메뉴 건너뛰기




Volumn 17, Issue 9, 2010, Pages 1227-1242

CAGE: Combinatorial analysis of gene-cluster evolution

Author keywords

algorithms; alignment; gene clusters; genomics; phylogenetic trees

Indexed keywords

DEFENSIN;

EID: 77958040819     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0094     Document Type: Article
Times cited : (13)

References (37)
  • 1
    • 0033867676 scopus 로고    scopus 로고
    • Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: A possible model for their origin
    • Achaz, G., Coissac, E., Viari, A., et al. 2000. Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin. Mol. Biol. Evol. 17, 1268-1275.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1268-1275
    • Achaz, G.1    Coissac, E.2    Viari, A.3
  • 2
    • 33846811438 scopus 로고    scopus 로고
    • Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats
    • Akhunov, E., Akhunova, A., and Dvorak, J. 2006. Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats. Mol. Biol. Evol. 24, 539-550.
    • (2006) Mol. Biol. Evol. , vol.24 , pp. 539-550
    • Akhunov, E.1    Akhunova, A.2    Dvorak, J.3
  • 3
    • 0142059650 scopus 로고    scopus 로고
    • An Alu transposition model for the origin and expansion of human segmental duplications
    • Bailey, J., Liu, G., and Eichler, E. 2006. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73, 823-834.
    • (2006) Am. J. Hum. Genet. , vol.73 , pp. 823-834
    • Bailey, J.1    Liu, G.2    Eichler, E.3
  • 4
    • 33750374575 scopus 로고    scopus 로고
    • Evolution of tandemly repeated sequences through duplication and inversion
    • Bertrand, D., Lajoie, M., El-Mabrouk, N., et al. 2006. Evolution of tandemly repeated sequences through duplication and inversion. Lect. Notes Comput. Sci. 4205, 129-140.
    • (2006) Lect. Notes Comput. Sci. , vol.4205 , pp. 129-140
    • Bertrand, D.1    Lajoie, M.2    El-Mabrouk, N.3
  • 5
  • 6
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette, M., Kent, W. J., Riemer, C., et al., 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715.
    • (2004) Genome Res. , vol.14 , pp. 708-715
    • Blanchette, M.1    Kent, W.J.2    Riemer, C.3
  • 8
    • 34548743476 scopus 로고    scopus 로고
    • Gene conversion: Mechanisms, evolution and human disease
    • Chen, J., Cooper, D., Chuzhanova, N., et al. 2007. Gene conversion: mechanisms, evolution and human disease. Nat. Rev. 8, 762-775.
    • (2007) Nat. Rev. , vol.8 , pp. 762-775
    • Chen, J.1    Cooper, D.2    Chuzhanova, N.3
  • 10
    • 0028557312 scopus 로고
    • Functional significance of different human CYP1A1 genotypes
    • Crofts, F., Taioli, E., Trachman, J., et al. 1994. Functional significance of different human CYP1A1 genotypes. Carcinogenesis 15, 2961-2963.
    • (1994) Carcinogenesis , vol.15 , pp. 2961-2963
    • Crofts, F.1    Taioli, E.2    Trachman, J.3
  • 11
    • 0036187352 scopus 로고    scopus 로고
    • Reconstructing the duplication history of tandemly repeated genes
    • Elemento, O., Gascuel, O., and Lefranc, M. P. 2002. Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 19, 278-278.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 278-278
    • Elemento, O.1    Gascuel, O.2    Lefranc, M.P.3
  • 12
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force, A., Lynch, M., Pickett, F. B., et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3
  • 13
    • 0035432364 scopus 로고    scopus 로고
    • Strategies for the systematic sequencing of complex genomes
    • Green, E. D. 2001. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2, 573-573.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 573-573
    • Green, E.D.1
  • 14
    • 77958060493 scopus 로고    scopus 로고
    • HLA class II protein expression in prostate cancer cells
