메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on drosophila genomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE DERIVATIVE; OLIGONUCLEOTIDE; PENTANUCLEOTIDE; TETRANUCLEOTIDE; UNCLASSIFIED DRUG;

EID: 84897523685     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/985706     Document Type: Article
Times cited : (4)

References (22)
  • 1
    • 0021759169 scopus 로고
    • Doublet frequencies in evolutionary distinct groups
    • 2-s2.0-0021759169 10.1093/nar/12.3.1749
    • Nussinov R., Doublet frequencies in evolutionary distinct groups. Nucleic Acids Research 1984 12 3 1749 1763 2-s2.0-0021759169 10.1093/nar/12.3.1749
    • (1984) Nucleic Acids Research , vol.12 , Issue.3 , pp. 1749-1763
    • Nussinov, R.1
  • 2
    • 0023664154 scopus 로고
    • Mono-through hexanucleotide composition of the Escherichia coli genome: A markov chain analysis
    • 2-s2.0-0023664154 10.1093/nar/15.6.2611
    • Phillips G. J., Arnold J., Ivarie R., Mono-through hexanucleotide composition of the Escherichia coli genome: a markov chain analysis. Nucleic Acids Research 1987 15 6 2611 2626 2-s2.0-0023664154 10.1093/nar/15.6.2611
    • (1987) Nucleic Acids Research , vol.15 , Issue.6 , pp. 2611-2626
    • Phillips, G.J.1    Arnold, J.2    Ivarie, R.3
  • 3
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin S., Mrázek J., Campbell A. M., Compositional biases of bacterial genomes and evolutionary implications. Journal of Bacteriology 1997 179 12 3899 3913 2-s2.0-1842332701 (Pubitemid 27259908)
    • (1997) Journal of Bacteriology , vol.179 , Issue.12 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 4
    • 0032173634 scopus 로고    scopus 로고
    • Global dinucleotide signatures and analysis of genomic heterogeneity
    • Karlin S., Global dinucleotide signatures and analysis of genomic heterogeneity. Current Opinion in Microbiology 1998 1 5 598 610 2-s2.0-0032173634 (Pubitemid 128433649)
    • (1998) Current Opinion in Microbiology , vol.1 , Issue.5 , pp. 598-610
    • Karlin, S.1
  • 5
    • 0032426005 scopus 로고    scopus 로고
    • Comparative DNA analysis across diverse genomes
    • DOI 10.1146/annurev.genet.32.1.185
    • Karlin S., Campbell A. M., Mrázek J., Comparative DNA analysis across diverse genomes. Annual Review of Genetics 1998 32 185 225 2-s2.0-0032426005 10.1146/annurev.genet.32.1.185 (Pubitemid 29045312)
    • (1998) Annual Review of Genetics , vol.32 , pp. 185-225
    • Karlin, S.1    Campbell, A.M.2    Mrazek, J.3
  • 6
    • 0032526323 scopus 로고    scopus 로고
    • Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons
    • DOI 10.1093/nar/26.12.2971
    • Rocha E. P. C., Viari A., Danchin A., Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Research 1998 26 12 2971 2980 2-s2.0-0032526323 10.1093/nar/26.12.2971 (Pubitemid 28297532)
    • (1998) Nucleic Acids Research , vol.26 , Issue.12 , pp. 2971-2980
    • Rocha, E.P.C.1    Viari, A.2    Danchin, A.3
  • 7
    • 0035049521 scopus 로고    scopus 로고
    • Genome-scale compositional comparisons in Eukaryotes
    • DOI 10.1101/gr.163101
    • Gentles A. J., Karlin S., Genome-scale compositional comparisons in Eukaryotes. Genome Research 2001 11 4 540 546 2-s2.0-0035049521 10.1101/gr.163101 (Pubitemid 32331551)
    • (2001) Genome Research , vol.11 , Issue.4 , pp. 540-546
    • Gentles, A.J.1    Karlin, S.2
  • 9
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • DOI 10.1007/BF00337288
    • Kohonen T., Self-organized formation of topologically correct feature maps. Biological Cybernetics 1982 43 1 59 69 2-s2.0-0020068152 (Pubitemid 12139984)
    • (1982) Biological Cybernetics , vol.43 , Issue.1 , pp. 59-69
    • Kohonen, T.1
  • 10
    • 0025489075 scopus 로고
    • The self-organizing map
    • 2-s2.0-0025489075 10.1109/5.58325
    • Kohonen T., The self-organizing map. Proceedings of the IEEE 1990 78 9 1464 1480 2-s2.0-0025489075 10.1109/5.58325
    • (1990) Proceedings of the IEEE , vol.78 , Issue.9 , pp. 1464-1480
    • Kohonen, T.1
  • 11
    • 0030270228 scopus 로고    scopus 로고
    • Engineering applications of the self-organizing map
    • PII S0018921996071769
    • Kohonen T., Oja E., Simula O., Visa A., Kangas J., Engineering applications of the self-organizing map. Proceedings of the IEEE 1996 84 10 1358 1383 2-s2.0-0030270228 10.1109/5.537105 (Pubitemid 126752592)
