|
|
Resource landscape shapes the composition and stability of the human vaginal microbiota
Tsukushi Kamiya
,
Mircea T Sofonea
,
Michael France
,
Nicolas Tessandier
,
Ignacio G Bravo
et al.
Article dans une revue
hal-05492290v1
|
|
|
High-risk human papillomavirus cervical infection prevalence: a nationwide retrospective study comparing opportunistic and organised screening, France, 2020 to 2023
Olivier Supplisson
,
Nicolas Tessandier
,
Mathilde Roussel
,
Stéphanie Haim-Boukobza
,
Sonia Burrel
et al.
Article dans une revue
hal-05191445v1
|
|
|
Incidence and duration of human papillomavirus infections in young women: insights from a bimonthly follow-up cohort
Thomas Bénéteau
,
Soraya Groc
,
Carmen Lía Murall
,
Vanina Boué
,
Baptiste Elie
et al.
Article dans une revue
hal-04822236v1
|
|
|
Mutant emergence timing and population immunisation status impact epidemiological dynamics
Bastien Reyné
,
Ramsès Djidjou-Demasse
,
Mircea T Sofonea
,
Samuel Alizon
Article dans une revue
hal-05069967v1
|
|
|
Leaky or polarised immunity: Non-Markovian modelling highlights the impact of immune memory assumptions
Bastien Reyné
,
Tsukushi Kamiya
,
Ramsès Djidjou-Demasse
,
Samuel Alizon
,
Mircea T Sofonea
Article dans une revue
hal-05283311v1
|
|
|
Viral and immune dynamics of genital human papillomavirus infections in young women with high temporal resolution
Nicolas Tessandier
,
Baptiste Elie
,
Vanina Boué
,
Christian Selinger
,
Massilva Rahmoun
et al.
Article dans une revue
hal-04906921v1
|
|
|
SARS-CoV-2 epidemiology, kinetics, and evolution: A narrative review
Samuel Alizon
,
Mircea T Sofonea
Article dans une revue
(article de synthèse)
hal-05025966v1
|
|
|
Importance scientifique, sanitaire et sociale du microbiome vaginal
Samuel Alizon
,
Jeanne Tamarelle
Article dans une revue
hal-05373992v1
|
|
|
Factors shaping vaginal microbiota long-term community dynamics in young adult women
Tsukushi Kamiya
,
Nicolas Tessandier
,
Baptiste Elie
,
Claire Bernat
,
Vanina Boué
et al.
Article dans une revue
hal-04987761v1
|
|
|
Seroprevalence of human herpes viruses in France, 2018–2022: a multilevel regression and poststratification approach
Olivier Supplisson
,
Benoit Visseaux
,
Stéphanie Haim-Boukobza
,
David Boutolleau
,
Samuel Alizon
et al.
Article dans une revue
hal-04710015v1
|
|
|
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model
Alexander Massey
,
Corentin Boennec
,
Claudia Ximena Restrepo-Ortiz
,
Christophe Blanchet
,
Samuel Alizon
et al.
Article dans une revue
hal-04710001v1
|
|
|
COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences
Gonché Danesh
,
Corentin Boennec
,
Laura Verdurme
,
Mathilde Roussel
,
Sabine Trombert-Paolantoni
et al.
Article dans une revue
hal-04246696v1
|
|
|
Within-host evolutionary dynamics of antimicrobial quantitative resistance
Ramsès Djidjou-Demasse
,
Mircea T Sofonea
,
Marc Choisy
,
Samuel Alizon
Article dans une revue
hal-03194023v4
|
|
|
Multiple infection theory rather than ‘socio‐virology’? A commentary on Leeks et al. 2023
Samuel Alizon
Article dans une revue
hal-04293988v1
|
|
|
Predicting the virulence of future emerging zoonotic viruses
Samuel Alizon
Article dans une revue
hal-04201651v1
|
|
|
Does exposure to different menstrual products affect the vaginal environment?
Nicolas Tessandier
,
Ilkay Başak Uysal
,
Baptiste Elie
,
Christian Selinger
,
Sophie Grasset
et al.
Molecular Ecology, 2023, EVOLUTIONARY ECOLOGY OF HUMAN‐ASSOCIATED MICROBES, 32 (10), pp.2592-2601. ⟨10.1111/mec.16678⟩
Article dans une revue
hal-03847887v1
|
|
|
Challenges for mathematical epidemiological modelling
Pascal Crepey
,
Harold Noël
,
Samuel Alizon
Article dans une revue
hal-03607991v1
|
|
|
Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics
Bastien Reyné
,
Quentin Richard
,
Christian Selinger
,
Mircea T Sofonea
,
Ramsès Djidjou-Demasse
et al.
