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42

Mircea T. SOFONEA - epidemiology & evolution of infectious diseases


postes

2018 — maître de conférences Univ. Montpellier
2017 — 2018 chercheur post-doctorant CNRS
2014 — 2017 doctorant moniteur Univ. Montpellier


formation

2021 DU stratégies anti-infectieuses (infectiologie hospitalière) Fac. Médecine, Univ. Montpellier
2017 doctorat en évolution des systèmes infectieux Univ. Montpellier
2014 diplôme de l'École normale supérieure Paris
2013 diplôme de l'Institut Pasteur Paris
2010 classes préparatoires Lyc. Henri-IV, Paris


concours & qualifications

2018 Qualifications MCU biologie des populations, biologie des organismes & mathématiques appliquées
2014 Agrégation SVSTU (spécialité biologie & physiologie des organismes), CAPES mathématiques
2010 École normale supérieure de la rue d'Ulm
2009 Olympiades Internationales de Biologie
2008 Olympiades de Physique France


Journal articles27 documents

  • Samuel Alizon, Christian Selinger, Mircea T Sofonea, Stéphanie Haim-Boukobza, Jean-Marc Giannoli, et al.. Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020. Eurosurveillance, European Centre for Disease Prevention and Control, 2022, 27 (6), pp.2100406. ⟨10.2807/1560-7917.ES.2022.27.6.2100406⟩. ⟨hal-03175551v3⟩
  • Baptiste Elie, Bénédicte Roquebert, Mircea T Sofonea, Sabine Trombert-Paolantoni, Vincent Foulongne, et al.. Variant‐specific SARS‐CoV‐2 within‐host kinetics. Journal of Medical Virology, Wiley-Blackwell, In press, ⟨10.1002/jmv.27757⟩. ⟨hal-03651890⟩
  • Bastien Reyné, Quentin Richard, Christian Selinger, Mircea T Sofonea, Ramsès Djidjou-Demasse, et al.. Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Mathematical Modelling of Natural Phenomena, EDP Sciences, 2022, 17, pp.7. ⟨10.1051/mmnp/2022008⟩. ⟨hal-03629334⟩
  • Mircea T Sofonea, Simon Cauchemez, Pierre-yves Boëlle. Epidemic models: why and how to use them. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2022, 41 (2), pp.101048. ⟨10.1016/j.accpm.2022.101048⟩. ⟨hal-03638186⟩
  • Samuel Alizon, Mircea T Sofonea. SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs. Journal of Evolutionary Biology, Wiley, 2021, 34 (12), pp.1867 - 1877. ⟨10.1111/jeb.13896⟩. ⟨hal-03289628⟩
  • Thomas Beneteau, Christian Selinger, Mircea T Sofonea, Samuel Alizon. Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), pp.e1009352. ⟨10.1371/journal.pcbi.1009352⟩. ⟨hal-03357550⟩
  • Mircea T Sofonea, Corentin Boennec, yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, 40 (3), pp.100881. ⟨10.1016/j.accpm.2021.100881⟩. ⟨hal-03289626⟩
  • Ramsès Djidjou-Demasse, Samuel Alizon, Mircea T Sofonea. Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. Journal of Mathematical Biology, Springer Verlag (Germany), 2021, ⟨10.1007/s00285-021-01571-9⟩. ⟨hal-02500420⟩
  • Benedicte Roquebert, Stéphanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. International Journal of Infectious Diseases, Elsevier, 2021, ⟨10.1016/j.ijid.2021.09.076⟩. ⟨hal-03366559⟩
  • Bastien Reyné, Christian Selinger, Mircea T Sofonea, Stéphanie Miot, Amandine Pisoni, et al.. Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities. International Journal of Epidemiology, Oxford University Press (OUP), 2021, 50 (6), pp.1788-1794. ⟨10.1093/ije/dyab121⟩. ⟨hal-03289625⟩
  • Bénédicte Roquebert, Sabine Trombert-Paolantoni, Stéphanie Haim-Boukobza, Emmanuel Lecorche, Laura Verdurme, et al.. 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, European Centre for Disease Prevention and Control, 2021, 26 (23), ⟨10.2807/1560-7917.es.2021.26.23.2100447⟩. ⟨hal-03289627⟩
  • Samuel Alizon, Stéphanie Haim-Boukobza, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, et al.. Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021. Eurosurveillance, European Centre for Disease Prevention and Control, 2021, 26 (28), ⟨10.2807/1560-⟩. ⟨hal-03289622⟩
  • Thomas Bénéteau, Elie ` Baptiste, Mircea T Sofonea, Samuel Alizon. Estimating dates of origin and end of COVID-19 epidemics. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e70. ⟨10.1101/2021.01.19.21250080⟩. ⟨hal-03120811v2⟩
  • Gonché Danesh, Baptiste Elie, yannis Michalakis, Mircea T Sofonea, Antonin Bal, et al.. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩. ⟨hal-03001114v2⟩
  • Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T Sofonea, Ramsès Djidjou-Demasse. Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLoS Computational Biology, Public Library of Science, 2021, ⟨10.1371/journal.pcbi.1008776⟩. ⟨hal-02879512v3⟩
  • Olivier Thomine, Samuel Alizon, Corentin Boennec, Marc Barthelemy, Mircea T Sofonea. Emerging dynamics from high-resolution spatial numerical epidemics. eLife, eLife Sciences Publication, 2021, 10, ⟨10.7554/elife.71417⟩. ⟨hal-03415297⟩
  • Mark P Zwart, Stéphane Blanc, Marcelle Johnson, Susanna Manrubia, yannis Michalakis, et al.. Unresolved advantages of multipartitism in spatially structured environments. Virus Evolution, Oxford University Press, 2021, 7 (1), ⟨10.1093/ve/veab004⟩. ⟨hal-03219672⟩
  • Mircea T Sofonea, Samuel Alizon. Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, ⟨10.1016/j.accpm.2021.100943⟩. ⟨hal-03366541⟩
  • Mircea T Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics, Elsevier, 2021, 35, pp.100459. ⟨10.1016/j.epidem.2021.100459⟩. ⟨hal-03289624⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon, Ignacio G. Bravo. SARS-CoV-2 viral RNA levels are not 'viral load'. Trends in Microbiology, Elsevier, 2021, 29 (11), pp.970-972. ⟨10.1016/j.tim.2021.08.008⟩. ⟨hal-03419147⟩
  • Stéphanie Haim-Boukobza, Bénédicte Roquebert, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021. Emerging Infectious Diseases, Centers for Disease Control and Prevention, 2021, 27 (5), pp.1496-1499. ⟨10.3201/eid2705.210397⟩. ⟨hal-03150819v3⟩
  • Mircea T Sofonea. A global asymptotic stability condition for a dimorphic Lotka-Volterra model with explicit indirect interactions. Applicable Analysis, Taylor & Francis, 2019, ⟨10.1080/00036811.2018.1437417⟩. ⟨hal-03366505⟩
  • Samuel Alizon, Carmen Lia Murall, Emma Saulnier, Mircea T Sofonea. Detecting within-host interactions from genotype combination prevalence data. Epidemics, Elsevier, 2019, 29, pp.100349. ⟨10.1016/j.epidem.2019.100349⟩. ⟨hal-02387765⟩
  • Romain Gallet, Frédéric Fabre, Gael Thébaud, Mircea T Sofonea, Anne Sicard, et al.. Small bottleneck size in a highly multipartite virus during a complete infection cycle. Journal of Virology, American Society for Microbiology, 2018, 92 (14), pp.e00139-18. ⟨10.1128/JVI.00139-18⟩. ⟨hal-01847886⟩
  • Mircea T Sofonea, L. Aldakak, Luis F. V. V. Boullosa, Samuel Alizon. Can Ebola Virus evolve to be less virulent in humans?. Journal of Evolutionary Biology, Wiley, 2018, 31 (3), pp.382 - 392. ⟨10.1111/jeb.13229⟩. ⟨hal-01897077⟩
  • Mircea T Sofonea, Samuel Alizon, yannis Michalakis. Exposing the diversity of multiple infection patterns. Journal of Theoretical Biology, Elsevier, 2017, 419, pp.278 - 289. ⟨10.1016/j.jtbi.2017.02.011⟩. ⟨hal-01567902⟩
  • Mircea T Sofonea, Samuel Alizon, yannis Michalakis. From within-host interactions to epidemiological competition: a general model for multiple infections. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩. ⟨hal-01571806⟩

