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We present a facile electrochemical method for synthesizing uniform sized graphene quantum dots (GQDs) with a strong yellow emission at 14% quantum yield. This approach has enabled a large-scale production of aqueous GQD solution without the need for polymeric or surfactant stabilizers. The structure and emission mechanism of the GQDs have been studied by combining extensive characterization techniques, rigorous control experiments and theoretical calculations. We further demonstrate the distinctive advantages of such GQDs for direct and efficient stem cell labeling, opening up great opportunities for their bio-medical applications.