Računarske metode particionisanja i grupisanja u biološkim mrežama
Computational methods for partitioning and grouping in biological networks
Author
Grbić, MilanaMentor
Pavlović-Lažetić, Gordana
Committee members
Filipović, Vladimir
Kartelj, Aleksandar
Matić, Dragan
Gemović, Branislava

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Show full item recordAbstract
U ovoj disertaciji se istražuju aktuelni problemi bioinformatike i računarske biologije i metode za njihovo rješavanje...
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 of
sparse biological networks into k-plex subnetworks, prediction of the role of metabolites in metabolic
reactions, partitioning of biological networks into highly connected components and the problem of
identification of significant groups of proteins by adding new edges to the weighted protein interactions
network. The aforementioned problems have theoretical importance in areas of machine learning
and optimization, and practical application in biological research. In addition to solving the aforementioned
problems from the computational aspect, the dissertation explores further application of
the obtained results in the fields of biology and biochemistry, as well as the integration of results
within existing bioinformatics tools.
The problem of predicting the role of metabolites in metabol...ic reactions is solved by a predictive
machine learning method based on the conditional random fields, while for the remaining three
problems the algorithams based on variable neighbourhood search are developed. For solving the
problem of identification of significant groups of proteins by adding new edges to the weighted protein
interactions network, the variable neighbourhood search is only the first phase of the proposed
solution, while in the second and the third phase of the proposed method, the integration with
additional biological information and bioinformatics tools are performed.
The proposed computational methods of partitioning and grouping in biological networks confirm
existing findings in a new manner and lead to new discoveries about biological elements and the
connections between them. By solving these problems and by interpreting the obtained results
in this dissertation, a scientific contribution was made to the scientific field of computer science,
particularly to the scientific disciplines of bioinformatics and computational biology.