    • Haque, A., Younger, A. R., Amria, S., et al. 2007. HLA class II protein expression in prostate cancer cells. J. Immunol. 178, 48. 22.
    • (2007) J. Immunol. , vol.178 , Issue.48 , pp. 22
    • Haque, A.1    Younger, A.R.2    Amria, S.3
  • 15
    • 77958053137 scopus 로고    scopus 로고
    • Personal communication
    • Hou, M. 2007. Personal communication.
    • (2007)
    • Hou, M.1
  • 16
    • 19344372749 scopus 로고    scopus 로고
    • Gene duplication: The genomic trade in spare parts
    • Hurles, M. 2004. Gene duplication: the genomic trade in spare parts. PLoS Biol. 2, e206.
    • (2004) PLoS Biol. , vol.2
    • Hurles, M.1
  • 17
    • 35649007348 scopus 로고    scopus 로고
    • Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    • Jiang, Z., Tang, H., Ventura, M., et al. 2007. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet. 39, 1361-1368.
    • (2007) Nat. Genet. , vol.39 , pp. 1361-1368
    • Jiang, Z.1    Tang, H.2    Ventura, M.3
  • 18
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E. S., Linton, L. M., Birren, B., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3
  • 19
    • 34347349069 scopus 로고    scopus 로고
    • Genomic rearrangements and sporadic disease
    • Lupski, J. R. 2007. Genomic rearrangements and sporadic disease. Nat. Genet. 39, S43-S47.
    • (2007) Nat. Genet. , vol.39
    • Lupski, J.R.1
  • 20
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M., and Conery, J. S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 21
    • 55549136564 scopus 로고    scopus 로고
    • The infinite sites model of genome evolution
    • Ma, J., Ratan, A., Raney, B. J., et al. 2008. The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. USA 105, 14254-14261.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 14254-14261
    • Ma, J.1    Ratan, A.2    Raney, B.J.3
  • 22
    • 34250365369 scopus 로고    scopus 로고
    • Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    • Margulies, E., Cooper, G. M., Asimenos, G., et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17, 760-764.
    • (2007) Genome Res. , vol.17 , pp. 760-764
    • Margulies, E.1    Cooper, G.M.2    Asimenos, G.3
  • 23
    • 0035011227 scopus 로고    scopus 로고
    • Comparison of genomic DNA sequences: Solved and unsolved problems
    • Miller, W. 2001. Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17, 391-397.
    • (2001) Bioinformatics , vol.17 , pp. 391-397
    • Miller, W.1
  • 24
    • 38849149795 scopus 로고    scopus 로고
    • 28-way vertebrate alignment and conservation track in the ucsc genome browser
    • Miller, W., Rosenbloom, K., Hardison, R. C., et al. 2007. 28-way vertebrate alignment and conservation track in the ucsc genome browser. Genome Res. 17, 1797-1808.
    • (2007) Genome Res. , vol.17 , pp. 1797-1808
    • Miller, W.1    Rosenbloom, K.2    Hardison, R.C.3
  • 25
    • 0000791476 scopus 로고
    • 1Lengths of chromosomal segments conserved since divergence of man and mouse
    • Nadeau, J. H., and Taylor, B. A. 1984. 1Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81, 814-818.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 814-818
    • Nadeau, J.H.1    Taylor, B.A.2
  • 26
    • 0034176716 scopus 로고    scopus 로고
    • Linkage of human narcolepsy with HLA association to chromosome 4p13-q21
    • Nakayama, J., Miura, M., Honda, M., et al. 2000. Linkage of human narcolepsy with HLA association to chromosome 4p13-q21. Genomics 65, 84-86.
    • (2000) Genomics , vol.65 , pp. 84-86
    • Nakayama, J.1    Miura, M.2    Honda, M.3
  • 28
    • 33644881888 scopus 로고    scopus 로고
    • Aldo-keto reductase (AKR) 1C3: Role in prostate disease and the development of specific inhibitors
