메뉴 건너뛰기




Volumn 9, Issue 6, 2008, Pages

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

EID: 47749155635     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-6-r104     Document Type: Article
Times cited : (13)

References (51)
  • 1
    • 0015895045 scopus 로고
    • An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugation
    • 10.1016/0022-2836(73)90240-4 4798988
    • Filipski J Thiery JP Bernardi G An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugation. J Mol Biol 1973, 80:177-197. 10.1016/0022-2836(73)90240-4 4798988
    • (1973) J Mol Biol , vol.80 , pp. 177-197
    • Filipski, J.1    Thiery, J.P.2    Bernardi, G.3
  • 2
    • 0017173987 scopus 로고
    • An approach to the organization of eukaryotic genomes at a macromolecular level
    • 10.1016/S0022-2836(76)80105-2 826644
    • Macaya G Thiery JP Bernardi G An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 1976, 108:237-254. 10.1016/S0022-2836(76)80105-2 826644
    • (1976) J Mol Biol , vol.108 , pp. 237-254
    • Macaya, G.1    Thiery, J.P.2    Bernardi, G.3
  • 3
    • 0017105287 scopus 로고
    • An analysis of eukaryotic genomes by density gradient centrifugation
    • 10.1016/S0022-2836(76)80104-0 826643
    • Thiery JP Macaya G Bernardi G An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 1976, 108:219-235. 10.1016/ S0022-2836(76)80104-0 826643
    • (1976) J Mol Biol , vol.108 , pp. 219-235
    • Thiery, J.P.1    Macaya, G.2    Bernardi, G.3
  • 5
    • 0025884418 scopus 로고
    • The distribution of genes in the human genome
    • 10.1016/0378-1119(91)90364-H 2055469
    • Mouchiroud D D'Onofrio G Aissani B Macaya G Gautier C Bernardi G The distribution of genes in the human genome. Gene 1991, 100:181-187. 10.1016/0378-1119(91)90364-H 2055469
    • (1991) Gene , vol.100 , pp. 181-187
    • Mouchiroud, D.1    D'Onofrio, G.2    Aissani, B.3    Macaya, G.4    Gautier, C.5    Bernardi, G.6
  • 6
    • 0028963020 scopus 로고
    • Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores
    • 10.1007/BF00163235 7723057
    • Duret L Mouchiroud D Gautier C Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol 1995, 40:308-317. 10.1007/BF00163235 7723057
    • (1995) J Mol Evol , vol.40 , pp. 308-317
    • Duret, L.1    Mouchiroud, D.2    Gautier, C.3
  • 7
    • 0030077335 scopus 로고    scopus 로고
    • Human coding and noncoding DNA: Compositional correlations
    • 10.1006/mpev.1996.0002 8673288
    • Clay O Caccio S Zoubak S Mouchiroud D Bernardi G Human coding and noncoding DNA: Compositional correlations. Mol Phylogenet Evol 1996, 5:2-12. 10.1006/mpev.1996.0002 8673288
    • (1996) Mol Phylogenet Evol , vol.5 , pp. 2-12
    • Clay, O.1    Caccio, S.2    Zoubak, S.3    Mouchiroud, D.4    Bernardi, G.5
  • 8
    • 0025775913 scopus 로고
    • Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins
    • 10.1007/BF02102652 1908021
    • D'Onofrio G Mouchiroud D Aissani B Gautier C Bernardi G Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 1991, 32:504-510. 10.1007/ BF02102652 1908021
    • (1991) J Mol Evol , vol.32 , pp. 504-510
    • D'Onofrio, G.1    Mouchiroud, D.2    Aissani, B.3    Gautier, C.4    Bernardi, G.5
  • 9
    • 0032509187 scopus 로고    scopus 로고
    • CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families
    • 10.1016/S0378-1119(98)00474-0 9931467
    • Jabbari K Bernardi G CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene 1998, 224:123-127. 10.1016/S0378-1119(98)00474-0 9931467
    • (1998) Gene , vol.224 , pp. 123-127
    • Jabbari, K.1    Bernardi, G.2
  • 10
    • 0343804994 scopus 로고
    • Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA
    • 345730 6281768 10.1073/pnas.79.2.355
    • Meunier-Rotival M Soriano P Cuny G Strauss F Bernardi G Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. Proc Natl Acad Sci USA 1982, 79:355-359. 345730 6281768 10.1073/pnas.79.2.355
    • (1982) Proc Natl Acad Sci USA , vol.79 , pp. 355-359
    • Meunier-Rotival, M.1    Soriano, P.2    Cuny, G.3    Strauss, F.4    Bernardi, G.5
