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Schlicker, Andreas

Ontology-based Similarity Measures and their Application in Bioinformatics

Universität des Saarlandes, November, 2010, 166 pages
Universität des Saarlandes

Genome-wide sequencing projects of many different organisms produce large
numbers of sequences that are functionally characterized using experimental and
bioinformatics methods. Following the development of the first bio-ontologies,
knowledge of the functions of genes and proteins is increasingly made available
in a standardized format. This allows for devising approaches that directly
exploit functional information using semantic and functional similarity
measures. This thesis addresses different aspects of the development and
application of such similarity measures.

First, we analyze semantic and functional similarity measures and apply them for
investigating the functional space in different taxa. Second, a new software
program and a new database are described, which overcome limitations of existing
tools and simplify the utilization of similarity measures for different

Third, we delineate two applications of our functional similarity measures. We
utilize them for analyzing domain and protein interaction datasets and derive
thresholds for grouping predicted domain interactions into low- and
high-confidence subsets. We also present the new MedSim method for
prioritization of candidate disease genes, which is based on the observation
that genes and proteins contributing to similar diseases are functionally
related. We demonstrate that the MedSim method performs at least as well as more
complex state-of-the-art methods and significantly outperforms current methods
that also utilize functional annotation.

Semantic Similarity, Functional Similarity, Ontology, Gene Ontology, Disease Gene Prioritization, FunSimMat
Prof. Dr. Dr. Thomas Lengauer
Dr. Mario Albrecht
Prof. Dr. Gerhard Weikum
Max-Planck-Institut für Informatik
Computational Biology and Applied Algorithmics
MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort

BibTeX Entry:
AUTHOR = {Schlicker, Andreas},
TITLE = {Ontology-based Similarity Measures and their Application in Bioinformatics},
PUBLISHER = {Universität des Saarlandes},
SCHOOL = {Universit{\"a}t des Saarlandes},
YEAR = {2010},
TYPE = {Doctoral dissertation}
PAGES = {166},
ADDRESS = {Saarbr{\"u}cken},
MONTH = {November},

Entry last modified by Ruth Schneppen-Christmann, 02/11/2011
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11/30/2010 11:02:51 AM

Ruth Schneppen-Christmann
Anja Becker
Andreas Schlicker

Edit Dates
11.02.2011 12:38:51
20.01.2011 14:57:03
11/30/2010 11:02:53 AM