    • Penning, T., Steckelbroeck, S., Bauman, D. R., et al. 2006. Aldo-keto reductase (AKR) 1C3: role in prostate disease and the development of specific inhibitors. Mol. Cell. Endocrinol. 248, 182-191.
    • (2006) Mol. Cell. Endocrinol. , vol.248 , pp. 182-191
    • Penning, T.1    Steckelbroeck, S.2    Bauman, D.R.3
  • 29
    • 8744312854 scopus 로고    scopus 로고
    • A novel method for multiple alignment of sequences with repeated and shuffled elements
    • Raphael, B., Zhi, D., Tang, H., et al. 2004. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 14, 2336-2336.
    • (2004) Genome Res. , vol.14 , pp. 2336-2336
    • Raphael, B.1    Zhi, D.2    Tang, H.3
  • 30
    • 33845617282 scopus 로고    scopus 로고
    • Comparing tandem repeats with duplications and excisions of variable degree
    • Sammeth, M., and Stoye, J. 2006. Comparing tandem repeats with duplications and excisions of variable degree. TCBB 3, 395-407.
    • (2006) TCBB , vol.3 , pp. 395-407
    • Sammeth, M.1    Stoye, J.2
  • 31
    • 0032848463 scopus 로고    scopus 로고
    • Genetic polymorphism of drug-metabolizing enzymes and susceptibility to oral cancer
    • Sato, M., Sato, T., Izumo, T., et al. 1999. Genetic polymorphism of drug-metabolizing enzymes and susceptibility to oral cancer. Carcinogenesis 20, 1927-1931.
    • (1999) Carcinogenesis , vol.20 , pp. 1927-1931
    • Sato, M.1    Sato, T.2    Izumo, T.3
  • 32
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz, S., Kent, W. J., Smit, A., et al. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
    • (2003) Genome Res. , vol.13 , pp. 103-107
    • Schwartz, S.1    Kent, W.J.2    Smit, A.3
  • 33
    • 0024492512 scopus 로고    scopus 로고
    • Evidence for a primary association of celiac disease to a particular HLA-DQ α?β heterodimer
    • Sollid, L., Markussen, G., Ek, J., et al. 2000. Evidence for a primary association of celiac disease to a particular HLA-DQ α?β heterodimer. J. Exp. Med. 169, 345-350.
    • (2000) J. Exp. Med. , vol.169 , pp. 345-350
    • Sollid, L.1    Markussen, G.2    Ek, J.3
  • 34
    • 33846006596 scopus 로고    scopus 로고
    • A comprehensive analysis of common copy-number variations in the human genome
    • Wong, K. K., de Leeuw, R. J., Dosanjh, N. S., et al. 2007. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80, 91-104.
    • (2007) Am. J. Hum. Genet. , vol.80 , pp. 91-104
    • Wong, K.K.1    De Leeuw, R.J.2    Dosanjh, N.S.3
  • 35
    • 0041886965 scopus 로고    scopus 로고
    • Greedy method for inferring tandem duplication history
    • Zhang, L., Ma, B., Wang, L., et al. 2003. Greedy method for inferring tandem duplication history. Bioinformatics 19, 1497-1504.
    • (2003) Bioinformatics , vol.19 , pp. 1497-1504
    • Zhang, L.1    Ma, B.2    Wang, L.3
  • 36
    • 61949256604 scopus 로고    scopus 로고
    • Simultaneous history reconstruction for complex gene clusters in multiple species
    • In Altman, R. B., Dunker, A. K., Hunter, L., et al., eds
    • Zhang, Y., Song, G., Hsu, C., et al. 2009. Simultaneous history reconstruction for complex gene clusters in multiple species. In Altman, R. B., Dunker, A. K., Hunter, L., et al., eds. Proc. Pac. Symp. Biocomput. 2009 162-173.
    • (2009) Proc. Pac. Symp. Biocomput. 2009 , pp. 162-173
    • Zhang, Y.1    Song, G.2    Hsu, C.3
  • 37
    • 47249087729 scopus 로고    scopus 로고
    • Reconstructing the evolutionary history of complex human gene clusters
    • In Vingron, M., and Wong, L., eds
    • Zhang, Y., Song, G., Vinar, T., et al. 2008. Reconstructing the evolutionary history of complex human gene clusters. In Vingron, M., and Wong, L., eds. Proc. 12th Annu. Int. Conf. Res. Comput. Mol. Biol. 29-49.
    • (2008) Proc. 12th Annu. Int. Conf. Res. Comput. Mol. Biol. , pp. 29-49
    • Zhang, Y.1    Song, G.2    Vinar, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.