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MOTIVATION: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is…
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Microarray is considered an important instrument and powerful new technology for large-scale gene sequence and gene expression analysis. One of the major challenges of this technique is the image processing phase. The accuracy of this phase…
Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. Identification of co-expressed genes and coherent patterns is the central goal in microarray or…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA…
Microarray data are often used to determine which genes are differentially expressed between groups, for example, between treatment and control groups. There are methods of determining which genes have a high probability of differential…
Gene expression is a complex phenomenon involving numerous interlinked variables, and studying these variables to control expression is essential in bioengineering and biomanufacturing. While cloning techniques for achieving plasmid…
Microarray technology is a new and powerful tool for the concurrent monitoring of a large number of gene expressions. Each microarray experiment produces hundreds of images. Each digital image requires a large storage space. Hence,…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively…
Artificial intelligence methods have often been applied to perform specific functions or tasks in the cyber-defense realm. However, as adversary methods become more complex and difficult to divine, piecemeal efforts to understand…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
Gene expression data is widely used in disease analysis and cancer diagnosis. However, since gene expression data could contain thousands of genes simultaneously, successful microarray classification is rather difficult. Feature selection…
We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant…
High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact…