메뉴 건너뛰기




Volumn 69, Issue 7, 2007, Pages 2429-2442

The mystery of two straight lines in bacterial genome statistics

Author keywords

Algebraic statistics; Codon usage; Context free approximation; Genome evolution; Mean field; Nucleotide frequency; Principal components

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA;

EID: 34548671660     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-007-9229-6     Document Type: Article
Times cited : (6)

References (27)
  • 1
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • 19
    • Besemer, J., Borodovsky, M., 1999. Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27(19), 3911-3920.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 2
    • 1342345235 scopus 로고    scopus 로고
    • Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species
    • Bharanidharan, D., Bhargavi, G.R., Uthanumallian, K., Gautham, N., 2004. Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species. Biochem. Biophys. Res. Commun. 315, 1097-1103.
    • (2004) Biochem. Biophys. Res. Commun. , vol.315 , pp. 1097-1103
    • Bharanidharan, D.1    Bhargavi, G.R.2    Uthanumallian, K.3    Gautham, N.4
  • 3
    • 34248203587 scopus 로고    scopus 로고
    • Component retention in principal component analysis with application to cDNA microarray data
    • doi:10.1186/1745-6150-2-2
    • Cangelosi, R., Goriely, A., 2007. Component retention in principal component analysis with application to cDNA microarray data. Biol. Direct 2, 2, doi:10.1186/1745-6150-2-2
    • (2007) Biol. Direct , vol.2 , pp. 2
    • Cangelosi, R.1    Goriely, A.2
  • 4
    • 14544301585 scopus 로고    scopus 로고
    • Codon bias signatures, organisation of microorganisms in codon space and lifestyle
    • Carbone, A., Kepes, F., Zinovyev, A., 2005. Codon bias signatures, organisation of microorganisms in codon space and lifestyle. Mol. Biol. Evol. 22, 547-561.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 547-561
    • Carbone, A.1    Kepes, F.2    Zinovyev, A.3
  • 5
    • 27144450646 scopus 로고    scopus 로고
    • Exons, introns, and DNA thermodynamics
    • Carlon, E., Malki, M.L., Blossey, R., 2005. Exons, introns, and DNA thermodynamics. Phys. Rev. Lett. 94, 178101.
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 178101
    • Carlon, E.1    Malki, M.L.2    Blossey, R.3
  • 6
    • 1542618322 scopus 로고    scopus 로고
    • Codon usage between genomes is constrained by genome-wide mutational processes
    • 10
    • Chen, S.L., Lee, W., Hottes, A.K., Shapiro, L., McAdams, H.H., 2004. Codon usage between genomes is constrained by genome-wide mutational processes. PNAS 101(10), 3480-3485.
    • (2004) PNAS , vol.101 , pp. 3480-3485
    • Chen, S.L.1    Lee, W.2    Hottes, A.K.3    Shapiro, L.4    McAdams, H.H.5
  • 8
    • 33745918349 scopus 로고    scopus 로고
    • Conspiracy in bacterial genomes
    • Frappat, L., Sciarrino, A., 2006. Conspiracy in bacterial genomes. Physica A 369, 699-713.
    • (2006) Physica a , vol.369 , pp. 699-713
    • Frappat, L.1    Sciarrino, A.2
  • 10
    • 23744452722 scopus 로고    scopus 로고
    • Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences
    • On-line:
    • Gorban, A.N., Zinovyev, A.Y., Popova, T.G., 2005a. Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences. In Silico Biol. 5, 0025. On-line: http://www.bioinfo.de/isb/2005/05/ 0025/
    • (2005) Silico Biol. , vol.5 , pp. 0025
    • Gorban, A.N.1    Zinovyev, A.Y.2    Popova, T.G.3
  • 11
    • 18844426538 scopus 로고    scopus 로고
    • Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences
    • Gorban, A., Popova, T., Zinovyev, A., 2005b. Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences. Physica A 353, 365-387.
    • (2005) Physica a , vol.353 , pp. 365-387
    • Gorban, A.1    Popova, T.2    Zinovyev, A.3
  • 12
    • 0035220937 scopus 로고    scopus 로고
    • A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
    • Knight, R.D., Freeland, S.J., Landweber, L.F., 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2, 0010.1-0010.13
    • (2001) Genome Biol. , vol.2 , pp. 00101-001013
    • Knight, R.D.1    Freeland, S.J.2    Landweber, L.F.3
  • 13
    • 0031593216 scopus 로고    scopus 로고
    • Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species