  • 11
    • 0010314873 scopus 로고
    • The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes
    • 393700 6572942 10.1073/pnas.80.7.1816
    • Soriano P Meunier-Rotival M Bernardi G The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. Proc Natl Acad Sci USA 1983, 80:1816-1820. 393700 6572942 10.1073/ pnas.80.7.1816
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 1816-1820
    • Soriano, P.1    Meunier-Rotival, M.2    Bernardi, G.3
  • 12
    • 33846609144 scopus 로고    scopus 로고
    • Human chromosomal bands: Nested structure, high-definition map and molecular basis
    • 10.1007/s00412-006-0078-0 17072634
    • Costantini M Clay O Federico C Saccone S Auletta F Bernardi G Human chromosomal bands: Nested structure, high-definition map and molecular basis. Chromosoma 2006, 116:29-40. 10.1007/s00412-006-0078-0 17072634
    • (2006) Chromosoma , vol.116 , pp. 29-40
    • Costantini, M.1    Clay, O.2    Federico, C.3    Saccone, S.4    Auletta, F.5    Bernardi, G.6
  • 13
    • 0026771276 scopus 로고
    • The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes
    • 49198 1594593 10.1073/pnas.89.11.4913
    • Saccone S De Sario A Della Valle G Bernardi G The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci USA 1992, 89:4913-4917. 49198 1594593 10.1073/pnas.89.11.4913
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 4913-4917
    • Saccone, S.1    De Sario, A.2    Della Valle, G.3    Bernardi, G.4
  • 14
    • 0027136190 scopus 로고
    • Correlations between isochores and chromosomal bands in the human genome
    • 48098 8265650 10.1073/pnas.90.24.11929
    • Saccone S De Sario A Wiegant J Raap AK Della Valle G Bernardi G Correlations between isochores and chromosomal bands in the human genome. Proc Natl Acad Sci USA 1993, 90:11929-11933. 48098 8265650 10.1073/pnas.90.24.11929
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11929-11933
    • Saccone, S.1    De Sario, A.2    Wiegant, J.3    Raap, A.K.4    Della Valle, G.5    Bernardi, G.6
  • 15
    • 0033804748 scopus 로고    scopus 로고
    • An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibrium
    • 1287892 10978227 10.1086/303085
    • Eisenbarth I Vogel G Krone W Vogel W Assum G An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibrium. Am J Hum Genet 2000, 67:873-880. 1287892 10978227 10.1086/303085
    • (2000) Am J Hum Genet , vol.67 , pp. 873-880
    • Eisenbarth, I.1    Vogel, G.2    Krone, W.3    Vogel, W.4    Assum, G.5
  • 16
    • 0034989085 scopus 로고    scopus 로고
    • Local rates of recombination are positively correlated with GC content in the human genome
    • 11371603
    • Fullerton SM Bernardo Carvalho A Clark AG Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol 2001, 18:1139-1142. 11371603
    • (2001) Mol Biol Evol , vol.18 , pp. 1139-1142
    • Fullerton, S.M.1    Bernardo Carvalho, A.2    Clark, A.G.3
  • 18
    • 33645530758 scopus 로고    scopus 로고
    • An isochore map of human chromosomes
    • 1457033 16597586 10.1101/gr.4910606
    • Costantini M Clay O Auletta F Bernardi G An isochore map of human chromosomes. Genome Res 2006, 16:536-541. 1457033 16597586 10.1101/ gr.4910606
    • (2006) Genome Res , vol.16 , pp. 536-541
    • Costantini, M.1    Clay, O.2    Auletta, F.3    Bernardi, G.4
  • 19
    • 34247118340 scopus 로고    scopus 로고
    • Discovering isochores by least-squares optimal segmentation
    • 10.1016/j.gene.2007.01.028 17389148
    • Haiminen N Mannila H Discovering isochores by least-squares optimal segmentation. Gene 2007, 394:53-60. 10.1016/j.gene.2007.01.028 17389148
    • (2007) Gene , vol.394 , pp. 53-60
    • Haiminen, N.1    Mannila, H.2
  • 20
    • 2942560068 scopus 로고    scopus 로고
    • IsoFinder: Computational prediction of isochores in genome sequences
    • 441537 15215396 10.1093/nar/gkh399
    • Oliver JL Carpena P Hackenberg M Bernaola-Galvan P IsoFinder: computational prediction of isochores in genome sequences. Nucleic Acids Res 2004, 32:W287-292. 441537 15215396 10.1093/nar/gkh399
