메뉴 건너뛰기




Volumn 105, Issue 38, 2008, Pages 14254-14261

The infinite sites model of genome evolution

Author keywords

Ancestral reconstruction; Gene duplication; Genome rearrangements

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME INSERTION; CHROMOSOME REARRANGEMENT; DNA SEQUENCE; EVOLUTION; GENOME; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; RECIPROCAL CHROMOSOME TRANSLOCATION; SIMULATION; X CHROMOSOME;

EID: 55549136564     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0805217105     Document Type: Article
Times cited : (74)

References (40)
  • 1
    • 0033391532 scopus 로고    scopus 로고
    • Genome rearrangement with gene families
    • Sankoff D (1999) Genome rearrangement with gene families. Bioinformatics 15:909-917.
    • (1999) Bioinformatics , vol.15 , pp. 909-917
    • Sankoff, D.1
  • 3
    • 0042027896 scopus 로고    scopus 로고
    • Structural dynamics of eukaryotic chromosome evolution
    • Eichler EE, Sankoff D (2003) Structural dynamics of eukaryotic chromosome evolution. Science 301:793-797.
    • (2003) Science , vol.301 , pp. 793-797
    • Eichler, E.E.1    Sankoff, D.2
  • 4
    • 4544242008 scopus 로고    scopus 로고
    • Genomic distances under deletions and insertions
    • Marron M, Swenson KM, Moret BME (2004) Genomic distances under deletions and insertions. Theor Comput Sci 325:347-360.
    • (2004) Theor Comput Sci , vol.325 , pp. 347-360
    • Marron, M.1    Swenson, K.M.2    Moret, B.M.E.3
  • 5
    • 0029976325 scopus 로고    scopus 로고
    • Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae
    • Moore JK, Haber JE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16:2164-2173.
    • (1996) Mol Cell Biol , vol.16 , pp. 2164-2173
    • Moore, J.K.1    Haber, J.E.2
  • 6
    • 0022976432 scopus 로고
    • Nonhomologous recombination in mammalian cells: Role for short sequence homologies in the joining reaction
    • Roth DB, Wilson JH (1986) Nonhomologous recombination in mammalian cells: Role for short sequence homologies in the joining reaction. Mol Cell Biol 6:4295-4304.
    • (1986) Mol Cell Biol , vol.6 , pp. 4295-4304
    • Roth, D.B.1    Wilson, J.H.2
  • 7
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations
    • Kimura M (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61:893-903.
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 8
    • 0020744702 scopus 로고
    • Properties of a neutral allele model with intragenic recombination
    • Hudson RR (1983) Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23:183-201.
    • (1983) Theor Popul Biol , vol.23 , pp. 183-201
    • Hudson, R.R.1
  • 9
    • 24044535485 scopus 로고    scopus 로고
    • Efficient sorting of genomic permutations by translocation, inversion and block interchange
    • Yancopoulos S, Attie O, Friedberg R (2005) Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21:3340-3346.
    • (2005) Bioinformatics , vol.21 , pp. 3340-3346
    • Yancopoulos, S.1    Attie, O.2    Friedberg, R.3
  • 10
    • 36949006683 scopus 로고    scopus 로고
    • Are there rearrangement hotspots in the human genome?
    • Alekseyev MA, Pevzner PA (2007) Are there rearrangement hotspots in the human genome? PLoS Comput Biol 3:e209.
    • (2007) PLoS Comput Biol , vol.3
    • Alekseyev, M.A.1    Pevzner, P.A.2
  • 11
    • 0037623969 scopus 로고    scopus 로고
    • The reconstruction of doubled genomes
    • El-Mabrouk N, Sankoff D (2003) The reconstruction of doubled genomes. SIAM J Comput 32:754-792.
    • (2003) SIAM J Comput , vol.32 , pp. 754-792
    • El-Mabrouk, N.1    Sankoff, D.2
  • 12
    • 33847709186 scopus 로고    scopus 로고
    • Whole genome duplications and contracted breakpoint graphs
    • Alekseyev MA, Pevzner PA (2007) Whole genome duplications and contracted breakpoint graphs. Soc Indust Appl Math J Comput 36:1748-1763.
    • (2007) Soc Indust Appl Math J Comput , vol.36 , pp. 1748-1763
    • Alekseyev, M.A.1    Pevzner, P.A.2
  • 13
  • 14
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 15
    • 0022376704 scopus 로고
    • Dating the human-ape split by amolecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape split by amolecular clock of mitochondrial DNA. J Mol Evol 22:160-174.
    • (1985) J Mol Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 18
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque G, Pevzner PA (2002) Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 12:26-36.
    • (2002) Genome Res , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.A.2
  • 19
    • 33750386912 scopus 로고    scopus 로고
    • Reconstructing contiguous regions of an ancestral genome
    • Ma J, et al. (2006) Reconstructing contiguous regions of an ancestral genome. Genome Res 16:1557-1565.
    • (2006) Genome Res , vol.16 , pp. 1557-1565
    • Ma, J.1
  • 20
    • 22744440499 scopus 로고    scopus 로고
    • Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
    • Murphy WJ, et al (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617.
    • (2005) Science , vol.309 , pp. 613-617
    • Murphy, W.J.1
  • 21
    • 34248576291 scopus 로고    scopus 로고
    • Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    • Mikkelsen TS, et al (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-177.
    • (2007) Nature , vol.447 , pp. 167-177
    • Mikkelsen, T.S.1
  • 22
    • 15344342569 scopus 로고    scopus 로고
    • A 1.5-approximation algorithm for sorting by transpositions and transreversals
    • Hartman T, Sharan R (2005) A 1.5-approximation algorithm for sorting by transpositions and transreversals. J Comput Syst Sci 70:300-320.
    • (2005) J Comput Syst Sci , vol.70 , pp. 300-320
    • Hartman, T.1    Sharan, R.2
  • 23
    • 0032444856 scopus 로고    scopus 로고
    • The leptotene-zygotene transition of meiosis
    • Zickler D, Kleckner N (1998) The leptotene-zygotene transition of meiosis. Annu Rev Genet 32:619-697.
    • (1998) Annu Rev Genet , vol.32 , pp. 619-697
    • Zickler, D.1    Kleckner, N.2
  • 24
    • 19944416873 scopus 로고    scopus 로고
    • Genetic analyses from ancient DNA
    • Paabo S, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645-679.
    • (2004) Annu Rev Genet , vol.38 , pp. 645-679
    • Paabo, S.1
  • 26
    • 0000116740 scopus 로고
    • A method for deducing branching sequences in phylogeny
    • Camin JH, Sokal RR (1965) A method for deducing branching sequences in phylogeny. Evolution (Lawrence, Kans) 19:311-326.
    • (1965) Evolution (Lawrence, Kans) , vol.19 , pp. 311-326
    • Camin, J.H.1    Sokal, R.R.2
  • 27
    • 0000927535 scopus 로고
    • Paths, trees, and flowers
    • Edmonds J (1965) Paths, trees, and flowers. Canad J Math 17:449-467.
    • (1965) Canad J Math , vol.17 , pp. 449-467
    • Edmonds, J.1
  • 28
    • 0001807019 scopus 로고
    • Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
    • ACM Press, New York, pp
    • Hannenhalli S, Pevzner PA (1995) Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proceedings of the 27th Annual ACM Symposium on the Theory of Computing. (ACM Press, New York), pp 178-189.
    • (1995) Proceedings of the 27th Annual ACM Symposium on the Theory of Computing , pp. 178-189
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 30
    • 0002275128 scopus 로고
    • Constructing a tree on the basis of a set of distances between the hanging vertices
    • Zaretskii KA (1965) Constructing a tree on the basis of a set of distances between the hanging vertices. Uspekhi Mat Nauk 20:90-92.
    • (1965) Uspekhi Mat Nauk , vol.20 , pp. 90-92
    • Zaretskii, K.A.1
  • 32
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19:99-113.
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 33
    • 0034178257 scopus 로고    scopus 로고
    • Homology - A personal view on some of the problems
    • Fitch WM (2000) Homology - A personal view on some of the problems. Trends Genet 16:227-231.
    • (2000) Trends Genet , vol.16 , pp. 227-231
    • Fitch, W.M.1
  • 34
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz S, et al. (2004) Human-mouse alignments with BLASTZ. Genome Res 13:103-107.
    • (2004) Genome Res , vol.13 , pp. 103-107
    • Schwartz, S.1
  • 35
    • 23844460187 scopus 로고    scopus 로고
    • Chromosomal breakpoint reuse in genome sequence rearrangement
    • Sankoff D, Trinh P (2005) Chromosomal breakpoint reuse in genome sequence rearrangement. J Comput Biol 12:812-821.
    • (2005) J Comput Biol , vol.12 , pp. 812-821
    • Sankoff, D.1    Trinh, P.2
  • 36
    • 52449090559 scopus 로고    scopus 로고
    • DUPCAR: Reconstructing contiguous ancestral regions with duplications
    • in press
    • Ma J, et al. (2008) DUPCAR: Reconstructing contiguous ancestral regions with duplications. J Comput Biol, in press.
    • (2008) J Comput Biol
    • Ma, J.1
  • 37
    • 12744263078 scopus 로고    scopus 로고
    • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    • Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2005) Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15:98-110.
    • (2005) Genome Res , vol.15 , pp. 98-110
    • Bourque, G.1    Zdobnov, E.M.2    Bork, P.3    Pevzner, P.A.4    Tesler, G.5
  • 39
    • 24044529257 scopus 로고    scopus 로고
    • Reconstructing tumor amplisomes
    • Raphael BJ, Pevzner PA (2004) Reconstructing tumor amplisomes. Bioinformatics 20:Suppl 1:I265-I273.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Raphael, B.J.1    Pevzner, P.A.2
  • 40
    • 43049143055 scopus 로고    scopus 로고
    • Mapping and sequencing of structural variation from eight human genomes
    • Kidd JM, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56-64.
    • (2008) Nature , vol.453 , pp. 56-64
    • Kidd, J.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.