infectious diseases modelling





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My research focuses on epidemiological and evolutionary implications of pathogens as well as on integrating the multiplicity of spatio-temporal scales in the fundamental study of infectious diseases. My work rely on various modelling approaches aligned along three axes: within-host microbial ecology, epidemiological dynamics and virulence evolution. In particular, I worked on Ebolavirus (EBOV), human papillomavirus (HPV), multipartite viruses, antibiotic resistance and SARS-CoV-2.

► Research work

   peer-reviewed international publications

• Danesh G., Elie B., Michalakis Y., Sofonea M. T., 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. (2020) Early phylodynamics analysis of the COVID-19 epidemics in France. PCI Evol. Biol. [pdf]

Alizon S., Murall C.-L., Saulnier E., Sofonea M. T. (2019) Detecting within-host interactions from genotype combination prevalence data. Epidemics. [pdf]

• Gallet R., Fabre F., Thébaud G., Sofonea M. T., Sicard A., Blanc S., Michalakis Y. (2018) Small bottleneck size  in a highly multipartite virus during a complete infectious cycle. J. Virol.

Sofonea M. T. (2018) A global asymptotic stability condition for a Lotka-Volterra model with indirect interactions. Applicable Analysis.

Sofonea M. T., Aldakak L., Boullosa L. F. V. V., Alizon S. (2018) Can Ebola Virus evolve to be less virulent in humans? J. Evol. Biol. [pdf] [sm]

Sofonea M. T., Alizon S., Michalakis Y. (2017) Exposing the diversity of multiple infection patterns. J. Theor. Biol. 419: 278--289. [pdf] [sm]

Sofonea M. T., Alizon S., Michalakis Y. (2015) From within-host interactions to epidemiological competition: a general model for multiple infections. Phil. Trans. R. Soc. B. 370(1675): 20140303. [pdf] [sm]


• Reyné B., Danesh G., Alizon S., Sofonea M. T. (2020) Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. medRxiv [pdf]

• Richard Q., Alizon S., Choisy M., Sofonea M. T., Djidjou-Demasse R. (2020) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. medRxiv [pdf]

Sofonea M. T., 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 [pdf]

• Djidjou-Demasse R., Michalakis Y., Choisy M., Sofonea M. T., Alizon S. (2020) Optimal COVID-19 epidemic control until vaccine deployment. medRxiv [pdf]

• Djidjou-Demasse R., Alizon S., Sofonea M. T. (2020) Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. arXiv [pdf]

Sofonea M. T., Alizon S, Michalakis Y. (2018) Why multiple infections favour virulent parasites. bioRxiv. [pdf][som]


Sofonea M. T. (2017) Virulence evolution and multiple infections. PhD thesis, University of Montpellier. [pdf]

► International communications

3 invitations, 9 selected talks

► Co-supervision of Phd theses

• Thomas Beneteau (French Fundation for Medical Research grant, 2019 - )

• Bastien Reyné (French Doctoral School grant, 2020 - )

► Co-supervision of Master internships

• Thomas Beneteau (M2 AgroParisTech, 2019)
• Julien Lombard (M1 Rennes, 2019)
• Luis F.V.V. Boullosa (M1 international MEME 2016)
• Lafi Aldakak (M1 international MEME, 2015)

► Responsabilities

• Head of the Theoretical & Experimental Evolution research group (MIVEGEC - Univ. Montpellier, CNRS, IRD - since 2021)
• PhD grant reviewer (ENS, Paris, since 2019)
• member of the organizing committee of the Evolution 2018 congress (Montpellier, 2016 - 2018)
• organizer of the weekly MIVEGEC lab seminar (Montpellier, 2015)