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  Integer linear programming approaches for non-unique probe selection.

Klau, G. W., Rahmann, S., Schliep, A., Vingron, M., & Reinert, K. (2007). Integer linear programming approaches for non-unique probe selection. In M. Anthony, E. Boros, P. Hammer, & A. Kogan (Eds.), Discrete Mathematics and Data Mining II - DM & DM II (pp. 840-856). Amsterdam et al: Elsevier.

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 Urheber:
Klau, Gunnar W., Autor
Rahmann, Sven1, Autor           
Schliep, Alexander1, Autor           
Vingron, Martin2, Autor           
Reinert, Knut, Autor
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Schlagwörter: Integer linear programming; Microarray; Probe; Oligonucleotide; Design; Group testing
 Zusammenfassung: In addition to their prevalent use for analyzing gene expression, DNA microarrays are an efficient tool for biological, medical, and industrial applications because of their ability to assess the presence or absence of biological agents, the targets, in a sample. Given a collection of genetic sequences of targets one faces the challenge of finding short oligonucleotides, the probes, which allow detection of targets in a sample by hybridization experiments. The experiments are conducted using either unique or non-unique probes, and the problem at hand is to compute a minimal design, i.e., a minimal set of probes that allows to infer the targets in the sample from the hybridization results. If we allow to test for more than one target in the sample, the design of the probe set becomes difficult in the case of non-unique probes. Building upon previous work on group testing for microarrays we describe the first approach to select a minimal probe set for the case of non-unique probes in the presence of a small number of multiple targets in the sample. The approach is based on an integer linear programming formulation and a branch-and-cut algorithm. Our implementation significantly reduces the number of probes needed while preserving the decoding capabilities of existing approaches.

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Sprache(n): eng - English
 Datum: 2007-04-01
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: eDoc: 336031
DOI: 10.1016/j.dam.2005.09.021
 Art des Abschluß: -

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Quelle 1

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Titel: Discrete Mathematics and Data Mining II - DM & DM II
Genre der Quelle: Buch
 Urheber:
Anthony, M.H.G., Herausgeber
Boros, E., Herausgeber
Hammer, P.L., Herausgeber
Kogan, A., Herausgeber
Affiliations:
-
Ort, Verlag, Ausgabe: Amsterdam et al : Elsevier
Seiten: - Band / Heft: - Artikelnummer: - Start- / Endseite: 840 - 856 Identifikator: -

Quelle 2

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Titel: Discrete Applied Mathematics
Genre der Quelle: Reihe
 Urheber:
Boros, Endre, Herausgeber
Affiliations:
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Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 155 Artikelnummer: - Start- / Endseite: - Identifikator: ISSN: 0166-218X