdf

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

Chapuis MP, Crespin L, Estoup A, Auge-Sabatier A, Foucart A, Lecoq M & Michalakis Y (2010) Parental crowding influences life-history traits in Locusta migratoria females. Bulletin of Entomological Research. 100: 9-17 pdf

Choisy M & de Roode JC (2010) Mixed infections and the evolution of virulence: effects of resource competition, parasite plasticity, and impaired host immunity. American Naturalist. 175: E105-E118

Darriet F, Marcombe S, Etienne M, Yebakima A, Agnew P, Yp-Tcha MM & Corbel V (2010) Field evalutation of pyriproxyfen and spinosad mixture for the control of insecticide resistant Aedes aegypti in Martinique (French West Indies). Parasites & Vectors. 3: 88 pdf

Djogbénou L, Noel V & Agnew P (2010) Costs of insensitive acetylcholinesterase insecticide resistance for the malaria vector Anopheles gambiae homozygous for the G119S mutation. Malaria Journal. 9: 12 pdf

Echaubard P, Duron O, Agnew P, Sidobre C, Noel V, Weill M & Michalakis Y (2010) Rapid evolution of Wolbachia density in insecticide resistant Culex pipiens. Heredity. 104: 15-19 pdf

Elena SF & Froissart R (2010) New experimental and theoretical approaches towards the understanding of the emergence of viral infections Introduction. Philosophical Transactions of the Royal Society B: Biological Sciences. 365: 1867-1869 pdf

Faye B, Bañuls, AL, Bucheton B, Dione MM, Bassanganam O, Hide M, Dereure J, Choisy M, Ndiaye JL, Konaté O, Claire M, Senghor MW, Faye MN, Sy I, Niang AA, Molez JF, Victoir K, Marty P, Delaunay P, Knecht R, Mellul S, Diedhiou S & Gaye O (2010) Canine visceral leishmaniasis caused by Leishmania infantum in Senegal: risk of emergence in humans? Microbes and Infection. 14: 1219-1225 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

Godreuil S, Renaud F, Choisy M, Depina JJ, Garnotel E, Morillon M, Van de Perre P & Bañuls AL (2010) Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti. Clinical Microbiology and Infection. 16: 1024-1026

Gutiérrez S, Yvon M, Thébaud G, Monsion B, Michalakis Y & Blanc S (2010) Dynamics of the multiplicity of cellular infection in a plant virus. PLoS Pathogens. 6: e1001113 pdf

Michalakis Y, Charmentier A, Gaillard JM, Sorci G, Tully T & O Ronce (2010) Evolution des traits d'histoire de vie. In Biologie Evolutive. Eds. Thomas F, Lefèvre T & Raymond M. pp. 339-386. De Boeck, Bruxelles.

Park AW, Jokela J & Michalakis Y (2010) Parasites and deleterious mutations: interactions influencing the evolutionary maintenance of sex. Journal of Evolutionary Biology. 23: 1013-1023 pdf


Chapuis MP, Loiseau A, Michalakis Y, Lecoq M, Franc A & Estoup A (2009) Outbreaks, gene flow and effective population size in the migratory locust, Locusta migratoria: a regional-scale comparative survey. Molecular Ecology. 18: 792-800 pdf

de Meeûs T, Prugnolle F & Agnew P (2009) Asexual reproduction in infectious diseases. In Lost Sex. Eds. Schön I, Martens K & Dijk P. pp 517-533. Springer, Netherlands

Marcombe S, Carron A, Darriet F, Etienne M, Agnew P, Tolosa M, Yp-Tcha MM, Lagneau C, Yébakima A & Corbel V (2009) Reduced efficacy of pyrethroid space sprays for dengue control in an area of Martinique with pyrethroid resistance. American Journal of Tropical Medicine and Hygiene. 80: 745-751 pdf

Michalakis Y & Renaud F (2009) Malaria: Evolution in vector control. Nature. 462: 298-300

Michalakis Y (2009) Parasitism and the evolution of life-history traits. In Ecology and evolution of parasitism. Eds. Thomas F, Guégan JF & Renaud F. pp. 19-30. Oxford University Press, Oxford.

Prugnolle F & Chevillon C (2009) Evolution adaptative des pathogènes, identification des mécanismes et conséquences épidémiologiques. In Introduction à l'épidémiologie intégrative des maladies infectieuses et parasitaire. (Eds. Guégan J & Choisy M). pp. 311-345. de Boeck.


