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The development of simple mathematical model for representing complicated real-life chemical reaction systems has been a fundamental issue in computational biology and bioinformatics. In particular, the accurate description of chemical events with multi-step chemical reactions has been regarded as an essential problem in chemistry and biophysics. To model chemical reaction systems in a manageable...
Message RNA (mRNA) is the template for protein synthesis. It carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell. The turnover process of mRNA is a chemical event with multiple small step reactions, and the degradation of mRNA molecules is an important step in gene expression. A number of mathematical models have been proposed to study the dynamics of...
microDoR Human is a web server tool based on machine learning algorithm to predict Human miRNA-mediated gene silencing: mRNA degradation or translational repression. For a miRNA-mRNA interaction, microDoR Human identifies whether the target mRNA is cleaved or translationally inhibite. microDoR Human is expected to serve as a useful tool for understanding of miRNA-mediated gene regulation. The microDoR...
MicroKNAs (miRNA) are essential 21-22 nucleotides regulatory RNAs produced from larger hairpin precursors (pre-miRNA), and regulate gene expression through mRNA degradation or translational inhibition. We applied functional strand support vector machine (FS-SVM), a new method for prediction of functional strand on the miRNA precursors, to classifying 5' and 3' pre-miRNAs and achieved about 94% accuracy...
The dynamic behavior of a cell model is affected by its structural complexity and parametric uncertainties. Two important issues in systems biology are how to quantitatively determine the relationship between system behaviors and parameter variations, and how to study the interactions between parameters. Using an NF-kB signaling pathway model as an example, and assuming that the parameters of this...
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