Xavier BAILLY

OrcId 0000-0001-6959-7974 
IdHal xavier-bailly 
ResearcherID C-6254-2011
E-mail xavier.bailly [at] inrae.fr

Profile

Xavier Bailly is an INRAE Research Engineer, accredited to supervise research (HDR), and has directed EPIA since 2018. EPIA is a joint INRAE–VetAgro Sup research unit dedicated to the epidemiology of animal and zoonotic diseases. His research aims to understand and anticipate how pathogens spread, diversify and evolve across host populations, ecological communities and structured territories.

He combines pathogen genomics, phylodynamics, spatial epidemiology, surveillance data and quantitative models. His current work notably integrates mechanistic models with artificial-intelligence approaches to improve inference, early detection of emerging threats and support for animal-health decision-making.

Research areas

• Genomic epidemiology and phylodynamics of animal and zoonotic pathogens.
• Multi-host transmission dynamics across territories and livestock networks.
• Integration of genomic, epidemiological, spatial, environmental and surveillance data.
• Simulation-based inference and hybrid AI–epidemiology approaches.
• Applications to animal and zoonotic diseases, including BVD, BTV, EHDV, Q Fever, Lyme borreliosis.

Genomic Epidemiology · Animal and zoonotic diseases · Phylodynamics · Spatial epidemiology · Surveillance · Inference and AI

Contributions to major collaborative projects and initiatives

• GeoAI4EI – GeoAI Toolbox for Epidemic Intelligence: contributing to the development of geospatial artificial-intelligence and inference approaches integrating epidemiological, environmental and surveillance data to strengthen emerging-threat anticipation and epidemic preparedness. GeoAI4EI builds on the European MOOD project.
• AVEEC – Pathogen adaptation to global changes: contributing to research on how climatic, environmental and agroecological changes affect the evolution and transmission of livestock pathogens, notably bluetongue and epizootic haemorrhagic disease viruses.
• PREZODE – Preventing Zoonotic Disease Emergence: contributing to this international initiative promoting One Health approaches that connect research, surveillance, field stakeholders and public policy to prevent zoonotic emergence, notably through the HODAS project.
• Q-Net-Assess: contributing to the characterisation of Coxiella burnetii genomic diversity and to the assessment of relationships between pathogen genotypes, host species, territories and zoonotic risk.
• CiTIQUE: contributing to the use of citizen-science data to investigate tick bites, tick-borne pathogens and territorial determinants of risk, notably across Borrelia genospecies.

Research, surveillance and decision support

As Director of EPIA, he helps structure a collective capacity connecting field observation, surveillance, genomics, ecology, modelling and artificial intelligence. EPIA works closely with the French National Animal Health Surveillance Platform (ESA Platform), part of whose coordination and engineering team is hosted within the unit. These collaborations support the development of methods, tools and results addressing the practical needs of animal-health stakeholders and decision-makers.

Teaching and supervision

He teaches genomic epidemiology and phylodynamics in university programmes, and supervises research at the interface of pathogen evolution, transmission, spatial analysis, and modelling.

Featured publications

• Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France - Veterinary Research, 2024. DOI: 10.1186/s13567-024-01377-9
• Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France - Microbial Genomics, 2023. DOI: 10.1099/mgen.0.001067
• Spatial modeling of Borrelia genospecies in human-biting ticks from the French citizen science programme CiTIQUE - Scientific Reports, 2026. DOI: 10.1038/s41598-026-42619-4
• Simulation-based inference of epidemiological and phylodynamic models via Neural Posterior Estimation - Proc. R. Soc. B, 2026. DOI: 10.1098/rspb.2026.1059
• PREZODE: a global co-designed collaboration for preventing zoonotic emergence - Nature Health, 2026. DOI: 10.1038/s44360-026-00103-3

Productions