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Full-Text Articles in Physical Sciences and Mathematics
Identifying Aging-Related Genes In Mouse Hippocampus Using Gateway Nodes, Kathryn Dempsey Cooper, Hesham Ali
Identifying Aging-Related Genes In Mouse Hippocampus Using Gateway Nodes, Kathryn Dempsey Cooper, Hesham Ali
Interdisciplinary Informatics Faculty Publications
Background: High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph …
On Mining Biological Signals Using Correlation Networks, Kathryn Dempsey Cooper, Ishwor Thapa, Claudia Cortes, Zack Eriksen, Dhundy Raj Bastola, Hesham Ali
On Mining Biological Signals Using Correlation Networks, Kathryn Dempsey Cooper, Ishwor Thapa, Claudia Cortes, Zack Eriksen, Dhundy Raj Bastola, Hesham Ali
Interdisciplinary Informatics Faculty Proceedings & Presentations
Correlation networks have been used in biological networks to analyze and model high-throughput biological data, such as gene expression from microarray or RNA-seq assays. Typically in biological network modeling, structures can be mined from these networks that represent biological functions; for example, a cluster of proteins in an interactome can represent a protein complex. In correlation networks built from high-throughput gene expression data, it has often been speculated or even assumed that clusters represent sets of genes that are coregulated. This research aims to validate this concept using network systems biology and data mining by identification of correlation network clusters …
A Parallel Template For Implementing Filters For Biological Correlation Networks, Kathryn Dempsey Cooper, Vladimir Ufimtsev, Sanjukta Bhowmick, Hesham Ali
A Parallel Template For Implementing Filters For Biological Correlation Networks, Kathryn Dempsey Cooper, Vladimir Ufimtsev, Sanjukta Bhowmick, Hesham Ali
Interdisciplinary Informatics Faculty Publications
High throughput biological experiments are critical for their role in systems biology – the ability to survey the state of cellular mechanisms on the broad scale opens possibilities for the scientific researcher to understand how multiple components come together, and what goes wrong in disease states. However, the data returned from these experiments is massive and heterogeneous, and requires intuitive and clever computational algorithms for analysis. The correlation network model has been proposed as a tool for modeling and analysis of this high throughput data; structures within the model identified by graph theory have been found to represent key players …
Parallel Adaptive Algorithms For Sampling Large Scale Networks, Kanimathi Duraisamy
Parallel Adaptive Algorithms For Sampling Large Scale Networks, Kanimathi Duraisamy
Student Work
The study of real-world systems, represented as networks, has important application in many disciplines including social sciences [1], bioinformatics [2] and software engineering [3]. These networks are extremely large, and analyzing them is very expensive. Our research work involves developing parallel graph sampling methods for efficient analysis of gene correlation networks. Our sampling algorithms maintain important structural and informational properties of large unstructured networks. We focus on preserving the relative importance, based on combinatorial metrics, rather than the exact measures. We use a special subgraph technique, based on finding triangles called maximal chordal subgraphs, which maintains the highly connected portions …
The Development Of Parallel Adaptive Sampling Algorithms For Analyzing Biological Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Sanjukta Bhowmick, Hesham Ali
The Development Of Parallel Adaptive Sampling Algorithms For Analyzing Biological Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Sanjukta Bhowmick, Hesham Ali
Interdisciplinary Informatics Faculty Proceedings & Presentations
The availability of biological data in massive scales continues to represent unlimited opportunities as well as great challenges in bioinformatics research. Developing innovative data mining techniques and efficient parallel computational methods to implement them will be crucial in extracting useful knowledge from this raw unprocessed data, such as in discovering significant cellular subsystems from gene correlation networks. In this paper, we present a scalable combinatorial sampling technique, based on identifying maximum chordal subgraphs, that reduces noise from biological correlation networks, thereby making it possible to find biologically relevant clusters from the filtered network. We show how selecting the appropriate filter …
A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick
A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick
Interdisciplinary Informatics Faculty Proceedings & Presentations
A correlation network is a graph-based representation of relationships among genes or gene products, such as proteins. The advent of high-throughput bioinformatics has resulted in the generation of volumes of data that require sophisticated in silico models, such as the correlation network, for in-depth analysis. Each element in our network represents expression levels of multiple samples of one gene and an edge connecting two nodes reflects the correlation level between the two corresponding genes in the network according to the Pearson correlation coefficient. Biological networks made in this manner are generally found to adhere to a scale-free structural nature, that …