Article dans une revue
hal-03629334v1
|
|
|
Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022
Mircea Sofonea
,
Bénédicte Roquebert
,
Vincent Foulongne
,
David Morquin
,
Laura Verdurme
et al.
Article dans une revue
hal-03714983v1
|
|
|
The source of individual heterogeneity shapes infectious disease outbreaks
Baptiste Elie
,
Christian Selinger
,
Samuel Alizon
Article dans une revue
hal-03175555v2
|
|
|
TiPS : Rapidly simulating trajectories and phylogenies from compartmental models
Gonché Danesh
,
Emma Saulnier
,
Olivier Gascuel
,
Marc Choisy
,
Samuel Alizon
Article dans une revue
hal-03903561v1
|
|
|
Concomitant and productive genital infections by HSV-2 and HPV in two young women: A case report
Ilkay Başak Uysal
,
Vanina Boué
,
Carmen Lia Murall
,
Christelle Graf
,
Christian Selinger
et al.
Article dans une revue
hal-03795483v1
|
|
|
Corrigendum to: Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities
Bastien Reyné
,
Christian Selinger
,
Mircea Sofonea
,
Stéphanie Miot
,
Amandine Pisoni
et al.
Article dans une revue
hal-04056156v1
|
|
|
Les lois de la contagion. Fake news, virus, tendances…
Samuel Alizon
Article dans une revue
hal-03664004v1
|
|
|
Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020
Samuel Alizon
,
Christian Selinger
,
Mircea T Sofonea
,
Stéphanie Haim-Boukobza
,
Jean-Marc Giannoli
et al.
Article dans une revue
hal-03175551v3
|
|
|
Variant‐specific SARS‐CoV‐2 within‐host kinetics
Baptiste Elie
,
Bénédicte Roquebert
,
Mircea T Sofonea
,
Sabine Trombert-Paolantoni
,
Vincent Foulongne
et al.
Article dans une revue
hal-03651890v1
|
|
|
Within-host bacterial growth dynamics with both mutation and horizontal gene transfer
Ramsès Djidjou-Demasse
,
Samuel Alizon
,
Mircea T Sofonea
Article dans une revue
hal-02500420v1
|
|
|
Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses
A. Debernardi
,
W. Jarassier
,
C. Soret
,
C. Mougin
,
Samuel Alizon
et al.
Article dans une revue
hal-03425708v1
|
|
|
Two waves and a high tide: the COVID-19 epidemic in France
Mircea T Sofonea
,
Corentin Boennec
,
Yannis Michalakis
,
Samuel Alizon
Article dans une revue
hal-03289626v2
|
|
|
SARS-CoV-2 viral RNA levels are not 'viral load
Yannis Michalakis
,
Mircea T Sofonea
,
Samuel Alizon
,
Ignacio G. Bravo
Article dans une revue
hal-03419147v1
|
|
|
Memory is key in capturing COVID-19 epidemiological dynamics
Mircea T Sofonea
,
Bastien Reyné
,
Baptiste Elie
,
Ramsès Djidjou-Demasse
,
Christian Selinger
et al.
Article dans une revue
hal-03289624v1
|
|
|
Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France
Mircea T Sofonea
,
Samuel Alizon
Article dans une revue
hal-03366541v1
|
|
|
Can we eradicate viral pathogens?
Samuel Alizon
,
Paul E Turner
Article dans une revue
hal-03500287v1
|
|
|
Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic
Quentin Richard
,
Samuel Alizon
,
Marc Choisy
,
Mircea T Sofonea
,
Ramsès Djidjou-Demasse
Article dans une revue
hal-02879512v3
|
|
|
Emerging dynamics from high-resolution spatial numerical epidemics
Olivier Thomine
,
Samuel Alizon
,
Corentin Boennec
,
Marc Barthelemy
,
Mircea T Sofonea
Article dans une revue
hal-03415297v1
|
|
|
Predicting COVID-19 incidence in French hospitals using human contact network analytics
Christian Selinger
,
Marc Choisy
,
Samuel Alizon
Article dans une revue
hal-03267059v2
|
|
|
Treating symptomatic infections and the co-evolution of virulence and drug resistance
Samuel Alizon
Article dans une revue
hal-03001103v2
|
|
|
Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021
Stéphanie Haim-Boukobza
,
Bénédicte Roquebert
,
Sabine Trombert-Paolantoni
,
Emmanuel Lecorche
,
Laura Verdurme
et al.
