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

More information

Created

10/7/2017