Hallou Group | Cell and Tissue Dynamics

Our work investigates how mechanical and biological signals, particularly those associated with the extracellular matrix and with epithelial, stromal, and immune cells, combine to regulate cell fate decisions and tissue dynamics during development, homeostasis, regeneration, and disease. To this end, we develop innovative experimental and computational approaches integrating mechanobiology, spatial genomics, advanced microscopy, machine learning/artificial intelligence, and mathematical modelling to study the mechanical and biochemical environments of in vivo tissues and organoid cultures at the level of individual cells. Our work is highly interdisciplinary, and we actively collaborate with clinicians, as well as mathematical biologists, biostatisticians, and computer scientists.

Aim

Develop new computational and experimental tools to understand and to study the role of mechanical and biological signals in cell fate decisions and tissue dynamics in development, homeostasis, regeneration and disease.

Objectives

1. To develop, building on our pioneer work on spatial mechano-transcriptomics (A. Hallou et al. Nature Methods 22, 737–750, 2025), an integrated spatial mechanomics platform to measure the molecular and mechanical state of cells in tissues at single resolution using spatial multi-omics (transcriptomics, proteomics, metabolomics, etc.), advanced microscopy, image-based force inference, atomic force microscopy (AFM), mathematical modelling, bioinformatics and ML/AI.

2. To map the mechanome of human and mouse tissues in development, homeostasis and disease, with a particular focus on inflammatory diseases (psoriasis, uveitis, IBD), fibrosis (IPF, systemic sclerosis, gut fibrosis) and cancer. 

3. To functionally characterise the biological and mechanical determinants of cell fate decisions and tissue dynamics in health and disease using lineage tracing, intravital imaging and human organoid co-cultures with immune and stromal cells, combined with genome editing and mechano-chemical perturbation experiments.