Emerg Infect Dis.
• Elie B, Lecorche E, Sofonea MT, Trombert-Paolantoni S, Foulongne V, Guedj J, Haim-Boukobza S, Roquebert B, Alizon S. (2021) Inferring SARS-CoV-2 variant within-host kinetics. J Med Virol.
• Sofonea MT, Cauchemez S, Boëlle PY. (2022) Epidemic models: why and how to use them. Anaesth Crit Care Pain Med.
• Reyné B, Richard Q, Noûs C, Selinger C=, Sofonea MT=, Djidjou-Demasse R=, Alizon S=. (2022) Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Math Model Nat Phenom.
• Alizon S, Selinger C=, Sofonea MT=, Haim-Boukobza S, Giannoli JM, Ninove L, Pillet S, Vincent T, de Rougemont A, Tumiotto C, Sollis M, Stephan R, Bressolette-Bodin C, Salmona M, L'Honneur AS, Behillil S, Lefeuvre C, Dina J, Hantz S, Hartard C, Veyer D, Delagreverie HM, Fourati S, Visseaux B, Henquell C, Lina B, Foulongne V, Burrel S. (2022) Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values. Eurosurveillance.
• Reyné B, Saby N, Sofonea MT. (2022) Principles of mathematical epidemiology and compartmental modelling application to COVID-19. Anaesth Crit Care Pain Med.
• Bénéteau T, Elie B, Sofonea MT, Alizon S. (2021) Estimating dates of origin and end of COVID-19 epidemics. Peer Community Journal.
• Djidjou-Demasse R=, Sofonea MT=, Choisy M, Alizon S. (2021) Within-host evolutionary dynamics of antimicrobial quantitative resistance. PCI Math Comp Biol.
• Danesh G, Elie B, Michalakis Y, Sofonea MT, Bal A, Behillil S, Destras G, Boutolleau D, Burrel S, Marcelin A-G, Plantier J-C, Thibault V, Simon-Loriere E, van der Werf S, Lina B, Josset L, Enouf V, Alizon S. (2021) Early phylodynamics analysis of the COVID-19 epidemics in France. Peer Community Journal.
• Kuschmierz P and 60 others. (2021) European first-year university students accept evolution but lack substantial knowledge about it: a standardized European cross-country assessment. Evo Edu Outreach.
• Thomine O, Alizon S, Barthelemy M, Boennec C, Sofonea MT. (2021) Emerging dynamics from high-resolution spatial numerical epidemics. eLife.
• Roquebert B, Haim-Boukobza S, Trombert-Paolantoni S, Lecorche E, Verdurme L, Foulongne V, Burrel S, Alizon S=, Sofonea MT=. (2021) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. Int J Infect Dis.
• Michalakis Y, Sofonea MT, Alizon S, Bravo IG. (2021) SARS-CoV-2 viral RNA levels are not “viral load”. Trends Microbiol.
• Sofonea MT & Alizon S (2021) Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesth Crit Care Pain Med.
• Alizon S, Haim-Boukobza S, Foulongne V, Verdurme L, Trombert-Paolantoni S, Lecorche E, Roquebert B, Sofonea MT. (2021) Rapid spread of the SARS-CoV-2 delta variant in French regions in June 2021. Eurosurveillance.
• Bénéteau T, Selinger C=, Sofonea MT=, Alizon S=. (2021) Episome partitioning and symmetric cell divisions: quantifying the role of random events in the persistence of HPV infections. PLOS Comput Biol.
• Alizon S & Sofonea MT. (2021) SARS-CoV-2 virulence evolution: avirulence theory, immunity, and trade-offs. J Evol Biol.
• Reyné B, Selinger C, Sofonea MT, Miot S, Pisoni A, Tuaillon E, Bousquet J, Blain H, Alizon S. (2021) Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary attack risk in aged care facilities. Int J Epidemiol.
• Roquebert B, Trombert-Paolantoni S, Haim-Boukobza S, Lecorche E, Verdurme L, Foulongne V, Sofonea MT=, Alizon S=. (2021)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. Eurosurveillance.
• Sofonea MT, Boennec C, Michalakis Y, Alizon S. (2021) Two waves and a high tide: the COVID-19 epidemic in France. Anaesth Crit Care Pain Med.
