Algorithms for effective querying of graph-based pathway databases

buir.advisorDoğrusöz, Uğur
dc.contributor.authorÇetintaş, Ahmet
dc.date.accessioned2016-01-08T18:01:54Z
dc.date.available2016-01-08T18:01:54Z
dc.date.issued2007
dc.descriptionAnkara : The Department of Computer Engineering and the Institute of Engineering and Science of Bilkent Univ., 2007.en_US
dc.descriptionThesis (Master's) -- Bilkent University, 2007.en_US
dc.descriptionIncludes bibliographical references leaves 81-83.en_US
dc.description.abstractAs the scientific curiosity shifts toward system-level investigation of genomicscale information, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. Graph-based pathway ontologies and databases have been in wide use for such data. This representation has made it possible to programmatically integrate cellular networks as well as investigating them using the well-understood concepts of graph theory to predict their structural and dynamic properties. In this regard, it is essential to effectively query such integrated large networks to extract the sub-networks of interest with the help of efficient algorithms and software tools. Towards this goal, we have developed a querying framework along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, applicable to all sorts of graph-based pathway databases from PPIs to metabolic pathways to signaling pathways. These algorithms can also account for compound or nested structures present in the pathway data, and have been implemented within the querying components of Patika (Pathway Analysis Tools for Integration and Knowledge Acquisition) tools and have proven to be useful for answering a number of biologically significant queries for a large graph-based pathway database.en_US
dc.description.provenanceMade available in DSpace on 2016-01-08T18:01:54Z (GMT). No. of bitstreams: 1 0003351.pdf: 4312537 bytes, checksum: 248dcb0ef7611e28ed16250574ff3224 (MD5)en
dc.description.statementofresponsibilityÇetintaş, Ahmeten_US
dc.format.extentxiv, 83 leaves, illustrations , tablesen_US
dc.identifier.itemidBILKUTUPB046426
dc.identifier.urihttp://hdl.handle.net/11693/14549
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGraph Algorithmsen_US
dc.subjectGraph Queryingen_US
dc.subjectBiological Pathwaysen_US
dc.subjectPathway Databasesen_US
dc.subject.lccQA166 .C48 2007en_US
dc.subject.lcshGraph theory.en_US
dc.subject.lcshAlgorithms.en_US
dc.titleAlgorithms for effective querying of graph-based pathway databasesen_US
dc.typeThesisen_US
thesis.degree.disciplineComputer Engineering
thesis.degree.grantorBilkent University
thesis.degree.levelMaster's
thesis.degree.nameMS (Master of Science)

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