Genome feature exploration using hyperbolic Self-Organizing Maps

Martin C, Díaz Solórzano NN, Ontrup J, Nattkemper TW (2007)
In: Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University.

Konferenzbeitrag | Veröffentlicht | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor/in
Abstract / Bemerkung
The advent of sequencing technologies allows to reassess the relationship between species in the hierarchically organized tree of life. Self-Organizing Maps (SOM) in Euclidean and hyperbolic space are applied to genomic signatures of 350 different organisms of the two superkingdoms Bacteria and Archaea to link the sequence signature space to pre-defined taxonomic levels, i.e. the tree of life. In the hyperbolic space the SOMs are trained by either the standard algorithm (HSOM) or in a hierarchical manner (H²SOM). For evaluating the SOM performances, distances between organisms in the feature space, on the SOM grid and in the taxonomy tree are compared pair-wise. We show that the structure recovered using the different SOMs reflects the gold standard of current taxonomy. The distances between species are better preserved when using the HSOM or H²SOM which makes the hyperbolic space better suited for embedding the high dimensional genomic signatures.
Stichworte
hyperbolic SOM; Metagenomics; information visualization; phylogenetics; self organization; tree of life; whole genome analysis
Erscheinungsjahr
2007
Titel des Konferenzbandes
Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007)
Konferenz
WSOM 2007
Konferenzort
Bielefeld, Germany
Konferenzdatum
2007-09-03 – 2007-09-06
ISBN
978-3-00-022473-7
Page URI
https://pub.uni-bielefeld.de/record/2018412

Zitieren

Martin C, Díaz Solórzano NN, Ontrup J, Nattkemper TW. Genome feature exploration using hyperbolic Self-Organizing Maps. In: Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University; 2007.
Martin, C., Díaz Solórzano, N. N., Ontrup, J., & Nattkemper, T. W. (2007). Genome feature exploration using hyperbolic Self-Organizing Maps. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007) Bielefeld: Bielefeld University. doi:10.2390/biecoll-wsom2007-140
Martin, C., Díaz Solórzano, N. N., Ontrup, J., and Nattkemper, T. W. (2007). “Genome feature exploration using hyperbolic Self-Organizing Maps” in Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007) (Bielefeld: Bielefeld University).
Martin, C., et al., 2007. Genome feature exploration using hyperbolic Self-Organizing Maps. In Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University.
C. Martin, et al., “Genome feature exploration using hyperbolic Self-Organizing Maps”, Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007), Bielefeld: Bielefeld University, 2007.
Martin, C., Díaz Solórzano, N.N., Ontrup, J., Nattkemper, T.W.: Genome feature exploration using hyperbolic Self-Organizing Maps. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld University, Bielefeld (2007).
Martin, Christian, Díaz Solórzano, Naryttza Namelly, Ontrup, Jörg, and Nattkemper, Tim Wilhelm. “Genome feature exploration using hyperbolic Self-Organizing Maps”. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University, 2007.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Suchen in

Google Scholar
ISBN Suche