TY - JOUR T1 - A Scalable Algorithm for Structure Identification of Complex Gene Regulatory Network from Temporal Expression Data JF - bioRxiv DO - 10.1101/073296 SP - 073296 AU - Shupeng Gui AU - Rui Chen AU - Liang Wu AU - Ji Liu AU - Hongyu Miao Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/09/04/073296.abstract N2 - Motivation Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. Moreover, recent work suggests that these methods still suffer from the curse of dimensionality if network size increases to 100 or higher.Result We present a novel scalable algorithm for identifying genome-wide regulatory network structures. The highlight of our method is that its superior performance does not degenerate even for a network size on the order of 104, and is thus readily applicable to large-scale complex networks. Such a breakthrough is achieved by considering both prior biological knowledge and multiple topological properties (i.e., sparsity and hub gene structure) of complex networks in the regularized formulation. We also illustrate the application of our algorithm in practice using the time-course expression data from an influenza infection study in respiratory epithelial cells.Availability and Implementation The algorithm described in this article is implemented in MATLABĀ®. The source code is freely available from https://github.com/Hongyu-Miao/DMI.git.Contact jliu{at}cs.rochester.edu; hongyu.miao{at}uth.tmc.eduSupplementary information Supplementary data are available online. ER -