Browsing by Author "Alkan, Ferhat"
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks Motivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks the informal goal is to group together related nodes. For the case of protein-protein interaction networks such groups are expected to form clusters of functionally orthologous proteins. Construction of such clusters for networks from different species may prove useful in determining evolutionary relationships in ...
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications Motivation: Analysis of protein-protein interaction (PPI) networks provides invaluable insight into several systems biology problems. High-throughput experimental techniques together with computational methods provide large-scale PPI networks. However a major issue with these networks is their erroneous nature
Motivation: Network prediction as applied to protein-protein interaction (PPI) networks has received considerable attention within the last decade. Because of the limitations of experimental techniques for interaction detection and network construction several computational methods for PPI network reconstruction and growth have been suggested. Such methods usually limit the scope of study to a single network employing data based on genomic context structure domain sequence information or existing ...