The paper presents a multi-objective mixed integer linear programming model for portfolio selection of research and development (R&D) projects with synergies. Partial assignment of funds is allowed to different tasks of the project, while synergies are considered at the task and the project level. A synergy is active if a number of its elements sufficiently supported is within certain bounds. The risk associated with insufficient support is introduced. Numerical results are presented to demonstrate the efficiency of the proposed approach for large scale instances.