Chengwei Lei

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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)
Many mammalian genes are occupied by paused RNA polymerase II (pol II) in the promoter-proximal region on both sides of the transcription start site. However, the impact of pol II pausing on gene expression and cell biology is not fully understood. In this study, we used a Cre-Lox system to conditionally knock out the b subunit of mouse negative elongation(More)
Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks are usually constructed and analyzed in an ad hoc manner. In this study, we propose a completely parameter-free and systematic method for(More)
Discovering DNA motifs from co-expressed or co-regulated genes is an important step towards deciphering complex gene regulatory networks and understanding gene functions. Despite significant improvement in the last decade, it still remains one of the most challenging problems in computational molecular biology. In this work, we propose a novel motif finding(More)
Identifying approximately repeated patterns, or motifs, in DNA sequences from a set of co-regulated genes is an important step towards deciphering the complex gene regulatory networks and understanding gene functions. In this work, we develop a novel motif finding algorithm (PSO+) using a population-based stochastic optimization technique called Particle(More)
DNA methylation, a well-studied mechanism of epigenetic regulation, plays important roles in cancer. Increased levels of global DNA methylation is observed in primary solid tumors including endometrial carcinomas and is generally associated with silencing of tumor suppressor genes. The role of DNA methylation in cancer recurrence after therapeutic(More)
Motivation: Recent advances in high-throughput technology have dramatically increased the availability of protein-protein interaction (PPI) data and stimulated the development of many methods for predicting protein complexes, which are important in understanding the functional organization of PPI networks. However, automated protein complex prediction from(More)
To understand the function of protein complexes and their association with biological processes, a lot of studies have been done towards analyzing the protein-protein interaction (PPI) networks. However, the advancement in high-throughput technology has resulted in a humongous amount of data for analysis. Moreover, high level of noise, sparseness, and(More)