Learn More
Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident(More)
Application-level protocol specifications (i.e., how a protocol should behave) are helpful for network security management, including intrusion detection and intrusion prevention. The knowledge of protocol specifications is also an effective way of detecting malicious code. However, current methods for obtaining unknown protocol specifications highly rely(More)
—Extracting the protocol message format specifications of unknown applications from network traces is important for a variety of applications such as application protocol parsing, vulnerability discovery, and system integration. In this paper, we propose ProDecoder, a network trace based protocol message format inference system that exploits the semantics(More)
Polyribosome sedimentation velocity centrifugation can be used to identify differential regulation of the translation of mRNAs. However, ultracentrifugation presents practical limitations on the number of sedimentation velocity gradients that can be run simultaneously. A method for sedimentation velocity analysis of polyribosomes is presented that is based(More)
BACKGROUND Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these(More)
MOTIVATION Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms. RESULTS An open source integrated microarray database and analysis suite, WebArrayDB(More)
BACKGROUND UV irradiation activates the epidermal growth factor receptor, induces Egr1 expression and promotes apoptosis in a variety of cell types. We examined the hypothesis that Egr1 regulates genes that mediate this process by use of a chip-on-chip protocol in human tumorigenic prostate M12 cells. RESULTS UV irradiation led to significant binding of(More)