• Sofonea MT, Reyné B, Elie B, Djidjou-Demasse R, Selinger C, Michalakis Y, Alizon S. (2021) Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics.
• Haim-Boukobza S, Roquebert B, Trombert-Paolantoni S, Lecorche E, Verdurme L, Foulongne V, Selinger C, Michalakis Y, Sofonea MT=, Alizon S=. (2021) Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021. Emerg Infect Dis.
• Richard Q, Alizon S, Choisy M, Sofonea MT, Djidjou-Demasse R. (2021) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLOS Comput Biol.
• Djidjou-Demasse R, Alizon S, Sofonea MT. (2021) Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. J Math Biol.
• Zwart MP, Blanc S, Johnson M, Manrubia S, Michalakis Y, Sofonea MT. (2021) Unresolved advantages of multipartitism in spatially structured environments. Virus Evol.
• Alizon S, Murall C-L, Saulnier E, Sofonea MT. (2019) Detecting within-host interactions from genotype combination prevalence data. Epidemics.
• Sofonea MT. (2019) A global asymptotic
stability condition for a Lotka-Volterra model with indirect
interactions. Applicable Analysis.
• Gallet R, Fabre F, Thébaud G, Sofonea MT,
Sicard A, Blanc S, Michalakis Y. (2018) Small bottleneck
size in a highly multipartite virus during a complete
infectious cycle. J Virol.
• Sofonea MT, Aldakak L, Boullosa LF VV, Alizon S. (2018) Can Ebola Virus evolve to be less virulent in
humans? J Evol Biol.
• Sofonea MT, Alizon S, Michalakis Y.
(2017) Exposing the diversity of multiple infection patterns. J
Theor Biol.
• Sofonea MT, Alizon S, Michalakis Y.
(2015) From within-host interactions to epidemiological competition: a general model for multiple infections. Phil Trans R Soc B.
preprints
• Reyné B, Sofonea MT, Alizon S. (2022) Modelling long-term COVID-19 hospital admission dynamics using immune protection waning data. medRxiv.
• Kamiya T, Alvarez-Iglesias A, Ferguson J, Sofonea MT, Fitz-Simon N. (2022) Estimating time-dependent infectious contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland. medRxiv.
• Fitz-Simon N, Ferguson J, Alvarez-Iglesias A, Sofonea MT, Kamiya T. (2022) Understanding the role of mask-wearing during COVID-19 on the island of Ireland. medRxiv.
• Verdume L, Danesh G, Trombert S, Sofonea MT, Noel V, Foulongne V, Montès B, Tuaillon E, Haim-Boukobza S, Roquebert B, Alizon S. (2021) Spread of SARS-CoV-2 Delta variant infections bearing the S:E484Q and S:T95I mutations in July and August 2021 in France. medRxiv.
• Boennec C, Alizon S, Sofonea MT. Anticipating the hospital burden of future COVID-19 epidemic waves. medRxiv..
• Sofonea MT, Boennec C, Fontalirant A, Regnat M, Lefrant JY, Alizon S, Fischer MO. (2021) Quantifying the real-life impacts of vaccination on critical COVID-19. OSF.
• Reyné B, Danesh G, Alizon S, Sofonea MT. (2020) Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. medRxiv.
• Sofonea MT, Reyné B, Elie B, Djidjou-Demasse R, Selinger C, Michalakis Y, Alizon S. (2020) Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France. medRxiv.
• Djidjou-Demasse R, Michalakis Y, Choisy M, Sofonea MT, Alizon S. (2020) Optimal COVID-19 epidemic control until vaccine deployment. medRxiv.
• Sofonea MT, Alizon S, Michalakis Y. (2018)
Why multiple infections favour virulent parasites. bioRxiv.
French publications
• Djidjou-Demasse R, Selinger C, Sofonea MT. (2020) Épidémiologie mathématique et modélisation de la pandémie de Covid-19 : enjeux et diversité. Revue Francophone des Laboratoires.
expert report
• Anses. (2021) Note d'appui scientifique et technique relative à la viabilité dans l'air et la dose infectante du virus SARS-CoV-2. (saisine 2021-SA-0018). Maisons-Alfort : Anses.
books
• Collective work (edited by Boudeau D, Caudron N, Delorme L, Fabre P, Godard F, Rilhac M, Sicard M, Sofonea MT). (2021) Du labo à la classe : l’évolution en action.