The induced pluripotent stem cells (iPSCs), generated from transcription factor-induced reprogramming, hold the great promise as the next generation materials for regenerative medicine. Intensive follow-up studies have accumulated a large amount of high-throughput data in transcription, proteomics, methylation, and other levels, which makes the computational studies feasible. Here we briefly review the recent bioinformatics efforts to study iPSCs. Specifically, we will summarize several comparison studies to determine how closely human iPSCs resemble human embryonic stem cells (ESCs) from sequence, gene expression profile, chromatin structure, DNA methylation, proteomics, and function aspects. Then computational methods to assess iPSC’s pluripotency in a cost-effective yet accurate way are introduced. Finally, we will indicate the further biomolecular network studies to understand the underlying mechanism for cell reprogramming and the dynamics within this biological process.
Keywords: Cell reprogramming, gene regulatory network, induced pluripotent stem cells, transcriptional similarity, dynamics, DNA methylation, proteomics, chromatin structure, gene expression profile, sequence, Forward Engineering Strategy