Article dans une revue
hal-03150819v3
|
|
|
Reconstructing contact network structure and cross-immunity patterns from multiple infection histories
Christian Selinger
,
Samuel Alizon
Article dans une revue
hal-03357549v1
|
|
|
Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities
Bastien Reyné
,
Christian Selinger
,
Mircea T Sofonea
,
Stéphanie Miot
,
Amandine Pisoni
et al.
Article dans une revue
hal-03289625v1
|
|
|
Estimating dates of origin and end of COVID-19 epidemics
Thomas Bénéteau
,
Elie ` Baptiste
,
Mircea T Sofonea
,
Samuel Alizon
Article dans une revue
hal-03120811v2
|
|
|
Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021
Samuel Alizon
,
Stéphanie Haim-Boukobza
,
Vincent Foulongne
,
Laura Verdurme
,
Sabine Trombert-Paolantoni
et al.
Article dans une revue
hal-03289622v1
|
|
|
SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France
Benedicte Roquebert
,
Stéphanie Haim-Boukobza
,
Sabine Trombert-Paolantoni
,
Emmanuel Lecorche
,
Laura Verdurme
et al.
Article dans une revue
hal-03366559v1
|
|
|
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
Bénédicte Roquebert
,
Sabine Trombert-Paolantoni
,
Stéphanie Haim-Boukobza
,
Emmanuel Lecorche
,
Laura Verdurme
et al.
Article dans une revue
hal-03289627v1
|
|
|
Early phylodynamics analysis of the COVID-19 epidemic in France
Gonché Danesh
,
Baptiste Elie
,
Yannis Michalakis
,
Mircea T Sofonea
,
Antonin Bal
et al.
Article dans une revue
hal-03001114v2
|
|
|
Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections
Thomas Beneteau
,
Christian Selinger
,
Mircea T Sofonea
,
Samuel Alizon
Article dans une revue
hal-03357550v1
|
|
|
SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs
Samuel Alizon
,
Mircea T Sofonea
Article dans une revue
hal-03289628v1
|
|
|
Superspreading genomes
Samuel Alizon
Article dans une revue
hal-03133445v1
|
|
|
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Gonché Danesh
,
Victor Virlogeux
,
Christophe Ramière
,
Caroline Charre
,
Laurent Cotte
et al.
Article dans une revue
hal-03357552v1
|
|
|
Cytokine response following perturbation of the cervicovaginal milieu during HPV genital infection
Christian Selinger
,
Massilva Rahmoun
,
Carmen Lia Murall
,
Claire Bernat
,
Vanina Boué
et al.
Article dans une revue
hal-03354891v1
|
|
|
10 Questions and 4 experts on Corona
Akiko Iwasaki
,
Gérard Krause
,
Samuel Alizon
,
Rino Rappuoli
Article dans une revue
hal-04053451v1
|
|
|
HPV cervical infections and serological status in vaccinated and unvaccinated women
Carmen Lia Murall
,
Bastien Reyné
,
Christian Selinger
,
Claire Bernat
,
Vanina Boué
et al.
Article dans une revue
hal-03001077v2
|
|
|
Analyses génomiques et phylodynamiques du SARS-Cov-2
Baptiste Elie
,
Samuel Alizon
Article dans une revue
hal-02893568v2
|
|
|
Detecting within-host interactions from genotype combination prevalence data
Samuel Alizon
,
Carmen Lia Murall
,
Emma Saulnier
,
Mircea T Sofonea
Article dans une revue
hal-02387765v1
|
|
|
Epithelial stratification shapes infection dynamics
Carmen Lia Murall
,
Robert Jackson
,
Ingeborg Zehbe
,
Nathalie Boulle
,
Michel Segondy
et al.
Article dans une revue
hal-02069914v1
|
|
|
Modelling the evolution of viral oncogenesis
Carmen Lia Murall
,
Samuel Alizon
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses, 374 (1773), pp.20180302. ⟨10.1098/rstb.2018.0302⟩
Article dans une revue
hal-02124893v1
|
|
|
COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences
Jérôme Bourret
,
Samuel Alizon
,
Ignacio Bravo
Article dans une revue
hal-02957623v1
|
|
|
Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study
Carmen Murall
,
Massilva Rahmoun
,
Christian Selinger
,
Monique Baldellou
,
Claire Bernat
et al.
