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

Leonid Molokov (Institutionen för data- och informationsteknik, Datavetenskap, Algoritmer (Chalmers))
Göteborg : Chalmers University of Technology, 2011. - 56 s.
[Licentiatavhandling]

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.

Nyckelord: Parameterized complexity, Hitting Set, Hypergraph, Set Cover, Union Editing, Fixed Parameter Tractable, Shotgun proteomics



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Denna post skapades 2011-03-28.
CPL Pubid: 138385

 

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Institutioner (Chalmers)

Institutionen för data- och informationsteknik, Datavetenskap, Algoritmer (Chalmers)

Ämnesområden

Informations- och kommunikationsteknik
Livsvetenskaper
Datalogi
Bioinformatik och systembiologi

Chalmers infrastruktur

Relaterade publikationer

Inkluderade delarbeten:


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


Application of Combinatorial Methods to Protein Identification in Peptide Mass Fingerprinting


Examination

Datum: 2011-04-29
Tid: 09:00
Lokal: EA
Opponent: Prof. Sebastian Böcker, Department of Mathematics and Computer Science, University of Jena