Berticat C, Bonnet J, Duchon S, Agnew P, Weill M & Corbel V (2008) Costs and benefits of multiple resistance to insecticides for Culex quinquefasciatus mosquitoes. BMC Evolutionary Biology. 8: 104 doi pdf

Chapuis MP, Estoup A, Augé-Sabatier A, Foucart A, Lecoq M & Michalakis Y (2008) Genetic variation for parental effects on the propensity to gregarize in Locusta migratoria. BMC Evolutionary Biology. 8: 37 pdf

Chapuis MP, Lecoq M, Michalakis Y, Loiseau A, Sword GA, Piry S & Estoup A (2008) Do outbreaks affect population structure? A worldwide survey in Locusta migratoria, a pest plagued by microsatellite null alleles. Molecular Ecology. 17: 3640 pdf

Gavrilets S & Michalakis Y (2008) Effects of environmental heterogeneity on victim-exploiter coevolution. Evolution. 62: 3100-3116 pdf

Michalakis Y, Bedhomme S, Biron DG, Rivero A, Sidobre C & Agnew P (2008) Virulence and resistance in a mosquito-microsporidium interaction. Evolutionary Applications. 1: 49-56 pdf

Monsion B, Froissart R, Michalakis Y & Blanc S (2008) Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization. PLoS Pathogens. 4: e1000174 pdf

Olivieri I, Singer MC, Magalhaes S, Courtiol A, Dubois Y, Carbonell D, Justy F, Beldade P, Parmesan C & Michalakis Y (2008) Genetic, ecological, behavioral, and geographic differentiation of populations in a thistle weevil: implications for speciation and biocontrol. Evolutionary Applications. 1: 112-128 pdf

Prugnolle F, Choisy M & de Meeûs T (2008) CLONALITY V.0.4: a randomization-based program to test for heterozygosity-genet size relationships in clonal organisms. Molecular Ecology Resources. 8: 954-956


Choisy M, Guégan JF & Rohani P (2007) Mathematical Modeling of Infectious Diseases Dynamics. In Encyclopedia of infectious diseases: Modern methodologies (Ed. Tibayrenc M). John Wiley & Sons,Inc. pdf

de Meeûs T, Prugnolle F & Agnew P (2007) Asexual reproduction: Genetics and evolutionary aspects. Cellular and Molecular Life Sciences. 64: 1355-1372 pdf

Michalakis Y (2007) Parasitisme et évolution des traits d'histoire de vie. In Ecologie et évolution des systèmes parasites. (Eds. Thomas F, Guégan JF & Renaud F) de Boeck, Bruxelles pdf

Nettle D, Grace JB, Choisy M, Cornell HV, Guégan JF & Hochberg ME (2007) Cultural diversity, economic development and societal instability. PLoS One. 9: e929 pdf

Rivero A, Agnew P, Bedhomme S, Sidobre C & Michalakis Y (2007) Resource depletion in Aedes aegypti mosquitoes infected by the microsporidia Vavraia culicis. Parasitology. 134: 1355-1362 pdf


Choisy M & Rohani P (2006) Harvesting can increase severity of wildlife disease epidemics. Proceedings of the Royal Society of London, Series B. 273: 2025-2034 pdf

Choisy M, Guégan JF & Rohani P (2006) Dynamics of infectious diseases and pulse vaccination: teasing apart the embedded resonance effects. Physica D. 223: 26-35 pdf


Bedhomme S, Agnew P, Sidobre C & Michalakis Y (2005) Pollution by conspecifics as a component of intraspecific competition among Aedes aegypti larvae. Ecological Entomology. 30: 1-7 pdf

Bedhomme S, Agnew P, Vital POY, Sidobre C & Michalakis Y (2005) Prevalence-dependent costs of parasite virulence. PLoS Biology. 3: e262 [- synopsis -] doi pdf

Biron DG, Agnew P, Marche L, Sidobre C & Michalakis Y (2005) Proteome of Aedes aegypti larvae in response to infection by the intracellular parasite Vavraia culicis. International Journal for Parasitology. 35: 1385-1397 pdf

Chapuis MP, Loiseau A, Michalakis Y, Lecoq M & Estoup A (2005) Characterization and PCR multiplexing of polymorphic microsatellite loci for the locust Locusta migratoria. Molecular Ecology Notes. 5: 554-557

Froissart R, Roze D, Uzest M, Galibert L, Blanc S & Michalakis Y (2005) Recombination every day: Abundant recombination in a virus during a single multi-cellular host infectiton. PLoS Biology. 3: e89 [- synopsis -] pdf

McCoy KD, Chapuis E, Tirard C, Boulinier T, Michalakis Y, Bohec CL, Maho YL & Gauthier-Clerc M (2005) Recurrent evolution of host-specialized races in a globally distributed parasite. Proceedings of the Royal Society of London, Series B. 272: 2389-95. pdf

Michalakis Y & Renaud F (2005) Malaria - fungal allies enlisted. Nature. 435: 891 pdf

Montville R, Froissart R, Remold SK, Tenaillon O & Turner PE (2005) Evolution of mutational robustness in an RNA virus PLoS Biology. 3: e381 [- synopsis -] pdf

Plisson C, Uzest M, Drucker M, Froissart R, Dumas C, Conway J, Thomas D, Blanc S & Bron P (2005) Structure of the mature P3-virus particle complex of cauliflower mosaic virus revealed by cryo-electron microscopy Journal of Molecular Biology. 346: 267-277 pdf

Roze D, Rousset F & Michalakis Y (2005) Germline bottlenecks, biparental inheritance and selection on mitochondrial variants: a two-level selection model. Genetics. 170: 1385-1399 pdf