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In diesel engines with EGR and VGT, the gas flow dynamics has significant nonlinear effects. This is shown by analyzing DC-gains in different operating points showing that these gains have large variations. To handle these nonlinear effects, a nonlinear state dependent input transformation is investigated. This input transformation is achieved through inversion of the models for EGR-flow and turbine flow. It is shown that the input transformation handles the nonlinear effects and decreases the variations in DC-gains substantially. The input transformation is combined with a new control structure that has a pumping work minimization feature and consists of PID controllers and min/max-selectors for coordinated control of EGR-fraction and oxygen/fuel ratio. The EGR flow and the exhaust manifold pressure are chosen as feedback variables in this structure. Further, the set-points for EGR-fraction and oxygen/fuel ratio are transformed to set-points for the feedback variables.