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Items: 1 to 50 of 60

1.

COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences.

Bourret J, Alizon S, Bravo IG.

Genome Biol Evol. 2019 Dec 1;11(12):3523-3528. doi: 10.1093/gbe/evz262.

2.

Detecting within-host interactions from genotype combination prevalence data.

Alizon S, Murall CL, Saulnier E, Sofonea MT.

Epidemics. 2019 Dec;29:100349. doi: 10.1016/j.epidem.2019.100349. Epub 2019 Jun 18.

3.

Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study.

Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boué V, Buisson M, Christophe G, D'Auria G, 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 É, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S.

BMJ Open. 2019 Jun 11;9(6):e025129. doi: 10.1136/bmjopen-2018-025129.

4.

Correction to 'Modelling the evolution of viral oncogenesis'.

Murall CL, Alizon S.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 8;374(1776):20190394. doi: 10.1098/rstb.2019.0394. No abstract available.

5.

Modelling the evolution of viral oncogenesis.

Murall CL, Alizon S.

Philos Trans R Soc Lond B Biol Sci. 2019 May 27;374(1773):20180302. doi: 10.1098/rstb.2018.0302. Erratum in: Philos Trans R Soc Lond B Biol Sci. 2019 Jul 8;374(1776):20190394.

PMID:
30955498
6.

Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence.

Alizon S, Bravo IG, Farrell PJ, Roberts S.

Philos Trans R Soc Lond B Biol Sci. 2019 May 27;374(1773):20190041. doi: 10.1098/rstb.2019.0041.

7.

Epithelial stratification shapes infection dynamics.

Murall CL, Jackson R, Zehbe I, Boulle N, Segondy M, Alizon S.

PLoS Comput Biol. 2019 Jan 23;15(1):e1006646. doi: 10.1371/journal.pcbi.1006646. eCollection 2019 Jan.

8.

Coevolution of virulence and immunosuppression in multiple infections.

Kamiya T, Mideo N, Alizon S.

J Evol Biol. 2018 Jul;31(7):995-1005. doi: 10.1111/jeb.13280. Epub 2018 May 11.

PMID:
29668109
9.

Inexpensive Research in the Golden Open-Access Era.

Alizon S.

Trends Ecol Evol. 2018 May;33(5):301-303. doi: 10.1016/j.tree.2018.02.005. Epub 2018 Apr 3.

PMID:
29625710
10.

Reconciling Pasteur and Darwin to control infectious diseases.

Alizon S, Méthot PO.

PLoS Biol. 2018 Jan 18;16(1):e2003815. doi: 10.1371/journal.pbio.2003815. eCollection 2018 Jan.

11.

Can Ebola virus evolve to be less virulent in humans?

Sofonea MT, Aldakak L, Boullosa LFVV, Alizon S.

J Evol Biol. 2018 Mar;31(3):382-392. doi: 10.1111/jeb.13229. Epub 2018 Feb 6.

PMID:
29288541
12.

Why Human Papillomavirus Acute Infections Matter.

Alizon S, Murall CL, Bravo IG.

Viruses. 2017 Oct 10;9(10). pii: E293. doi: 10.3390/v9100293. Review.

13.

Correction: Introducing the Outbreak Threshold in Epidemiology.

Hartfield M, Alizon S.

PLoS Pathog. 2017 May 31;13(5):e1006415. doi: 10.1371/journal.ppat.1006415. eCollection 2017 May.

14.

Phylodynamique des infections virales.

Alizon S, Saulnier E.

Virologie (Montrouge). 2017 Jun 1;21(3):119-129. doi: 10.1684/vir.2017.0696.

PMID:
31967559
15.

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study.

Saulnier E, Gascuel O, Alizon S.

PLoS Comput Biol. 2017 Mar 6;13(3):e1005416. doi: 10.1371/journal.pcbi.1005416. eCollection 2017 Mar.

16.

Exposing the diversity of multiple infection patterns.

Sofonea MT, Alizon S, Michalakis Y.

J Theor Biol. 2017 Apr 21;419:278-289. doi: 10.1016/j.jtbi.2017.02.011. Epub 2017 Feb 11.

PMID:
28193485
17.

