Transition to turbulence in two-dimensional laminar separation bubbles on a flat plate is investigated by Direct Numerical Simulations (DNS). In laminar separation bubbles transition and separation are present simultaneously and interact in a physically complex manner. A set of numerical simulations has been carried out to investigate the transition process, and in particular to shed light on the development of large coherent structures, which arise during the transition. For the separation bubbles investigated, transition to turbulence appeared to be self-sustained, i.e., in contrast to zero pressure gradient boundary layers, no external forcing was required to initiate or sustain the transition process. The DNS results reveal that the streamwise vortices ('braids'), which evolve between two neighboring spanwise coherent vortical structures, may be with a consequence of a similar instability mechanisms as observed in bluff-body wakes (mode B instability). The simulation results also suggest that the development of three-dimensional disturbances is due to an absolute secondary instability. High-amplitude 2D waves were introduced through a spanwise slot to control the separation. It was shown that strong 2D forcing significantly alters the flow filed. With large amplitude two-dimensional forcing the temporal growth of 3D disturbances inside the separated flow region can be suppressed and as a consequence, the secondary absolute instability can be prevented. Consequently, the flow remains laminar in almost the entire computational domain.