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Author:Riihimäki, Vesa
Title:Graph Algorithms in Computational Systems Biology
Graafialgoritmit laskennallisessa systeemibiologiassa
Publication type:Master's thesis
Publication year:2004
Pages:iv + 58      Language:   eng
Department/School:Teknillisen fysiikan ja matematiikan osasto
Main subject:Tietoliikennetekniikka   (S-72)
Supervisor:Östergård, Patric
Instructor:
OEVS:
Electronic archive copy is available via Aalto Thesis Database.
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Location:P1 Ark TF80     | Archive
Keywords:algorithm
bioinformatics
computation
graph theory
genomics
molecule structure
NP-complete
proteomics
systems biology
algoritmi
bioinformatiikka
graafiteoria
genomiikka
laskenta
molekyylirakenne
NP-täydellisyys
proteomiikka
systeemibiologia
Abstract (eng): This thesis is a literary research in the field of systems biology.
The aim of the study is both to scan the use of graph theory in biology, or bioinformatics, and collect methods to solve those problems.

The systems biology field, which was established half a century ago, became interesting for engineers as the amount of biological data started increasing dramatically in the last few years.
In the field there are many workers having different academic backgrounds.

The current problems in the field mainly concern genome sequencing and molecule structure prediction.
In the future, when one knows more about regulations and interactions between genes and cells, one will perhaps be able to simulate living organisms.
As a basis for the models are often networks and graphs, which emphasises the importance of studying these concepts.
The role of graph theory in genomics and proteomics and clinical studies, i.e. in systems biology, differs from modelling the biological systems to giving methods for solving the biological problem.

The graph problems arising from biology cover the whole graph theory field.
There are both easy problems that can be solved using methods available and hard problems, e.g., NP-complete problems, for which the algorithms have to be developed further.

Examples of problems arising in systems biology include shortest path problem, finding connected components, structure graphs, matching, Eulerian path problem, Chinese postman problem, Hamiltonian path problem, graph isomorphism problem, maximum clique and independent set problems.
Abstract (fin): Tämä diplomityö on kirjallisuusselvitys eräistä systeemibiologian avoimista ongelmista.
Tutkielman tavoitteena on kartoittaa graafiteorian sovellusaluetta biologisessa tutkimuksessa ja bioinformatiikassa, sekä koota ratkaisumenetelmiä sieltä nouseviin ongelmiin.

Systeemibiologian tutkimusalue, joka on ideoitu jo puoli vuosisataa sitten, alkoi kiinnostaa tekniikan tutkijoita biologisen aineiston kasvun myötä viime vuosina.
Tutkimusalalla on paljon tekijöitä, joiden koulutustausta vaihtelee biologiasta tietojenkäsittelyyn.

Systeemibiologian tämän päivän keskeisimmät ongelmat käsittelevät genomin sekvensointia ja molekyylirakennetta.
Tulevaisuudessa tietämyksen kasvaessa geenien ja solujen säätelystä ja vaikutuksista, laskennalliset menetelmät mahdollistavat eliöiden simuloimisen.
Eliömallien pohjana ovat verkot ja graafit, jolloin tässä käsiteltävän aiheen merkitys korostuu.
Graafiteorian anti genomiikalle, proteomiikalle ja kliiniselle tutkimukselle vaihteleekin graafien tarjotessa niin malleille pohjan, kuin myös menetelmiä yksittäisten ongelmien ratkaisemiseen.

Biologisten ongelmien laajuutta kuvaa se, että esiin nousevat ongelmat kattavat koko graafiteorian tutkimusalan.
Joihinkin ongelmiin on hyvin tehokkaita algoritmejä, mutta alalla esiintyy myös haastavampia ongelmia, kuten NP-täydelliset ongelmat, joiden ratkaisumenetelmiä on vielä kehitettävä.

Systeemibiologiassa esiintyviä graafisongelmia ovat muun muassa lyhimmän polun ongelma, yhtenäisten komponenttien etsintä, rakennegraafin etsintä, pariustusongelmat, Eulerin polun määrittäminen, kiinalainen postimiehen ongelma, Hamiltonin polun etsintä, klikkiongelmat, sekä graafien isomorfismi.
ED:2004-07-14
INSSI record number: 25449
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