The explosion of interest in stem cells, over the past decade or so, in both basic and translational research has encouraged three of BioMed Central's flagship journals, BMC Biology, BMC Medicine and Genome Medicine, to come together to present a series of specially commissioned comment and review articles on stem cell biology and medicine. In this thematic series we aim to highlight some of the most important and topical issues - including recent advances, controversies and challenges in stem cell research, and of course their clinical implications. To supplement the comment and review, relevant original research articles will be added to the series as they are published. Stem cell genomics: new thematic series. Genome Medicine 2011, 3:34. An editorial by Guest Editor Stuart Orkin introduces this new series of articles, highlighting progress in genomic-scale studies of stem cells and cellular reprogramming that could impact medicine. Stem cell therapy clinical trials. BMC Medicine 2011, 9:52. Trounson and colleagues review recent developments and future prospects of clinical trials for stem cell therapies, highlighting usage of mesenchymal and neural stem cells, and reporting on the start of trials involving lines derived from pluripotent cells. Focus on stem cell individuality. BMC Biology 2011, 9:40. Arthur Lander reflects on how current assumptions that stem cells divide asymmetrically and are programmed to produce the right differentiated cell types at the right times may fail to acknowledge a fundamental contribution of stem cell individuality.