Bilgisayar Mühendisliği Bölümü Koleksiyonu

Permanent URI for this collectionhttps://gcris.khas.edu.tr/handle/20.500.12469/45

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Citation Count: 54
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
(Oxford University Press, 2014) Erten, Cesim; Erten, Cesim
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 predicting the functions of proteins with unknown functions and in verifying those with estimated functions. Results: A central informal objective in constructing clusters of orthologous proteins is to guarantee that each cluster is composed of members with high homological similarity usually determined via sequence similarities and that the interactions of the proteins involved in the same cluster are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based on backbone extraction and merge strategy (BEAMS) for the problem. We finally show through experiments based on biological significance tests that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore the computational burden of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms.
Citation Count: 7
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
(Oxford University Press, 2017) Erten, Cesim; Erten, Cesim
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
Citation Count: 9
SiPAN: simultaneous prediction and alignment of protein-protein interaction networks
(Oxford University Press, 2015) Erten, Cesim; Erten, Cesim
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 network topology. Incorporating multiple species network data for network reconstruction and growth entails the design of novel models encompassing both network reconstruction and network alignment since the goal of network alignment is to provide functionally orthologous proteins from multiple networks and such orthology information can be used in guiding interolog transfers. However such an approach raises the classical chicken or egg problem

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Browsing Bilgisayar Mühendisliği Bölümü Koleksiyonu by Author "Alkan, Ferhat"