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Abstract:
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In this dissertation some actual problems of bioinformatics and computational biology are explored,together with the methods for solving them. The following problems are considered: partitioning ofsparse biological networks intok-plexsubnetworks, prediction of the role of metabolites in metabolicreactions, partitioning of biological networks into highly connectedcomponents and the problem ofidentification of significant groups of proteins by adding new edges to the weighted protein interacti-ons network. The aforementioned problems have theoretical importance in areas of machine learningand optimization, and practical application in biological research. Inaddition to solving the afore-mentioned problems from the computational aspect, the dissertation explores further application ofthe obtained results in the fields of biology and biochemistry, as well as the integration of resultswithin existing bioinformatics tools.The problem of predicting the role of metabolites in metabolic reactions is solved by a predictivemachine learning method based on the conditional random fields, whilefor the remaining threeproblems the algorithams based on variable neighbourhood search are developed. For solving theproblem of identification of significant groups of proteins by adding new edges to the weighted proteininteractions network, the variable neighbourhood search is only the first phase of the proposedsolution, while in the second and the third phase of the proposed method, the integration withadditional biological information and bioinformatics tools are performed.The proposed computational methods of partitioning and groupingin biological networks confirmexisting findings in a new manner and lead to new discoveries about biological elements and theconnections between them. By solving these problems and by interpreting the obtained resultsin this dissertation, a scientific contribution was made to the scientific field of computer science,particularly to the scientific disciplines of bioinformatics and computational biology. |