Article dans une revue
hal-02157154v1
|
|
|
Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence
Samuel Alizon
,
Ignacio G Bravo
,
Paul Farrell
,
Sally Roberts
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1773), pp.20190041. ⟨10.1098/rstb.2019.0041⟩
Article dans une revue
hal-02108649v3
|
|
|
Coevolution of virulence and immunosuppression in multiple infections
Tsukushi Kamiya
,
Nicole Mideo
,
Samuel Alizon
Article dans une revue
hal-01898496v1
|
|
|
Simulating the effect of public health interventions using dated virus sequences and geographical data
Samuel Alizon
Article dans une revue
(compte-rendu de lecture)
hal-01705816v1
|
|
|
Inexpensive Research in the Golden Open-Access Era
Samuel Alizon
Article dans une revue
hal-01788084v1
|
|
|
Can Ebola Virus evolve to be less virulent in humans?
Mircea T Sofonea
,
L. Aldakak
,
Luis F. V. V. Boullosa
,
Samuel Alizon
Article dans une revue
hal-01897077v1
|
|
|
Reconciling Pasteur and Darwin to control infectious diseases
Samuel Alizon
,
Pierre-Olivier Méthot
Article dans une revue
hal-01737461v1
|
|
|
Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study
Emma Saulnier
,
Olivier Gascuel
,
Samuel Alizon
Article dans une revue
hal-01567904v1
|
|
|
Predicting HIV virulence evolution in response to widespread treatment
Samuel Alizon
,
Roger Kouyos
Article dans une revue
hal-01467624v1
|
|
|
Exposing the diversity of multiple infection patterns
Mircea T Sofonea
,
Samuel Alizon
,
Yannis Michalakis
Article dans une revue
hal-01567902v1
|
|
|
Phylodynamique des infections virales
Samuel Alizon
,
Emma Saulnier
Article dans une revue
hal-01638067v1
|
|
|
Modelling the evolution of how vector-borne parasites manipulate the vector's host choice
Samuel Alizon
Article dans une revue
hal-01560018v1
|
|
|
Why Human Papillomavirus Acute Infections Matter
Samuel Alizon
,
Carmen Murall
,
Ignacio G Bravo
Article dans une revue
hal-01638068v1
|
|
|
A Visionary Pioneer of Parasite Ecology and Evolution
Samuel Alizon
Article dans une revue
hal-01567905v1
|
|
|
Within-host stochastic emergence dynamics of immune-escape mutants
Matthew Hartfield
,
Samuel Alizon
Article dans une revue
hal-01567908v1
|
|
|
Adaptive virulence evolution: the good old fitness-based approach
Samuel Alizon
,
Yannis Michalakis
Article dans une revue
hal-01567907v1
|
|
|
From within-host interactions to epidemiological competition: a general model for multiple infections
Mircea T Sofonea
,
Samuel Alizon
,
Yannis Michalakis
Philosophical Transactions of the Royal Society B: Biological Sciences, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩
Article dans une revue
hal-01571806v1
|
|
|
Clinical applications of pathogen phylogenies
Matthew Hartfield
,
Carmen Lia Murall
,
Samuel Alizon
Article dans une revue
hal-01567914v1
|
|
|
What is a pathogen? Toward a process view of host-parasite interactions
Pierre-Olivier Methot
,
Samuel Alizon
Article dans une revue
hal-01567912v1
|
|
|
Parasite evolution in response to sex-based host heterogeneity in resistance and tolerance
Susan V Cousineau
,
Samuel Alizon
Article dans une revue
hal-01567915v1
|
|
|
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective
Christophe Fraser
,
Katrina Lythgoe
,
Gabriel E Leventhal
,
George Shirreff
,
T Deirdre Hollingsworth
et al.
Article dans une revue
hal-01567910v1
|
|
|
Evidence that hepatitis C virus genome partly controls infection outcome
Matthew Hartfield
,
Rowena Bull
,
Peter A White
,
Andrew Lloyd
,
Fabio Luciani
et al.
Article dans une revue
hal-01567913v1
|
|
|
Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics
Samuel Alizon
,
Sébastien Lion
,
Carmen Lia Murall
,
Jessica Lee Abbate
Article dans une revue
hal-01567909v1
|
|
|
Epidemiological feedbacks affect evolutionary emergence of pathogens
Matthew Hartfield
,
Samuel Alizon
Article dans une revue
hal-01567911v1
|
|
|
Co-infection and super-infection models in evolutionary epidemiology
Samuel Alizon
Article dans une revue
hal-01567919v1
|
|
|
Within-host and between-host evolutionary rates across the HIV-1 genome
Samuel Alizon
,
Christophe Fraser
Article dans une revue
hal-01567922v1
|
|
|
How effectively can HIV phylogenies be used to measure heritability?
