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Volumn 2015, Issue , 2015, Pages

Development of Self-Compressing BLSOM for Comprehensive Analysis of Big Sequence Data

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

EID: 84944339989     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2015/506052     Document Type: Article
Times cited : (7)

References (24)
  • 1
    • 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
    • S. Kanaya, M. Kinouchi, T. Abe et al., "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, no. 1-2,pp. 89-99, 2001
    • (2001) Gene , vol.276 , Issue.1-2 , pp. 89-99
    • Kanaya, S.1    Kinouchi, M.2    Abe, T.3
  • 3
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • 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 Research, vol. 12, no. 5, pp. 281-290, 2005
    • (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
  • 4
    • 68749105319 scopus 로고    scopus 로고
    • Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a largescale self-organizingmap constructed with the earth simulator
    • 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 largescale self-organizingmap constructed with the earth simulator," Journal of the Earth Simulator, vol. 6, pp. 7-23, 2006
    • (2006) Journal of the Earth Simulator , vol.6 , pp. 7-23
    • Abe, T.1    Sugawara, H.2    Kanaya, S.3    Ikemura, T.4
  • 5
    • 19144369096 scopus 로고    scopus 로고
    • Substrateinduced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes
    • T. Uchiyama, T. Abe, T. Ikemura, and K. Watanabe, "Substrateinduced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes," Nature Biotechnology, vol. 23, no. 1, pp. 88-93, 2005
    • (2005) Nature Biotechnology , vol.23 , Issue.1 , pp. 88-93
    • Uchiyama, T.1    Abe, T.2    Ikemura, T.3    Watanabe, K.4
  • 6
    • 84876865275 scopus 로고    scopus 로고
    • A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks
    • R. Nakao, T. Abe, A. M. Nijhof et al., "A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks," ISME Journal, vol. 7, no. 5, pp. 1003-1015, 2013
    • (2013) ISME Journal , vol.7 , Issue.5 , pp. 1003-1015
    • Nakao, R.1    Abe, T.2    Nijhof, A.M.3
  • 8
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • T. Kohonen, "Self-organized formation of topologically correct feature maps," Biological Cybernetics, vol. 43, no. 1, pp. 59-69, 1982
    • (1982) Biological Cybernetics , vol.43 , Issue.1 , pp. 59-69
    • Kohonen, T.1
  • 9
    • 0025489075 scopus 로고
    • Theself-organizingmap
    • T. Kohonen, "Theself-organizingmap," Proceedings of the IEEE, vol. 78, no. 9, pp. 1464-1480, 1990
    • (1990) Proceedings of the IEEE , vol.78 , Issue.9 , pp. 1464-1480
    • Kohonen, T.1
  • 10
    • 0030270228 scopus 로고    scopus 로고
    • Engineering applications of the self-organizing map
    • T. Kohonen, E. Oja, O. Simula, A. Visa, and J. Kangas, "Engineering applications of the self-organizing map," Proceedings of the IEEE, vol. 84, no. 10, pp. 1358-1383, 1996
    • (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
  • 11
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • D. T. Pride, R. J. Meinersmann, T. M. Wassenaar, and M. J. Blaser, "Evolutionary implications of microbial genome tetranucleotide frequency biases," Genome Research, vol. 13, no. 2, pp. 145-158, 2003
    • (2003) Genome Research , vol.13 , Issue.2 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 12
    • 58749086048 scopus 로고    scopus 로고
    • Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes
    • H. Suzuki, M. Sota, C. J. Brown, and E. M. Top, "Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes," Nucleic Acids Research, vol. 36, no. 22, article e147, 2008
    • (2008) Nucleic Acids Research , vol.36 , Issue.22
    • Suzuki, H.1    Sota, M.2    Brown, C.J.3    Top, E.M.4
  • 13
    • 77958476427 scopus 로고    scopus 로고
    • Distinguishing microbial genome fragments based on their composition: Evolutionary and comparative genomic perspectives
    • S. C. Perry and R. G. Beiko, "Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives," Genome Biology and Evolution, vol. 2, no. 1, pp. 117-131, 2010
    • (2010) Genome Biology and Evolution , vol.2 , Issue.1 , pp. 117-131
    • Perry, S.C.1    Beiko, R.G.2
  • 14
    • 79952303267 scopus 로고    scopus 로고
    • A novel method of characterizing genetic sequences: Genome space with biological distance and applications