    • (1996) Proceedings of the IEEE , vol.84 , Issue.10 , pp. 1358-1383
    • Kohonen, T.1    Oja, E.2    Simula, O.3    Visa, A.4    Kangas, J.5
  • 12
    • 0035802405 scopus 로고    scopus 로고
    • 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
    • DOI 10.1016/S0378-1119(01)00673-4, PII S0378111901006734
    • Kanaya S., Kinouchi M., Abe T., Kudo Y., Yamada Y., Nishi T., Mori H., Ikemura T., 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 2001 276 1-2 89 99 2-s2.0-0035802405 10.1016/S0378-1119(01)00673-4 (Pubitemid 32925263)
    • (2001) Gene , vol.276 , Issue.1-2 , pp. 89-99
    • Kanaya, S.1    Kinouchi, M.2    Abe, T.3    Kudo, Y.4    Yamada, Y.5    Nishi, T.6    Mori, H.7    Ikemura, T.8
  • 13
    • 0242500968 scopus 로고    scopus 로고
    • Informatics for unveiling hidden genome signatures
    • DOI 10.1101/gr.634603
    • Abe T., Kanaya S., Kinouchi M., Ichiba Y., Kozuki T., Ikemura T., Informatics for unveiling hidden genome signatures. Genome Research 2003 13 4 693 702 2-s2.0-0242500968 10.1101/gr.634603 (Pubitemid 36511927)
    • (2003) Genome Research , vol.13 , Issue.4 , pp. 693-702
    • Abe, T.1    Kanaya, S.2    Kinouchi, M.3    Ichiba, Y.4    Kozuki, T.5    Ikemura, T.6
  • 14
    • 31844456638 scopus 로고    scopus 로고
    • Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes
    • DOI 10.1016/j.gene.2005.09.040, PII S0378111905006463
    • Abe T., Sugawara H., Kanaya S., Kinouchi M., Ikemura T., Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 2006 365 1-2 27 34 2-s2.0-31844456638 10.1016/j.gene.2005.09.040 (Pubitemid 43185220)
    • (2006) Gene , vol.365 , Issue.1-2 SPEC. ISS. , pp. 27-34
    • Abe, T.1    Sugawara, H.2    Kanaya, S.3    Kinouchi, M.4    Ikemura, T.5
  • 15
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • 2-s2.0-33646569088 10.1093/dnares/dsi015
    • Abe T., Sugawara H., Kinouchi M., Kanaya S., Ikemura T., Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Research 2005 12 5 281 290 2-s2.0-33646569088 10.1093/dnares/dsi015
    • (2005) DNA Research , vol.12 , Issue.5 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3    Kanaya, S.4    Ikemura, T.5
  • 16
    • 84876865275 scopus 로고    scopus 로고
    • A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks
    • Nakao R., Abe T., Nijhof A. M., Yamamoto S., Jongejan F., Ikemura T., Sugimoto C., A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks. ISME Journal 2013 7 5 1003 1015
    • (2013) ISME Journal , vol.7 , Issue.5 , pp. 1003-1015
    • Nakao, R.1    Abe, T.2    Nijhof, A.M.3    Yamamoto, S.4    Jongejan, F.5    Ikemura, T.6    Sugimoto, C.7
  • 18
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phaylogeny
    • Drosophila 12 Genomes Consortium
    • Drosophila 12 Genomes Consortium, Evolution of genes and genomes on the Drosophila phaylogeny. Nature 2007 450 7167 203 218
    • (2007) Nature , vol.450 , Issue.7167 , pp. 203-218
  • 20
    • 36048950933 scopus 로고    scopus 로고
    • Gene family evolution across 12 Drosophila genomes
    • DOI 10.1371/journal.pgen.0030197
    • Hahn M. W., Han M. V., Han S.-G., Gene family evolution across 12 Drosophila genomes. PLoS genetics 2007 3 11 e197 2-s2.0-43549091647 10.1371/journal.pgen.0030197 (Pubitemid 350291574)
    • (2007) PLoS Genetics , vol.3 , Issue.11 , pp. 2135-2146
    • Hahn, M.W.1    Han, M.V.2    Han, S.-G.3
  • 21
    • 84884286094 scopus 로고    scopus 로고
    • Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance
    • Iwasaki Y., Wada K., Wada Y., Abe T., Ikemura T., Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance. Chromosome Research 2013 21 461 474
    • (2013) Chromosome Research , vol.21 , pp. 461-474
    • Iwasaki, Y.1    Wada, K.2    Wada, Y.3    Abe, T.4    Ikemura, T.5
  • 22
    • 74949101957 scopus 로고    scopus 로고
    • A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses
    • 2-s2.0-74949101957 10.1093/dnares/dsp018
    • Abe T., Kanaya S., Uehara H., Ikemura T., A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. DNA Research 2009 16 5 287 298 2-s2.0-74949101957 10.1093/dnares/dsp018
    • (2009) DNA Research , vol.16 , Issue.5 , pp. 287-298
    • Abe, T.1    Kanaya, S.2    Uehara, H.3    Ikemura, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.