Background:More and more high-throughput datasets are available from multiple levels of measuring gene regulations.The reverse engineering of gene regulatory networks from these data offers a valuable research paradigm to decipher regulatory mechanisms.So far,numerous methods have been developed for reconstructing gene regulatory networks.Results:In this paper,we provide a review of bioinformatics methods for inferring gene regulatory network from omics data.To achieve the precision reconstruction of gene regulatory networks,an intuitive alteative is to integrate these available resources in a rational framework.We also provide computational perspectives in the endeavors of inferring gene regulatory networks from heterogeneous data.We highlight the importance of multi-omics data integration with prior knowledge in gene regulatory network inferences.Conclusions:We provide computational perspectives of inferring gene regulatory networks from multiple omics data and present theoretical analyses of existing challenges and possible solutions.We emphasize on prior knowledge and data integration in network inferences owing to their abilities of identifying regulatory causality.