Browsing by Author "Abaka, Gamze"

Now showing 1 - 2 of 2

Citation Count: 14
Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways
(Oxford University Press, 2013) Abaka, Gamze; Biyikoglu, Turker; Erten, Cesim
Motivation: Given a pair of metabolic pathways an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction drug design and overall may enhance our understanding of cellular metabolism. Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database we demonstrate that when compared with a state-of-the-art alternative the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.
Global Alignment of Metabolic Pathways and Protein-Protein Interaction Networks
(Kadir Has Üniversitesi, 2014) Abaka, Gamze; Erten, Cesim
Metabolic pathways and protein interaction networks are essential at almost every function for living organisms. Simply, while reactions produce life energy within cells, protein interaction networks provide biological functions. Also, abnormal reactions or interactions cause various disorders. Thus, in bioinformatics, most of the studies are based on these networks in order to find hopeful results for these disorders and biological challenges. Solving alignment problem is one of these studies such that it tries to find similar reactions, proteins or functions. In this thesis, we focus on that problem within both metabolic pathways and protein interaction networks. Firstly, we propose a constrained alignment algorithm, CAMPways, for one-to-many alignment of metabolic pathways and we extend the framework, CAPPI, for one-to-one protein interaction network alignment with necessary changes. Afterwards, we provide the computational intractability of the problem and finally we compare our algorithm with different algorithms on actual metabolic pathways and protein interaction networks.