Preprints, Working Papers, ...5 documents

  • Ramsès Djidjou-Demasse, Mircea T Sofonea, Marc Choisy, Samuel Alizon. Within-host evolutionary dynamics of antimicrobial quantitative resistance. 2021. ⟨hal-03194023v4⟩
  • Mircea T Sofonea, Corentin Boennec, yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. 2021. ⟨hal-03322646⟩
  • Ramsès Djidjou-Demasse, Christian Selinger, Mircea T Sofonea. Épidémiologie mathématique & modélisation de la pandémie de COVID-19 : enjeux et diversité. 2020. ⟨hal-02924338⟩
  • Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea T Sofonea. Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. 2020. ⟨hal-03045490⟩
  • Mircea T Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France. 2020. ⟨hal-02619546⟩

Reports9 documents

  • Samuel Alizon, Mircea T Sofonea. De Delta à Omicron, scénarios de tendances hospitalières pour l'hiver 2021-2022. [Rapport de recherche] 16, CNRS - Centre National de la Recherche Scientifique; IRD - Institut de recherche pour le developpement; Université de Montpellier. 2021. ⟨hal-03502127⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France et l’implication potentielle des déficits en G6PD. [Rapport de recherche] 11, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950702⟩
  • Samuel Alizon, Mircea T Sofonea. Analyse de l’épidémie de COVID-19 en France et scénarios de contrôle. [Rapport de recherche] 9, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950665⟩
  • Samuel Alizon, Mircea T Sofonea, yannis Michalakis. Modéliser l'épidémie de COVID-19 (résumé). [Rapport de recherche] 7, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950651⟩
  • Samuel Alizon, Bastien Reyné, Mircea T Sofonea. Limites et délais dans l’estimation du nombre de reproduction. [Rapport de recherche] 5, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882697⟩
  • Mircea T Sofonea, Samuel Alizon. Immunité de groupe et contrôle de l’épidémie de COVID-19. [Rapport Technique] 2, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882682⟩
  • Thomas Bénéteau, Baptiste Elie, Samuel Alizon, Mircea T Sofonea. Stochasticité et épidémie de COVID-19. [Rapport de recherche] 8, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950660⟩
  • yannis Michalakis, Mircea T Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France pourraient-ils être expliqués par des comorbidités ?. [Rapport de recherche] 10, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950676⟩
  • Samuel Alizon, yannis Michalakis, Mircea T Sofonea. Évolution de la virulence et COVID-19. [Rapport de recherche] 12, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950712⟩

Theses1 document