    • M. Deng, C. Yu, Q. Liang, R. L. He, and S. S.-T. Yau, "A novel method of characterizing genetic sequences: genome space with biological distance and applications," PLoS ONE, vol. 6, no. 3, Article ID e17293, 2011
    • (2011) PLoS ONE , vol.6 , Issue.3
    • Deng, M.1    Yu, C.2    Liang, Q.3    He, R.L.4    Yau, S.S.-T.5
  • 15
    • 84860265013 scopus 로고    scopus 로고
    • Microbial lifestyle and genome signatures
    • C. Dutta and S. Paul, "Microbial lifestyle and genome signatures," Current Genomics, vol. 13, no. 2, pp. 153-162, 2012
    • (2012) Current Genomics , vol.13 , Issue.2 , pp. 153-162
    • Dutta, C.1    Paul, S.2
  • 16
    • 84864101124 scopus 로고    scopus 로고
    • A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses
    • K. Kryukov, K. Sumiyama, K. Ikeo, T. Gojobori, and N. Saitou, "A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses," Genome Biology and Evolution, vol. 4, no. 4, pp. 501-512, 2012
    • (2012) Genome Biology and Evolution , vol.4 , Issue.4 , pp. 501-512
    • Kryukov, K.1    Sumiyama, K.2    Ikeo, K.3    Gojobori, T.4    Saitou, N.5
  • 17
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • H. Teeling, A. Meyerdierks, M. Bauer, R. Amann, and F. O. Glöckner, "Application of tetranucleotide frequencies for the assignment of genomic fragments," Environmental Microbiology, vol. 6, no. 9, pp. 938-947, 2004
    • (2004) Environmental Microbiology , vol.6 , Issue.9 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3    Amann, R.4    Glöckner, F.O.5
  • 18
    • 38649143159 scopus 로고    scopus 로고
    • Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing
    • C.-K. K. Chan, A. L. Hsu, S.-L. Tang, and S. K. Halgamuge, "Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing," Journal of Biomedicine and Biotechnology, vol. 2008, Article ID 513701, 10 pages, 2008
    • (2008) Journal of Biomedicine and Biotechnology , vol.2008
    • Chan, C.-K.K.1    Hsu, A.L.2    Tang, S.-L.3    Halgamuge, S.K.4
  • 19
    • 47049115023 scopus 로고    scopus 로고
    • Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification
    • C. Martin, N. N. Diaz, J. Ontrup, and T. W. Nattkemper, "Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification," Bioinformatics, vol. 24, no. 14, pp. 1568-1574, 2008
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1568-1574
    • Martin, C.1    Diaz, N.N.2    Ontrup, J.3    Nattkemper, T.W.4
  • 20
    • 70350015324 scopus 로고    scopus 로고
    • Community-wide analysis of microbial genome sequence signatures
    • G. J. Dick, A. F. Andersson, B. J. Baker et al., "Community-wide analysis of microbial genome sequence signatures," Genome Biology, vol. 10, no. 8, article R85, 2009
    • (2009) Genome Biology , vol.10 , Issue.8
    • Dick, G.J.1    Andersson, A.F.2    Baker, B.J.3
  • 21
    • 77955836327 scopus 로고    scopus 로고
    • Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self-organizing map (SOM)
    • M. Mitsumori, S. Nakagawa, H. Matsui, T. Shinkai, and A. Takenaka, "Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self-organizing map (SOM)," Journal of Applied Microbiology, vol. 109, no. 3, pp. 763-770, 2010
    • (2010) Journal of Applied Microbiology , vol.109 , Issue.3 , pp. 763-770
    • Mitsumori, M.1    Nakagawa, S.2    Matsui, H.3    Shinkai, T.4    Takenaka, A.5
  • 22
    • 79955071957 scopus 로고    scopus 로고
    • Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
    • M. Weber, H. Teeling, S. Huang et al., "Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics," ISME Journal, vol. 5, no. 5, pp. 918-928, 2011
    • (2011) ISME Journal , vol.5 , Issue.5 , pp. 918-928
    • Weber, M.1    Teeling, H.2    Huang, S.3
  • 23
    • 79954568885 scopus 로고    scopus 로고
    • Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case
    • Y. Iwasaki, T. Abe, K. Wada, M. Itoh, and T. Ikemura, "Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case," DNA Research, vol. 18, no. 2, pp. 125-136, 2011
    • (2011) DNA Research , vol.18 , Issue.2 , pp. 125-136
    • Iwasaki, Y.1    Abe, T.2    Wada, K.3    Itoh, M.4    Ikemura, T.5
  • 24
    • 74949101957 scopus 로고    scopus 로고
    • Anovel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses
    • T. Abe, S. Kanaya,H. Uehara, and T. Ikemura, "Anovel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses," DNA Research, vol. 16, no. 5, pp. 287-298, 2009.
    • (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.