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Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and Cþþ, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic userdoi:10.1093/bioinformatics/btv137 pmid:25755273 pmcid:PMC4495295 fatcat:x45x6p6nnjcnflyzf4bngogizi