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Pluripotent stem cells, such as embryonic stem (ES) cells and induced pluripotent stem (iPS) cells, hold great promise as a cell source for regenerative therapies to treat many major diseases characterized by an irreversible loss of functional tissues. However, the future clinical application of pluripotent stem cells faces a number of obstacles regarding the safety, efficiency and long-term benefits. Some of these challenges are being addressed by the chemical biology approach using small molecules. In this paper, we review the recent progress and patents on small molecules which promote pluripotent stem cell maintenance, reprogramming, and direct differentiation with a focus on cardiomyogenesis.