Multicellular systems rely on the coordinated activity of individual cells, each integrating intrinsic molecular processes and external signals to maintain survival, adapt to its environment, and contribute to collective functions. This coordination emerges from the tight interdependence of cellular metabolism, cell-cell communication, and intracellular signaling, whose perturbation can disrupt tissue organization and function.

This talk will explore how systems biology and single-cell and spatial transcriptomics can be used to investigate different aspects of multicellular systems, from cellular functions and intercellular interactions to tissue organization. In particular, I will present scCellFie, a computational framework for inferring metabolic activities, and Tensor-cell2cell, which characterizes context-dependent patterns of cell-cell communication. Finally, the generation and analysis of a spatial transcriptomic atlas of ectopic pregnancy will illustrate how spatial information can be leveraged to characterize cellular organization, spatial relationships, and tissue architecture.