Jianhua Ruan

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MOTIVATION Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On the other hand, comparative methods are more reliable, but(More)
MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize,(More)
MOTIVATION A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This problem can be referred to as targeted gene finding. Since gene regulation is mainly determined by the binding of transcription factors and cis-regulatory DNA sequences, most existing gene annotation(More)
Community structure is an important property of complex networks. The automatic discovery of such structure is a fundamental task in many disciplines, including sociology, biology, engineering, and computer science. Recently, several community discovery algorithms have been proposed based on the optimization of a modularity function (Q) . However, the(More)
MOTIVATION Recent advances in technology have dramatically increased the availability of protein-protein interaction (PPI) data and stimulated the development of many methods for improving the systems level understanding the cell. However, those efforts have been significantly hindered by the high level of noise, sparseness and highly skewed degree(More)
Co-expression network-based approaches have become popular in analyzing microarray data, such as for detecting functional gene modules. However, co-expression networks are often constructed by ad hoc methods, and network-based analyses have not been shown to outperform the conventional cluster analyses, partially due to the lack of an unbiased evaluation(More)
BACKGROUND Diagnosis of acute infection in the critically ill remains a challenge. We hypothesized that circulating leukocyte transcriptional profiles can be used to monitor the host response to and recovery from infection complicating critical illness. METHODOLOGY/PRINCIPAL FINDINGS A translational research approach was employed. Fifteen mice underwent(More)
Identifying gene functional modules is an important step towards elucidating gene functions at a global scale. In this paper, we introduce a simple method to construct gene co-expression networks from microarray data, and then propose an efficient spectral clustering algorithm to identify natural communities, which are relatively densely connected(More)
Damage initiates a pleiotropic cellular response aimed at cellular survival when appropriate. To identify genes required for damage survival, we used a cell-based RNAi screen against the Drosophila genome and the alkylating agent methyl methanesulphonate (MMS). Similar studies performed in other model organisms report that damage response may involve(More)
Automatic discovery of community structures in complex networks is a fundamental task in many disciplines, including social science, engineering, and biology. A quantitative measure called modularity (Q) has been proposed to effectively assess the quality of community structures. Several community discovery algorithms have since been developed based on the(More)