Open Access. Powered by Scholars. Published by Universities.®

Philosophy Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 3 of 3

Full-Text Articles in Philosophy

Identifying Pathway Proteins In Networks Using Convergence, Kathryn Dempsey Cooper, Hesham Ali Jan 2013

Identifying Pathway Proteins In Networks Using Convergence, Kathryn Dempsey Cooper, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

One of the key goals of systems biology concerns the analysis of experimental biological data available to the scientific public. New technologies are rapidly developed to observe and report whole-scale biological phenomena; however, few methods exist with the ability to produce specific, testable hypotheses from this noisy ‘big’ data. In this work, we propose an approach that combines the power of data-driven network theory along with knowledge-based ontology to tackle this problem. Network models are especially powerful due to their ability to display elements of interest and their relationships as internetwork structures. Additionally, ontological data actually supplements the confidence of ...


A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali Jan 2011

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data ...


Identifying Modular Function Via Edge Annotation In Gene Correlation Networks Using Gene Ontology Search, Kathryn Dempsey Cooper, Ishwor Thapa, Dhundy Raj Bastola, Hesham Ali Jan 2011

Identifying Modular Function Via Edge Annotation In Gene Correlation Networks Using Gene Ontology Search, Kathryn Dempsey Cooper, Ishwor Thapa, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks provide a powerful tool for analyzing large sets of biological information. This method of high-throughput data modeling has important implications in uncovering novel knowledge of cellular function. Previous studies on other types of network modeling (protein-protein interaction networks, metabolomes, etc.) have demonstrated the presence of relationships between network structures and organization of cellular function. Studies with correlation network further confirm the existence of such network structure and biological function relationship. However, correlation networks are typically noisy and the identified network structures, such as clusters, must be further investigated to verify actual cellular function. This is traditionally done using ...