Our research aims to understand the role of long intergenic non-coding RNAs (lincRNAs) in establishing the distinct epigenetic states of adult and embryonic cells and their misregulation in diseases such as cancer. To further explore how lincRNAs may define and or drive cell fate decisions we developed computational methods to provide initial hypothesis of their functions. This “guilt by association method” pointed to a clear connection of lincRNAs and numerous cellular pathways ranging from pluripotency, cancer, adipogenesis to parasitology. We have employed systematic computational and experimental approaches that have unraveled a myriad of functional roles for lincRNAs in these pathways. Collectively our studies point to key regulatory roles for lincRNAs across diverse biological pathways, with a common theme of forming ribonucleic-protein complexes that in turn modulate cell fate decisions.