A Visionary Pioneer of Parasite Ecology and Evolution.

Alizon S.

Am Nat. 2016 Jun;187(6):ii-iii. doi: 10.1086/686526. Epub 2016 Apr 1. No abstract available.

PMID:
27172602
18.

From within-host interactions to epidemiological competition: a general model for multiple infections.

Sofonea MT, Alizon S, Michalakis Y.

Philos Trans R Soc Lond B Biol Sci. 2015 Aug 19;370(1675). pii: 20140303. doi: 10.1098/rstb.2014.0303.

19.

Adaptive virulence evolution: the good old fitness-based approach.

Alizon S, Michalakis Y.

Trends Ecol Evol. 2015 May;30(5):248-54. doi: 10.1016/j.tree.2015.02.009. Epub 2015 Mar 30. Review.

PMID:
25837917
20.

Within-host stochastic emergence dynamics of immune-escape mutants.

Hartfield M, Alizon S.

PLoS Comput Biol. 2015 Mar 18;11(3):e1004149. doi: 10.1371/journal.pcbi.1004149. eCollection 2015 Mar.

21.

Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics.

Alizon S, Lion S, Murall CL, Abbate JL.

Virulence. 2014;5(8):825-7. doi: 10.4161/21505594.2014.976514.

22.

What is a pathogen? Toward a process view of host-parasite interactions.

Méthot PO, Alizon S.

Virulence. 2014;5(8):775-85. doi: 10.4161/21505594.2014.960726. Review.

23.

Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance.

Cousineau SV, Alizon S.

J Evol Biol. 2014 Dec;27(12):2753-66. doi: 10.1111/jeb.12541. Epub 2014 Dec 4.

24.

Evidence that hepatitis C virus genome partly controls infection outcome.

Hartfield M, Bull R, White PA, Lloyd A, Luciani F, Alizon S; HITS investigators.

Evol Appl. 2014 May;7(5):533-47. doi: 10.1111/eva.12151. Epub 2014 Mar 26.

25.

Clinical applications of pathogen phylogenies.

Hartfield M, Murall CL, Alizon S.

Trends Mol Med. 2014 Jul;20(7):394-404. doi: 10.1016/j.molmed.2014.04.002. Epub 2014 May 1. Review.

PMID:
24794010
26.

Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.

Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S.

Science. 2014 Mar 21;343(6177):1243727. doi: 10.1126/science.1243727. Review.

27.

Epidemiological feedbacks affect evolutionary emergence of pathogens.

Hartfield M, Alizon S.

Am Nat. 2014 Apr;183(4):E105-17. doi: 10.1086/674795. Epub 2014 Feb 12.

PMID:
24642501
28.

Co-infection and super-infection models in evolutionary epidemiology.

Alizon S.

Interface Focus. 2013 Dec 6;3(6):20130031. doi: 10.1098/rsfs.2013.0031. Review.

29.

How effectively can HIV phylogenies be used to measure heritability?

Shirreff G, Alizon S, Cori A, Günthard HF, Laeyendecker O, van Sighem A, Bezemer D, Fraser C.

Evol Med Public Health. 2013 Jan;2013(1):209-24. doi: 10.1093/emph/eot019. Epub 2013 Sep 13.

30.

Epidemic spread on weighted networks.

Kamp C, Moslonka-Lefebvre M, Alizon S.

PLoS Comput Biol. 2013;9(12):e1003352. doi: 10.1371/journal.pcbi.1003352. Epub 2013 Dec 12.

31.

On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison.

Alizon S.

J Evol Biol. 2013 Sep;26(9):2051-6. doi: 10.1111/jeb.12199. Epub 2013 Jul 13.

32.

Introducing the outbreak threshold in epidemiology.

Hartfield M, Alizon S.

PLoS Pathog. 2013;9(6):e1003277. doi: 10.1371/journal.ppat.1003277. Epub 2013 Jun 6. Erratum in: PLoS Pathog. 2017 May 31;13(5):e1006415.

33.

Within-host and between-host evolutionary rates across the HIV-1 genome.

Alizon S, Fraser C.

Retrovirology. 2013 May 2;10:49. doi: 10.1186/1742-4690-10-49.