    • (2004) Nucleic Acids Res , vol.32
    • Oliver, J.L.1    Carpena, P.2    Hackenberg, M.3    Bernaola-Galvan, P.4
  • 21
    • 0035186281 scopus 로고    scopus 로고
    • Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software
    • 10.1093/bioinformatics/17.11.1065 11724737
    • Ramensky VE Makeev VJ Roytberg MA Tumanyan VG Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software. Bioinformatics 2001, 17:1065-1066. 10.1093/bioinformatics/ 17.11.1065 11724737
    • (2001) Bioinformatics , vol.17 , pp. 1065-1066
    • Ramensky, V.E.1    Makeev, V.J.2    Roytberg, M.A.3    Tumanyan, V.G.4
  • 23
    • 0034755052 scopus 로고    scopus 로고
    • A novel method to calculate the G+C content of genomic DNA sequences
    • 11697737
    • Zhang CT Wang J Zhang R A novel method to calculate the G+C content of genomic DNA sequences. J Biomol Struct Dyn 2001, 19:333-341. 11697737
    • (2001) J Biomol Struct Dyn , vol.19 , pp. 333-341
    • Zhang, C.T.1    Wang, J.2    Zhang, R.3
  • 24
    • 0035407214 scopus 로고    scopus 로고
    • The evolution of isochores
    • 10.1038/35080577 11433361
    • Eyre-Walker A Hurst LD The evolution of isochores. Nat Rev Genet 2001, 2:549-555. 10.1038/35080577 11433361
    • (2001) Nat Rev Genet , vol.2 , pp. 549-555
    • Eyre-Walker, A.1    Hurst, L.D.2
  • 25
    • 47749115552 scopus 로고    scopus 로고
    • IsoBase http://www.geneinfo.eu/isobase/
    • IsoBase
  • 26
    • 0024805395 scopus 로고
    • The isochore organization of the human genome
    • 10.1146/annurev.ge.23.120189.003225 2694946
    • Bernardi G The isochore organization of the human genome. Annu Rev Genet 1989, 23:637-661. 10.1146/annurev.ge.23.120189.003225 2694946
    • (1989) Annu Rev Genet , vol.23 , pp. 637-661
    • Bernardi, G.1
  • 27
    • 0030603239 scopus 로고    scopus 로고
    • The gene distribution of the human genome
    • 10.1016/0378-1119(96)00393-9 8863734
    • Zoubak S Clay O Bernardi G The gene distribution of the human genome. Gene 1996, 174:95-102. 10.1016/0378-1119(96)00393-9 8863734
    • (1996) Gene , vol.174 , pp. 95-102
    • Zoubak, S.1    Clay, O.2    Bernardi, G.3
  • 28
    • 34347222211 scopus 로고    scopus 로고
    • The neoselectionist theory of genome evolution
    • 1866311 17494746 10.1073/pnas.0701652104
    • Bernardi G The neoselectionist theory of genome evolution. Proc Natl Acad Sci USA 2007, 104:8385-8390. 1866311 17494746 10.1073/ pnas.0701652104
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 8385-8390
    • Bernardi, G.1
  • 29
    • 0030560766 scopus 로고    scopus 로고
    • Base composition and gene distribution: Critical patterns in mammalian genome organization
    • 10.1016/S0168-9525(97)81400-X 9257535
    • Gardiner K Base composition and gene distribution: Critical patterns in mammalian genome organization. Trends Genet 1996, 12:519-524. 10.1016/ S0168-9525(97)81400-X 9257535
    • (1996) Trends Genet , vol.12 , pp. 519-524
    • Gardiner, K.1
  • 30
    • 33847343427 scopus 로고    scopus 로고
    • Isochores and replication time zones: A perfect match
    • 10.1159/000098182 17317955
    • Schmegner C Hameister H Vogel W Assum G Isochores and replication time zones: A perfect match. Cytogenet Genome Res 2007, 116:167-172. 10.1159/ 000098182 17317955
    • (2007) Cytogenet Genome Res , vol.116 , pp. 167-172
    • Schmegner, C.1    Hameister, H.2    Vogel, W.3    Assum, G.4
  • 31
    • 13744263543 scopus 로고    scopus 로고
    • Noncoding DNA, isochores and gene expression: Nucleosome formation potential
    • 548339 15673716 10.1093/nar/gki184
    • Vinogradov AE Noncoding DNA, isochores and gene expression: Nucleosome formation potential. Nucleic Acids Res 2005, 33:559-563. 548339 15673716 10.1093/nar/gki184
    • (2005) Nucleic Acids Res , vol.33 , pp. 559-563
    • Vinogradov, A.E.1
  • 32
    • 40449128815 scopus 로고    scopus 로고
    • Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions
    • 10.1101/gr.7010208 18230801
    • Darai-Ramqvist E Sandlund A Muller S Klein G Imreh S Kost-Alimova M Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res 2008, 18:370-379. 10.1101/gr.7010208 18230801
