PhD in Computational Systems Biology / Bioinformatics (M/F)

This PhD position is part of the MSCA Doctoral Network PANDORA, focusing on pathological mechanisms and drug optimization for Age-Related Macular Degeneration (AMD). The successful candidate will create a predictive multi-scale digital twin of the retina affected by AMD, integrating large-scale molecular interaction maps, boolean models, and agent-based models (ABM). The project aims to simulate cellular communication and tissue homeostasis, predict experimental perturbations, and identify novel therapeutic targets for AMD. Conducted at the Centre de Biologie Intégrative (CBI) in Toulouse, the research will leverage advanced computational frameworks to model up to 1,000 biomolecules and thousands of agents, advancing translational biomedical research.

• Develop large-scale molecular interaction maps for retinal mechanisms linked to AMD and the complement system.
• Convert interaction maps into executable boolean models using the 'map-to-model' framework developed at CNRS/UPS and INRIA.
• Adjust boolean models to specific AMD conditions using omics data generated within the PANDORA consortium.
• Integrate boolean models into multi-scale agent-based models (ABM) to create a predictive digital twin of the AMD-affected retina.
• Simulate experimental perturbations (e.g., environmental stress, extracellular matrix composition, genetic inactivation) in silico and compare predictions with in vitro data from PANDORA partners.
• Use the digital twin to identify and prioritize novel therapeutic targets for AMD, facilitating experimental validation by the consortium.
• Collaborate with interdisciplinary teams to ensure integration of biological, computational, and clinical perspectives.