The identification of microRNA (miRNA) target sites is an important and challenging problem. In the past decade, dozens of computational methods have been developed to predict miRNA target sites. Despite their existence, rarely is there a method that considers the well-known competition and cooperation among miRNAs when attempts to discover target sites. To fill this gap, we developed a new approach called CCmiR, which takes the cooperation and competition of multiple miRNAs into account in a statistical model to predict their target sites. Tested on 4 different types of datasets, CCmiR predicted miRNA target sites with a high recall and a reasonable precision. Moreover, we demonstrated that CCmiR identified known and new cooperative and competitive miRNAs supported by literature. Compared with three state-of-the-art computational methods, CCmiR had a higher recall and a higher precision than these popular methods
