Parameterized algorithms for hitting set variants applied to protein identification in shotgun proteomics
Licentiate thesis, 2011
This work is dedicated to problem of protein identification in bottom-up proteomics, and in particular, in shotgun proteomics. It is aimed on
providing a new way of interpretation of peak lists. Several computational problems are outlined and it is shown by simulations that despite NP-hardness, the problems in question can be relatively fast solved for practical cases. Problems are also studied from parameterized complexity theory perspective.
Union Editing
Fixed Parameter Tractable
Shotgun proteomics
Hitting Set
Parameterized complexity
Hypergraph
Set Cover
EA
Opponent: Prof. Sebastian Böcker, Department of Mathematics and Computer Science, University of Jena
Author
Leonid Molokov
Chalmers, Computer Science and Engineering (Chalmers), Computing Science (Chalmers)
Application of Combinatorial Methods to Protein Identification in Peptide Mass Fingerprinting
KDIR 2010 - International Conference on Knowledge Discovery and Information Retrieval, Valencia, Spain,;(2010)p. 307-313
Paper in proceeding
The union of minimal hitting sets: parameterized combinatorial bounds and counting
Journal of Discrete Algorithms,;Vol. 7(2009)p. 391-401
Journal article
Areas of Advance
Information and Communication Technology
Life Science Engineering (2010-2018)
Subject Categories
Bioinformatics and Systems Biology
Computer Science
EA
Opponent: Prof. Sebastian Böcker, Department of Mathematics and Computer Science, University of Jena