The attached disclosure provides a systems approach based on mathematical modelling of the kinetics of essential biochemical pathways involved in organ homeostasis. When this in silico model is coupled with in-vitro and/or in-vivo measurements to quantify drug-induced perturbations, a powerful platform that allows accurate and mechanistic-level prediction of drug-induced organ injury can be generated. The method described in this disclosure demonstrates that several physiological situations can also be accurately modelled in addition to the effect of perturbations induced by drugs. It can also be used along with high-throughput “omics” data to generate testable hypotheses leading to informed decision-making in drug development.