George Shirreff
,
Samuel Alizon
,
Anne Cori
,
Huldrych F Guenthard
,
Oliver Laeyendecker
et al.
Article dans une revue
hal-01567924v1
|
|
|
On the limits of interpreting some plastic responses through a cooperator/cheater prism. A comment on Harrison
Samuel Alizon
Article dans une revue
hal-01567920v1
|
|
|
Epidemic spread on weighted networks
Christel Kamp
,
Mathieu Moslonka-Lefebvre
,
Samuel Alizon
Article dans une revue
hal-01567923v1
|
|
|
Parasite co-transmission and the evolutionary epidemiology of virulence
Samuel Alizon
Article dans une revue
istex
hal-01567917v1
|
|
|
Multiple infections and the evolution of virulence
Samuel Alizon
,
Jacobus C De Roode
,
Yannis Michalakis
Article dans une revue
hal-01567918v1
|
|
|
Introducing the outbreak threshold in epidemiology
Matthew Hartfield
,
Samuel Alizon
Article dans une revue
hal-01567921v1
|
|
|
Modelling the course of an HIV infection: Insights from ecology and evolution
Samuel Alizon
,
Carsten Magnus
Article dans une revue
hal-01567926v1
|
|
|
Weighting for sex acts to understand the spread of STI on networks
Mathieu Moslonka-Lefebvre
,
Sebastian Bonhoeffer
,
Samuel Alizon
Article dans une revue
hal-01567925v1
|
|
|
Within-host parasite cooperation and the evolution of virulence
Samuel Alizon
,
Sébastien Lion
Article dans une revue
hal-01567928v1
|
|
|
Inclusive fitness theory and eusociality
Patrick Abbot
,
Jun Abe
,
John Alcock
,
Samuel Alizon
,
Joao a C Alpedrinha
et al.
Article dans une revue
hal-01567932v1
|
|
|
Virulence evolution in response to anti-infection resistance: toxic food plants can select for virulent parasites of monarch butterflies
Jacobus C De Roode
,
C Lopez Fernandez De Castillejo
,
T Faits
,
Samuel Alizon
Article dans une revue
hal-01567929v1
|
|
|
Bridging scales in the evolution of infectious disease life histories: theory
Troy Day
,
Samuel Alizon
,
Nicole Mideo
Article dans une revue
hal-01567927v1
|
|
|
Epidemiological and clinical consequences of within-host evolution
Samuel Alizon
,
Fabio Luciani
,
Roland R. Regoes
Article dans une revue
istex
hal-01567931v1
|
|
|
The transmission-virulence trade-off and superinfection: comments to smith
Samuel Alizon
,
Yannis Michalakis
Article dans une revue
hal-01567930v1
|
|
|
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load
Samuel Alizon
,
Viktor Von Wyl
,
Tanja Stadler
,
Roger D. Kouyos
,
Sabine Yerly
et al.
Article dans une revue
hal-01567934v1
|
|
|
Within-host viral evolution in a heterogeneous environment. Insights into the HIV co-receptor switch
Samuel Alizon
,
Barbara Boldin
Article dans une revue
hal-01567935v1
|
|
|
The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies
R Froissart
,
J Doumayrou
,
F Vuillaume
,
Samuel Alizon
,
Y Michalakis
Philosophical Transactions of the Royal Society B: Biological Sciences, 2010, 365 (1548), pp.1907-18. ⟨10.1098/rstb.2010.0068⟩
Article dans une revue
hal-01567933v1
|
|
|
The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus
Fabio Luciani
,
Samuel Alizon
Article dans une revue
hal-01567937v1
|
|
|
Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future
Samuel Alizon
,
Amy Hurford
,
Nicole Mideo
,
Minus van Baalen
Article dans une revue
hal-01567938v1
|
|
|
The Price equation framework to study disease within-host evolution
Samuel Alizon
Article dans une revue
hal-01567936v1
|
|
|
Competition between cryptic species explains variations in rates of lineage evolution
Samuel Alizon
,
Michal Kucera
,
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Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (34), pp.12382-12386. ⟨10.1073/pnas.0805039105⟩
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