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Volumn 69, Issue , 2016, Pages 308-314

Set of rules for genomic signal downsampling

Author keywords

Compression; Cumulated phase; Downsampling; DWT; Genomic signal; Phylogeny; Sequence identification

Indexed keywords

BIOINFORMATICS; BIOLOGY; COMPACTION; DNA; DNA SEQUENCES; GENES; SIGNAL SAMPLING; WAVELET TRANSFORMS;

EID: 84957845077     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2015.05.022     Document Type: Article
Times cited : (13)

References (32)
  • 1
    • 0036936190 scopus 로고    scopus 로고
    • Classifications and other ordering systems
    • Mayr E., Bock W.J. Classifications and other ordering systems. J. Zool. Syst. Evol. Res. 2002, 40(4):169-194. 10.1046/j.1439-0469.2002.00211.x.
    • (2002) J. Zool. Syst. Evol. Res. , vol.40 , Issue.4 , pp. 169-194
    • Mayr, E.1    Bock, W.J.2
  • 2
    • 33845335476 scopus 로고    scopus 로고
    • Finding a maximum likelihood tree is hard
    • Chor B., Tuller T. Finding a maximum likelihood tree is hard. J. ACM 2006, 53(5):722-744. 10.1145/1183907.1183909.
    • (2006) J. ACM , vol.53 , Issue.5 , pp. 722-744
    • Chor, B.1    Tuller, T.2
  • 3
    • 84873801934 scopus 로고    scopus 로고
    • High-throughput sequencing for biology and medicine
    • Soon W.W., Hariharan M., Snyder M.P. High-throughput sequencing for biology and medicine. Mol. Syst. Biol. 2013, 9(1):1-14. 10.1038/msb.2012.61.
    • (2013) Mol. Syst. Biol. , vol.9 , Issue.1 , pp. 1-14
    • Soon, W.W.1    Hariharan, M.2    Snyder, M.P.3
  • 4
    • 85032750863 scopus 로고    scopus 로고
    • Genomic signal processing
    • Anastassiou D. Genomic signal processing. IEEE Signal Process. Mag. 2001, 18(4):8-20. 10.1109/79.939833.
    • (2001) IEEE Signal Process. Mag. , vol.18 , Issue.4 , pp. 8-20
    • Anastassiou, D.1
  • 5
    • 0020659327 scopus 로고
    • H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences
    • Hamori E., Ruskin J. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 1983, 258(2):1318-1327.
    • (1983) J. Biol. Chem. , vol.258 , Issue.2 , pp. 1318-1327
    • Hamori, E.1    Ruskin, J.2
  • 6
    • 85032751617 scopus 로고    scopus 로고
    • Genomic signal processing [Life Sciences]
    • Dougherty E. Genomic signal processing [Life Sciences]. IEEE Signal Process. Mag. 2012, 29(3):124-129. 10.1109/MSP.2012.2185868.
    • (2012) IEEE Signal Process. Mag. , vol.29 , Issue.3 , pp. 124-129
    • Dougherty, E.1
  • 7
    • 80051666385 scopus 로고    scopus 로고
    • Feature selection for genomic signal processing: unsupervised, supervised, and self-supervised scenarios
    • Kung S.Y., Luo Y., Mak M-W. Feature selection for genomic signal processing: unsupervised, supervised, and self-supervised scenarios. J. Signal Process. Syst. 2010, 61(1):3-20. 10.1007/s11265-008-0273-8.
    • (2010) J. Signal Process. Syst. , vol.61 , Issue.1 , pp. 3-20
    • Kung, S.Y.1    Luo, Y.2    Mak, M.-W.3
  • 8
    • 84901006893 scopus 로고    scopus 로고
    • A novel representation of DNA sequence based on CMI coding
    • Hou W., Pan Q., He M. A novel representation of DNA sequence based on CMI coding. Phys. A: Stat. Mech. Appl. 2014, 409:87-96. 10.1016/j.physa.2014.04.030.
    • (2014) Phys. A: Stat. Mech. Appl. , vol.409 , pp. 87-96
    • Hou, W.1    Pan, Q.2    He, M.3
  • 10
    • 84897886684 scopus 로고    scopus 로고
    • Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis
    • Ding X., Cao C-C., Sun X. Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis. J. Theor. Biol. 2014, 353:9-18. 10.1016/j.jtbi.2014.02.039.
    • (2014) J. Theor. Biol. , vol.353 , pp. 9-18
    • Ding, X.1    Cao, C.-C.2    Sun, X.3
  • 11
    • 84899894712 scopus 로고    scopus 로고
    • A novel 2D representation of genome sequence and its application
