Stem cells are central to emerging concepts in health, medicine and therapy. The realization that specific cell reservoirs retain multipotency for tissue establishment and replenishment has implications for both the emerging field of regenerative therapy and the long standing problems of cancer, ageing and degenerative diseases. Recently the prospects for regenerative therapy have been boosted by the breakthrough finding that somatic cells can be reprogrammed into pluripotent embryonic stem (ES) cells upon expression of ES cell transcription factors. This astonishing finding further emphasizes the need to understand stem cell biology. Most of the information acquired on stem cells so far is empirical. Recent progress in systematic and computational methodologies, including seminal contributions by the applicants, permits a new approach to stem cell biology. We can now describe the systems biology of stem cells. This proposal is based on the importance of stem cells in future medicine and the need to understand the fundamental mechanisms that regulate their potential to differentiate towards specific lineages. We aim to gather the information required to understand the regulomes of key stem cells, particularly the transition between embryonic (ES) and neural (NS) cells. NS cells can be readily reprogrammed back to ES cells. We will systematically gather proteomic, transcriptomic, regulomic, live cell and cell cycle data to understand the ES – NS axis comprehensively (in both directions). We will validate the regulatory data by functional interrogation using RNAi screens and tests, complemented by quantitative fluorescent read-outs. To broaden the fundamental and medical relevance of the insights, we will pursue selected studies on other stem cells (e.g. HSCs), and their differentiated products. Thereby we will acquire a broader grasp on stem cell issues and also significantly advance mammalian systems biology.