34.

Parasite co-transmission and the evolutionary epidemiology of virulence.

Alizon S.

Evolution. 2013 Apr;67(4):921-33. doi: 10.1111/j.1558-5646.2012.01827.x. Epub 2012 Nov 16.

PMID:
23550745
35.

Multiple infections and the evolution of virulence.

Alizon S, de Roode JC, Michalakis Y.

Ecol Lett. 2013 Apr;16(4):556-67. doi: 10.1111/ele.12076. Epub 2013 Jan 24. Review.

PMID:
23347009
36.

Modelling the course of an HIV infection: insights from ecology and evolution.

Alizon S, Magnus C.

Viruses. 2012 Oct 4;4(10):1984-2013. doi: 10.3390/v4101984. Review.

37.

Weighting for sex acts to understand the spread of STI on networks.

Moslonka-Lefebvre M, Bonhoeffer S, Alizon S.

J Theor Biol. 2012 Oct 21;311:46-53. doi: 10.1016/j.jtbi.2012.06.031. Epub 2012 Jul 3. Erratum in: J Theor Biol. 2013 Jan 21;317:429.

38.

The transmission-virulence trade-off and superinfection: comments to Smith.

Alizon S, Michalakis Y.

Evolution. 2011 Dec;65(12):3633-8; discussion 3639-41. doi: 10.1111/j.1558-5646.2011.01432.x. Epub 2011 Sep 9. No abstract available.

PMID:
22133231
39.

Bridging scales in the evolution of infectious disease life histories: theory.

Day T, Alizon S, Mideo N.

Evolution. 2011 Dec;65(12):3448-61. doi: 10.1111/j.1558-5646.2011.01394.x. Epub 2011 Jul 19.

PMID:
22133217
40.

Within-host parasite cooperation and the evolution of virulence.

Alizon S, Lion S.

Proc Biol Sci. 2011 Dec 22;278(1725):3738-47. doi: 10.1098/rspb.2011.0471. Epub 2011 May 11.

41.

Inclusive fitness theory and eusociality.

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, Kümmerli 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, Noë 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, Sundström 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.

Nature. 2011 Mar 24;471(7339):E1-4; author reply E9-10. doi: 10.1038/nature09831.

42.

Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies.

de Roode JC, de Castillejo CL, Faits T, Alizon S.

J Evol Biol. 2011 Apr;24(4):712-22. doi: 10.1111/j.1420-9101.2010.02213.x. Epub 2011 Jan 24.

43.

Epidemiological and clinical consequences of within-host evolution.

Alizon S, Luciani F, Regoes RR.

Trends Microbiol. 2011 Jan;19(1):24-32. doi: 10.1016/j.tim.2010.09.005. Epub 2010 Nov 4. Review.

PMID:
21055948
44.

Within-host viral evolution in a heterogeneous environment: insights into the HIV co-receptor switch.

Alizon S, Boldin B.

J Evol Biol. 2010 Dec;23(12):2625-35. doi: 10.1111/j.1420-9101.2010.02139.x. Epub 2010 Oct 21.

45.

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.

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; Swiss HIV Cohort Study.

PLoS Pathog. 2010 Sep 30;6(9):e1001123. doi: 10.1371/journal.ppat.1001123.

46.

The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies.

Froissart R, Doumayrou J, Vuillaume F, Alizon S, Michalakis Y.

Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27;365(1548):1907-18. doi: 10.1098/rstb.2010.0068. Review.

47.

The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

Luciani F, Alizon S.

PLoS Comput Biol. 2009 Nov;5(11):e1000565. doi: 10.1371/journal.pcbi.1000565. Epub 2009 Nov 13.

48.
49.

Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future.

Alizon S, Hurford A, Mideo N, Van Baalen M.

J Evol Biol. 2009 Feb;22(2):245-59. doi: 10.1111/j.1420-9101.2008.01658.x.

50.

Acute or chronic? Within-host models with immune dynamics, infection outcome, and parasite evolution.

Alizon S, van Baalen M.

Am Nat. 2008 Dec;172(6):E244-56. doi: 10.1086/592404. Review.

PMID:
18999939

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