Publications by authors named "Ray Walshe"
A theoretical analysis of the prodrug delivery system for treating antibiotic-resistant bacteria.
IEEE/ACM Trans Comput Biol Bioinform
August 2011
Simulations were carried out to analyze a promising new antimicrobial treatment strategy for targeting antibiotic-resistant bacteria called the β-lactamase-dependent prodrug delivery system. In this system, the antibacterial drugs are delivered as inactive precursors that only become activated after contact with an enzyme characteristic of many species of antibiotic-resistant bacteria (β-lactamase enzyme). The addition of an activation step contributes an extra layer of complexity to the system that can lead to unexpected emergent behavior.
View Article and Find Full Text PDFArticle Synopsis
- Eukaryotic promoter prediction is a challenging aspect of computational genomics, crucial for understanding genetic regulatory networks, and requires improved tools due to the growing sequence data.
- A novel method is introduced that utilizes 128 unique DNA motifs and a Support Vector Machine (SVM) to effectively differentiate between promoter and non-promoter sequences across various organisms, achieving high accuracy rates and low false positives.
- The study concludes that using 4-mer frequencies along with machine learning can significantly enhance the identification of RNA polymerase II promoters compared to existing methods.
An agent-based model of bacteria-antibiotic interactions has been developed that incorporates the antibiotic-resistance mechanisms of Methicillin-Resistant Staphylococcus aureus (MRSA). The model, called the Micro-Gen Bacterial Simulator, uses information about the cell biology of bacteria to produce global information about population growth in different environmental conditions. It facilitates a detailed systems-level investigation of the dynamics involved in bacteria-antibiotic interactions and a means to relate this information to traditional high-level properties such as the Minimum Inhibitory Concentration (MIC) of an antibiotic.
View Article and Find Full Text PDF