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Metabolic Syndrome (MetSyn) is a cluster of metabolic abnormalities: hypertension, obesity, insulin resistance, and dyslipidemia (increased plasma triglyceride and (V)LDL-cholesterol levels, and decreased HDL cholesterol). Common comorbidities include cardiovascular diseases, liver steatosis and type 2 diabetes. The current pharmacological strategies are inadequate to deal with the growing rate of metabolic disorders, and lifestyle modulation including diet adjustment remains the fundamental approach to combat MetSyn. In several projects systems medicine approaches are used to make diagnosis more precise and contribute to the development of novel and personalized treatments. Underlying disease mechanisms are complex and partly unknown. This impacts the development of predictive computational models. Approaches to quantify variability and uncertainty in multi-level systems medicine models will be addressed. Recent findings will be discussed, focusing on the contribution of computational modelling in understanding the metabolic effects of bariatric surgery and pharmacological activation of the Liver X Receptor (LXR).