Characterization of genetic signal sequences with batch-learning SOM

WSOM 2007 - 6th Int. Workshop on Self-Organizing Maps

Volumn , Issue , 2007, Pages

  Abe, Takashi ^a,b   Ikeda, Shun ^a   Kanaya, Shigehiko ^c   Wada, Kennosuke ^d   Ikemura, Toshimichi ^a  

^a NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^d Untrod Inc   (Japan)

Author keywords

Batch learning SOM; BL SOM; Genome informatics; Oligonucleotide frequency; The Earth Simulator

Indexed keywords

BATCH LEARNING; BL-SOM; EARTH SIMULATORS; GENOME INFORMATICS; OLIGONUCLEOTIDE FREQUENCIES;

CLUSTERING ALGORITHMS; CONFORMAL MAPPING; INFORMATION SCIENCE; OLIGONUCLEOTIDES;

GENES;

EID: 84893437784     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (18)

1. T. Abe, S. Kanaya, M. Kinouchi, Y. Ichiba, T. Kozuki and T. Ikemura, "Informatics for unveiling hidden genome signatures,", Genome Res., Vol. 13, pp. 693-702, 2003.
2. T. Kohonen, "Self-organized formation of topologically correct feature maps,", Biol. Cybern., Vol. 43, pp. 59-69, 1982.
3. T. Kohonen, "The self-organizing map,", Proc. IEEE, Vol. 78, pp. 1464-1480, 1990.
4. T. Kohonen, E. Oja, O. Simula, A. Visa and J. Kangas, "Engineering applications of the self-organizing map,", Proc. IEEE, Vol. 84, pp. 1358-1384, 1996.
5. S. Kanaya, Y. Kudo, T. Abe, T. Okazaki, D.C. Carlos, and T. Ikemura, "Gene classification by self-organization mapping of codon usage in bacteria with completely sequenced genome,", Genome Informatics Series, Vol. 9, pp. 369-371, 1998.
6. S. Kanaya, M. Kinouchi, T. Abe, Y. Kudo, Y. Yamada, T. Nishi, H. Mori and T. Ikemura, "Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome,", Gene, Vol. 276, pp. 89-99, 2001.
7. T. Abe, S. Kanaya, M. Kinouchi, Y. Ichiba, T. Kozuki, and T. Ikemura, "A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency,", Genome Informatics Series, Vol. 13, pp. 12-20, 2002.
8. T. Abe, T. Kozuki, Y. Kosaka, A. Fukushima, S. Nakagawa, and T. Ikemura, "Self-organizing map reveals sequence characteristics of 90 prokaryotic and eukaryotic genomes on a single map,", WSOM 2003, pp. 95-100, 2003.
9. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya, Y. Matsuura, H. Tokutaka, and T. Ikemura, "A large-scale Self-Organizing Map (SOM) constructed with the Earth Simulator unveils sequence characteristics of a wide range of eukaryotic genomes," WSOM 2005, pp. 187-194, 2005.
10. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya, and T. Ikemura, "A large-scale Self-Organizing Map (SOM) unveils sequence characteristics of a wide range of eukaryote genomes,", Gene, Vol. 365, pp. 27-34, 2006.
11. T. Abe, H. Sugawara, S. Kanaya, and T. Ikemura, "Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator,", Journal of the Earth Simulator, Vol. 6, pp. 17-23, 2006.
12. A. Huttenhofer, M. Kiefmann, S. Meier-Ewert, J. O'Brien, H. Lehrach, J. Bachellerie, and J. Brosius, "RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse,", EMBO Vol. 20, pp. 2943-2953, 2001.
13. C. Marker, A. Zemmann, T. Terhorst, M. Kiefman, J. Kastenmayer, P. Green, J. Bachellerie, J. Brosius, and A. Huttenhofer, "Experimental RNomics: Identification of 140 Candidates for Small Non-Messenger RNAs in the Plant Arabidopsis thaliana,", Current Biology Vol. 12, pp. 2002-2013, 2002.
14. Y. Okazaki, M. Furuno, T. Kasukawa, et al, "Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs,", Nature Vol. 420, pp. 563-573, 2002.
15. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya, and T. Ikemura, "Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples,", DNA Res., Vol. 12, pp. 281-290, 2005.
16. H. Hayashi, T. Abe, M. Sakamoto, et al, "Direct cloning of genes encoding novel xylanases from human gut,", Can. J. Microbiol., Vol. 51, 251-259, 2005.
17. T. Uchiyama, T. Abe, T. Ikemura and K. Watanabe, "Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes,", Nature Biotech., Vol. 23, pp. 88-93, 2005.
18. T. Abe, H. Sugawara, S. Kanaya, and T. Ikemura, "A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of environmental uncultured microbes,", Polar Bioscience, Vol. 20, pp. 103-112, 2006.