Parameterized algorithms for hitting set variants applied to protein identification in shotgun proteomics
Licentiatavhandling, 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

Författare

Leonid Molokov

Chalmers, Data- och informationsteknik, Datavetenskap

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 i proceeding

The union of minimal hitting sets: parameterized combinatorial bounds and counting

Journal of Discrete Algorithms,; Vol. 7(2009)p. 391-401

Artikel i vetenskaplig tidskrift

Styrkeområden

Informations- och kommunikationsteknik

Livsvetenskaper och teknik

Ämneskategorier

Bioinformatik och systembiologi

Datavetenskap (datalogi)

EA

Opponent: Prof. Sebastian Böcker, Department of Mathematics and Computer Science, University of Jena