Selecting genotyping oligo probes via logical analysis of data

Kwangsoo Kim; Hong Seo Ryoo

doi:10.1007/978-3-540-72665-4_8

Selecting genotyping oligo probes via logical analysis of data

Kwangsoo Kim, Hong Seo Ryoo

School of Industrial Management Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Citation (Scopus)

Abstract

Based on the general framework of logical analysis of data, we develop a probe design method for selecting short oligo probes for genotyping applications in this paper. When extensively tested on genomic sequences downloaded from the Lost Alamos National Laboratory and the National Center of Biotechnology Information websites in various monospecific and polyspecific in silico experimental settings, the proposed probe design method selected a small number of oligo probes of length 7 or 8 nucleotides that perfectly classified all unseen testing sequences. These results well illustrate the utility of the proposed method in genotyping applications.

Original language	English
Title of host publication	Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings
Publisher	Springer Verlag
Pages	86-97
Number of pages	12
ISBN (Print)	9783540726647
DOIs	https://doi.org/10.1007/978-3-540-72665-4_8
Publication status	Published - 2007
Event	20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007 - Montreal, Canada Duration: 2007 May 28 → 2007 May 30

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4509 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007
Country	Canada
City	Montreal
Period	07/5/28 → 07/5/30

Keywords

LAD
Learning theory
Microarrays
Oligo probes
Optimization
Set covering
Viral pathogens

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-540-72665-4_8

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Cite this

Kim, K., & Ryoo, H. S. (2007). Selecting genotyping oligo probes via logical analysis of data. In Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings (pp. 86-97). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4509 LNAI). Springer Verlag. https://doi.org/10.1007/978-3-540-72665-4_8

Selecting genotyping oligo probes via logical analysis of data. / Kim, Kwangsoo; Ryoo, Hong Seo.

Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings. Springer Verlag, 2007. p. 86-97 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4509 LNAI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Kim, K & Ryoo, HS 2007, Selecting genotyping oligo probes via logical analysis of data. in Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4509 LNAI, Springer Verlag, pp. 86-97, 20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007, Montreal, Canada, 07/5/28. https://doi.org/10.1007/978-3-540-72665-4_8

Kim K, Ryoo HS. Selecting genotyping oligo probes via logical analysis of data. In Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings. Springer Verlag. 2007. p. 86-97. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-540-72665-4_8

Kim, Kwangsoo ; Ryoo, Hong Seo. / Selecting genotyping oligo probes via logical analysis of data. Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings. Springer Verlag, 2007. pp. 86-97 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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