    • Hou W., Pan Q., He M. A novel 2D representation of genome sequence and its application. J. Comput. Theor. Nanosci. 2014, 11(8):1745-1749. 10.1166/jctn.2014.3561.
    • (2014) J. Comput. Theor. Nanosci. , vol.11 , Issue.8 , pp. 1745-1749
    • Hou, W.1    Pan, Q.2    He, M.3
  • 12
    • 84896715949 scopus 로고    scopus 로고
    • A novel descriptor of protein sequences and its application
    • Yao Y., Yan S., Han J., Dai Q., He P. A novel descriptor of protein sequences and its application. J. Theor. Biol. 2014, 347:109-117. 10.1016/j.jtbi.2014.01.001.
    • (2014) J. Theor. Biol. , vol.347 , pp. 109-117
    • Yao, Y.1    Yan, S.2    Han, J.3    Dai, Q.4    He, P.5
  • 13
    • 84894634969 scopus 로고    scopus 로고
    • A graphical representation of protein based on a novel iterated function system
    • Ma T., Liu Y., Dai Q., Yao Y., He P. A graphical representation of protein based on a novel iterated function system. Phys. A: Stat. Mech. Appl. 2014, 403:21-28. 10.1016/j.physa.2014.01.067.
    • (2014) Phys. A: Stat. Mech. Appl. , vol.403 , pp. 21-28
    • Ma, T.1    Liu, Y.2    Dai, Q.3    Yao, Y.4    He, P.5
  • 14
    • 84957849861 scopus 로고    scopus 로고
    • Prokaryotic DNA signal downsampling for fast whole genome comparison
    • Advances in Intelligent Systems and Computing
    • Sedlar K., Skutkova H., Vitek M., Provaznik I. Prokaryotic DNA signal downsampling for fast whole genome comparison. Information Technologies in Biomedicine 2014, Vol. 3:373. Advances in Intelligent Systems and Computing. 10.1007/978-3-319-06593-9_33.
    • (2014) Information Technologies in Biomedicine , vol.3 , pp. 373
    • Sedlar, K.1    Skutkova, H.2    Vitek, M.3    Provaznik, I.4
  • 15
    • 84875382083 scopus 로고    scopus 로고
    • Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences
    • Yu HJ. Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences. Gene 2013, 518(2):419-424. 10.1016/j.gene.2012.12.079.
    • (2013) Gene , vol.518 , Issue.2 , pp. 419-424
    • Yu, H.J.1
  • 16
    • 84866159705 scopus 로고    scopus 로고
    • Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping
    • Kolekar P., Kale M., Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping. Mol. Phylogenet. Evol. 2012, 65(2):510-522. 10.1016/j.ympev.2012.07.003.
    • (2012) Mol. Phylogenet. Evol. , vol.65 , Issue.2 , pp. 510-522
    • Kolekar, P.1    Kale, M.2    Kulkarni-Kale, U.3
  • 17
    • 84904625905 scopus 로고    scopus 로고
    • A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering
    • Yin C., Chen Y., Yau S.S-T. A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering. J. Theor. Biol. 2014, 359:18-28. 10.1016/j.jtbi.2014.05.043.
    • (2014) J. Theor. Biol. , vol.359 , pp. 18-28
    • Yin, C.1    Chen, Y.2    Yau, S.S.-T.3
  • 18
    • 84957851904 scopus 로고    scopus 로고
    • Relationship of bacteria using comparison of whole genome sequences in frequency domain
    • Advances in Intelligent Systems and Computing
    • Kubicova V., Provaznik I. Relationship of bacteria using comparison of whole genome sequences in frequency domain. Information Technologies in Biomedicine 2014, Vol. 3:397. Advances in Intelligent Systems and Computing. 10.1007/978-3-319-06593-9_35.
    • (2014) Information Technologies in Biomedicine , vol.3 , pp. 397
    • Kubicova, V.1    Provaznik, I.2
  • 19
    • 84900812082 scopus 로고    scopus 로고
    • Applications of alignment-free methods in epigenomics
    • Pinello L., Lo Bosco G., Yuan G.-C. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014, 15(3):419-430. 10.1093/bib/bbt078.
    • (2014) Brief Bioinform. , vol.15 , Issue.3 , pp. 419-430
    • Pinello, L.1    Lo Bosco, G.2    Yuan, G.-C.3
  • 20
    • 84886837893 scopus 로고    scopus 로고
