I am an Assistant Professor of Bioinformatics at Aix-Marseille University (AMU), within the IBDM (Institut de Biologie du Développement de Marseille). I received my PhD in Computer Science, with a focus on bioinformatics, and I develop computational methods and tools to extract biological insight from complex data, using tools from network sciences and machine learning.

My research revolves around three main themes:

• multi-omics data integration,
• analysis of biological networks and knowledge graphs,
• integration of experimental omics data with prior knowledge.

Research

My current research direction is to develop knowledge-guided AI models for multi-omics data analysis and integration, combining experimental measurements with structured biological knowledge (networks, knowledge graphs, ontologies). Rather than relying on purely black-box predictions, I aim to build models guided by prior knowledge, providing explanations in terms of causal pathways and regulatory mechanisms. At IBDM, I am working on developing such approaches to uncover regulatory drivers of cell fate decisions from multi-omics profiles in developing tissues.

Previously, during my Ph.D. at LaBRI (University of Bordeaux), I developed network-based multi-omics integration methods for disease subtyping and biomarker identification. During my postdoctoral research at Marseille Medical Genetics (MMG), I applied Random Walk with Restart approaches on biomedical multilayer networks for phenotype prioritization in rare diseases. I also worked with biomedical knowledge graphs, evaluating knowledge graph embedding models for drug repurposing in rare diseases with a particular focus on data leakage and reliable model assessment.

Teaching

I teach computer science and bioinformatics at Aix-Marseille University (AMU).

Together with Benjamin Loire, I developed a serious game for kids and adults on molecular networks: https://gitlab.com/Rumengol/network_game