In this paper,we present a brief review of the existing computational methods for predicting proteome-wide protein-protein interaction networks from highthroughput data,The availability of various types of omics data provides great opportunity and also unprecedented challenge to infer the interactome in cells.Reconstructing the interactome or interaction network is a crucial step for studying the functional relationship among proteins and the involved biological processes.The protein interaction network will provide valuable resources and alteatives to decipher the mechanisms of these functionally interacting elements as well as the running system of cellular operations.In this paper,we describe the main steps of predicting protein-protein interaction networks and categorize the available approaches 1o couple the physical and functional linkages.The future topics and the analyses beyond prediction are also discussed and concluded.