    • Classification of genomic signals using dynamic time warping
    • Skutkova H., Vitek M., Babula P., Kizek R., Provaznik I. Classification of genomic signals using dynamic time warping. BMC Bioinform. 2013, 14(Suppl 10):S1. 10.1186/1471-2105-14-S10-S1.
    • (2013) BMC Bioinform. , vol.14 , pp. S1
    • Skutkova, H.1    Vitek, M.2    Babula, P.3    Kizek, R.4    Provaznik, I.5
  • 21
    • 33846197539 scopus 로고    scopus 로고
    • Settling the intractability of multiple alignment
    • ELIAS I. Settling the intractability of multiple alignment. J. Comput. Biol. 2006, 13(7):1323-1339. 10.1089/cmb.2006.13.1323.
    • (2006) J. Comput. Biol. , vol.13 , Issue.7 , pp. 1323-1339
    • ELIAS, I.1
  • 23
    • 0037460960 scopus 로고    scopus 로고
    • The Z curve database: a graphic representation of genome sequences
    • Zhang C.-T., Zhang R., Ou H.-Y. The Z curve database: a graphic representation of genome sequences. Bioinformatics 2003, 19(5):593-599. 10.1093/bioinformatics/btg041.
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 593-599
    • Zhang, C.-T.1    Zhang, R.2    Ou, H.-Y.3
  • 24
    • 0022428479 scopus 로고
    • Simpler DNA sequence representations
    • Gates M.A. Simpler DNA sequence representations. Nature 1985, 316(6025):219. 10.1038/316219a0.
    • (1985) Nature , vol.316 , Issue.6025 , pp. 219
    • Gates, M.A.1
  • 25
    • 0037901854 scopus 로고    scopus 로고
    • DNA sequence representation without degeneracy
    • Yau S.S-T. DNA sequence representation without degeneracy. Nucleic Acids Res. 2003, 31(12):3078-3080. 10.1093/nar/gkg432.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.12 , pp. 3078-3080
    • Yau, S.S.-T.1
  • 26
    • 1542637179 scopus 로고    scopus 로고
    • Visualization and analysis of DNA sequences using DNA walks
    • Berger J.A., Mitra S.K., Carli M., Neri A. Visualization and analysis of DNA sequences using DNA walks. J. Frankl. Inst. 2004, 341(1-2):37-53. 10.1016/j.jfranklin.2003.12.002.
    • (2004) J. Frankl. Inst. , vol.341 , Issue.1-2 , pp. 37-53
    • Berger, J.A.1    Mitra, S.K.2    Carli, M.3    Neri, A.4
  • 27
    • 0036550319 scopus 로고    scopus 로고
    • Conversion of nucleotides sequences into genomic signals
    • Cristea P.D. Conversion of nucleotides sequences into genomic signals. J. Cell. Mol. Med. 2002, 6(2):279-303. 10.1111/j.1582-4934.2002.tb00196.x.
    • (2002) J. Cell. Mol. Med. , vol.6 , Issue.2 , pp. 279-303
    • Cristea, P.D.1
  • 28
    • 0037399772 scopus 로고    scopus 로고
    • Large scale features in DNA genomic signals
    • Cristea P.D. Large scale features in DNA genomic signals. Signal Process. 2003, 83(4):871-888. 10.1016/S0165-1684(02)00477-2.
    • (2003) Signal Process. , vol.83 , Issue.4 , pp. 871-888
    • Cristea, P.D.1
  • 29
    • 78650855113 scopus 로고    scopus 로고
    • Impact of Alu repeats on the evolution of human p53 binding sites
    • Cui F., Sirotin M.V., Zhurkin V.B. Impact of Alu repeats on the evolution of human p53 binding sites. Biol. Direct 2011, 6(1):2. 10.1186/1745-6150-6-2.
    • (2011) Biol. Direct , vol.6 , Issue.1 , pp. 2
    • Cui, F.1    Sirotin, M.V.2    Zhurkin, V.B.3
  • 31
    • 0041386069 scopus 로고    scopus 로고
    • ClustalW-MPI: ClustalW analysis using distributed and parallel computing
    • LI K.-B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 2003, 19(12):1585-1586. 10.1093/bioinformatics/btg192.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1585-1586
    • LI, K.-B.1
  • 32
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D.F., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 1981, 53(1-2):131-147. 10.1016/0025-5564(81)90043-2.
    • (1981) Math. Biosci. , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2


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