    • 1-2
    • Lobry, J., 1997. Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene 205(1-2), 309-316.
    • (1997) Gene , vol.205 , pp. 309-316
    • Lobry, J.1
  • 14
    • 0037179524 scopus 로고    scopus 로고
    • Asymmetric directional mutation pressures in bacteria
    • 10
    • Lobry, J.R., Sueoka, N., 2002. Asymmetric directional mutation pressures in bacteria. Genome Biol. 3(10), 0058.
    • (2002) Genome Biol. , vol.3 , pp. 0058
    • Lobry, J.R.1    Sueoka, N.2
  • 15
    • 0038480747 scopus 로고    scopus 로고
    • Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria
    • 2
    • Lobry, J.R., Chessel, D., 2003. Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J. Appl. Genet. 44(2), 235-261.
    • (2003) J. Appl. Genet. , vol.44 , pp. 235-261
    • Lobry, J.R.1    Chessel, D.2
  • 16
    • 0036796799 scopus 로고    scopus 로고
    • Synonymous codon usage is subject to selection in thermophilic bacteria
    • 19
    • Lynn, D.J., Gregory, A.C., Singer, G.A.C., Hickey, D.A., 2002. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30(19), 4272-4277.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4272-4277
    • Lynn, D.J.1    Gregory, A.C.2    Singer, G.A.C.3    Hickey, D.A.4
  • 17
    • 33646475124 scopus 로고    scopus 로고
    • Mutation model for nucleotide sequences based on crystal basis
    • arXiv q-bio.BM/0506010
    • Minichini, C., Sciarrino, A., 2006. Mutation model for nucleotide sequences based on crystal basis. Biosystems 84, 191-206, arXiv q-bio.BM/0506010
    • (2006) Biosystems , vol.84 , pp. 191-206
    • Minichini, C.1    Sciarrino, A.2
  • 18
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial evolution
    • Muto, A., Osawa, S., 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84, 166-169.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 20
    • 33847687699 scopus 로고    scopus 로고
    • The mathematics of phylogenomics
    • 1
    • Pachter, L., Sturmfels, B., 2007. The mathematics of phylogenomics. SIAM Rev. 49(1), 3-31.
    • (2007) SIAM Rev. , vol.49 , pp. 3-31
    • Pachter, L.1    Sturmfels, B.2
  • 21
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
    • Singer, G.A.C., Hickey, D.A., 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17, 1581-1588.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1581-1588
    • Singer, G.A.C.1    Hickey, D.A.2
  • 22
    • 3643052747 scopus 로고
    • On the genetic basis of variation and heterogeneity of DNA base composition
    • Sueoka, N., 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA 48, 582-592.
    • (1962) Proc. Natl. Acad. Sci. USA , vol.48 , pp. 582-592
    • Sueoka, N.1
  • 23
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • 8
    • Sueoka, N., 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85(8), 2653-2657.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2653-2657
    • Sueoka, N.1
  • 24
    • 13444269018 scopus 로고    scopus 로고
    • Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
    • 1
    • Wan, X.F., Xu, D., Kleinhofs, A., Zhou, J., 2004. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol. Biol. 4(1), 19.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 19
    • Wan, X.F.1    Xu, D.2    Kleinhofs, A.3    Zhou, J.4
  • 25
    • 0034687143 scopus 로고    scopus 로고
    • Genes and the physics of the DNA double-helix
    • Yeramian, E., 2000a. Genes and the physics of the DNA double-helix. Gene 255, 139-150.
    • (2000) Gene , vol.255 , pp. 139-150
    • Yeramian, E.1
  • 26
    • 0034687101 scopus 로고    scopus 로고
    • The physics of DNA and the annotation of the Plasmodium falsiparum genome
    • Yeramian, E., 2000b. The physics of DNA and the annotation of the Plasmodium falsiparum genome. Gene 255, 151-168.
    • (2000) Gene , vol.255 , pp. 151-168
    • Yeramian, E.1
  • 27
    • 4043120425 scopus 로고    scopus 로고
    • Self-organizing approach for automated gene identification
    • Zinovyev, A.Y., Gorban, A.N., Popova, T.G., 2003. Self-organizing approach for automated gene identification. Open Syst. Inf. Dyn. 10, 321-333.
    • (2003) Open Syst. Inf. Dyn. , vol.10 , pp. 321-333
    • Zinovyev, A.Y.1    Gorban, A.N.2    Popova, T.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.