The art of modeling gene regulatory circuits.

The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame and develop our understanding of their properties. Here, we present some fundamental considerations to develop and analyze a model of a gene regulatory circuit of interest, either representing a natural, synthetic, or theoretical system. A mathematical model allows us to effectively evaluate the logical implications of our hypotheses.

Integrating Genome-Scale Metabolic Models with Patient Plasma Metabolome to Study Endothelial Metabolism In Situ.

Patient blood samples are invaluable in clinical omics databases, yet current methodologies often fail to fully uncover the molecular mechanisms driving patient pathology. While genome-scale metabolic models (GEMs) show promise in systems medicine by integrating various omics data, having only exometabolomic data remains a limiting factor. To address this gap, we introduce a comprehensive pipeline integrating GEMs with patient plasma metabolome.