We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the method by first developing a comprehensively cu rated kinetic model of sphingolipid biosynthesis in the yeast Saccharomyces cerevisiae. Next we apply IMCA using the model and integrating lipidomics data. The combinatorial complexity of the synthesis of sphingolipid molecules, along with the operational complexity of the participating enzymes of the pathway, presents an excellent case study for testing the capabilities of the IMCA. The exceptional agreement of the predictions of the method with genome-wide data highlights the importance and value of a comprehensive and consistent engineering approach for the development of such methods and models. Based on the analysis, we identified the class of enzymes regulating the distribution of sphin-golipids among species and hydroxylation states, with the D-phospholipase SP014 being one of the most prominent. The method and the applications presented here can be used for a broader, model-based inverse metabolic engineering approach. (C) 2016 The Authors. Published by Elsevier Inc. On behalf of International Metabolic Engineering Society. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nci/4.0/).