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.

   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]

   preprints

• 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]

   thesis

• 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)