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More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. We develop a bi-colored network based(More)
Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which(More)
Studying protein complexes is very important in biological processes since it helps reveal the structure-functionality relationships in biological networks and much attention has been paid to accurately predict protein complexes from the increasing amount of protein-protein interaction (PPI) data. Most of the available algorithms are based on the assumption(More)
MOTIVATION Disease progression is driven by dynamic changes in both the activity and connectivity of molecular pathways. Understanding these dynamic events is critical for disease prognosis and effective treatment. Compared with activity dynamics, connectivity dynamics is poorly explored. RESULTS We describe the M-module algorithm to identify gene modules(More)
In the past two decades, great efforts have been devoted to extract the dependence and interplay between structure and functions in biological networks because they have strong relevance to biological processes. In this article, we reviewed the recent development in the biological network analysis. In detail, we first reviewed the interactome topological(More)
Discovering evolving communities in dynamic networks is essential to important applications such as analysis for dynamic web content and disease progression. Evolutionary clustering uses the temporal smoothness framework that simultaneously maximizes the clustering accuracy at the current time step and minimizes the clustering drift between two successive(More)
The effectiveness of rapid rail transit system is analyzed using tools of complex network for the first time. We evaluated the effectiveness of the system in Beijing quantitatively from different perspectives, including descriptive statistics analysis, bridging property, centrality property, ability of connecting different part of the system and ability of(More)
Determining the dynamics of pathways associated with cancer progression is critical for understanding the etiology of diseases. Advances in biological technology have facilitated the simultaneous genomic profiling of multiple patients at different clinical stages, thus generating the dynamic genomic data for cancers. Such data provide enable investigation(More)
Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network(More)