    • (2008) Genome Res , vol.18 , pp. 370-379
    • Darai-Ramqvist, E.1    Sandlund, A.2    Muller, S.3    Klein, G.4    Imreh, S.5    Kost-Alimova, M.6
  • 33
    • 0035802383 scopus 로고    scopus 로고
    • Compositional heterogeneity within and among isochores in mammalian genomes. II. Some general comments
    • 10.1016/S0378-1119(01)00668-0 11591468
    • Clay O Bernardi G Compositional heterogeneity within and among isochores in mammalian genomes. II. Some general comments. Gene 2001, 276:25-31. 10.1016/S0378-1119(01)00668-0 11591468
    • (2001) Gene , vol.276 , pp. 25-31
    • Clay, O.1    Bernardi, G.2
  • 35
    • 0347503105 scopus 로고    scopus 로고
    • Statistical methods for DNA sequence segmentation
    • 10.1214/ss/1028905933
    • Braun JV Müller H-G Statistical methods for DNA sequence segmentation. Stat Sci 1998, 13:142-162. 10.1214/ss/1028905933
    • (1998) Stat Sci , vol.13 , pp. 142-162
    • Braun, J.V.1    Müller, H.-G.2
  • 36
    • 37849187605 scopus 로고    scopus 로고
    • A computational prediction of isochores based on hidden Markov models
    • 10.1016/j.gene.2006.04.032 17020791
    • Melodelima C Guéguen L Piau D Gautier C A computational prediction of isochores based on hidden Markov models. Gene 2006, 385:41-49. 10.1016/j.gene.2006.04.032 17020791
    • (2006) Gene , vol.385 , pp. 41-49
    • Melodelima, C.1    Guéguen, L.2    Piau, D.3    Gautier, C.4
  • 42
    • 33748680771 scopus 로고    scopus 로고
    • PROMPT: A protein mapping and comparison tool
    • 1569443 16817977 10.1186/1471-2105-7-331
    • Schmidt T Frishman D PROMPT: A protein mapping and comparison tool. BMC Bioinformatics 2006, 7:331. 1569443 16817977 10.1186/1471-2105-7-331
    • (2006) BMC Bioinformatics , vol.7 , pp. 331
    • Schmidt, T.1    Frishman, D.2
  • 44
    • 34347390455 scopus 로고    scopus 로고
    • Comparing segmentations by applying randomization techniques
    • 1904250 17521423 10.1186/1471-2105-8-171
    • Haiminen N Mannila H Terzi E Comparing segmentations by applying randomization techniques. BMC Bioinformatics 2007, 8:171. 1904250 17521423 10.1186/1471-2105-8-171
    • (2007) BMC Bioinformatics , vol.8 , pp. 171
    • Haiminen, N.1    Mannila, H.2    Terzi, E.3
  • 46
    • 34547493467 scopus 로고    scopus 로고
    • Isochore patterns and gene distributions in fish genomes
    • 10.1016/j.ygeno.2007.05.006 17590311
    • Costantini M Auletta F Bernardi G Isochore patterns and gene distributions in fish genomes. Genomics 2007, 90:364-371. 10.1016/ j.ygeno.2007.05.006 17590311
    • (2007) Genomics , vol.90 , pp. 364-371
    • Costantini, M.1    Auletta, F.2    Bernardi, G.3
  • 47
    • 18844379386 scopus 로고    scopus 로고
    • The biased distribution of Alus in human isochores might be driven by recombination
    • 10.1007/s00239-004-0197-2 15871047
    • Hackenberg M Bernaola-Galvan P Carpena P Oliver JL The biased distribution of Alus in human isochores might be driven by recombination. J Mol Evol 2005, 60:365-377. 10.1007/s00239-004-0197-2 15871047
    • (2005) J Mol Evol , vol.60 , pp. 365-377
    • Hackenberg, M.1    Bernaola-Galvan, P.2    Carpena, P.3    Oliver, J.L.4
  • 48
    • 0019085555 scopus 로고
    • An analysis of fish genomes by density gradient centrifugation
    • 10.1111/j.1432-1033.1980.tb07195.x 7460919
    • Hudson AP Cuny G Cortadas J Haschemeyer AE Bernardi G An analysis of fish genomes by density gradient centrifugation. Eur J Biochem 1980, 112:203-210. 10.1111/j.1432-1033.1980.tb07195.x 7460919
    • (1980) Eur J Biochem , vol.112 , pp. 203-210
    • Hudson, A.P.1    Cuny, G.2    Cortadas, J.3    Haschemeyer, A.E.4    Bernardi, G.5
  • 49
    • 0037036937 scopus 로고    scopus 로고
    • An ultracentrifugation analysis of two hundred fish genomes
    • 10.1016/S0378-1119(02)00733-3 12354649
    • Bucciarelli G Bernardi G Bernardi G An ultracentrifugation analysis of two hundred fish genomes. Gene 2002, 295:153-162. 10.1016/ S0378-1119(02)00733-3 12354649
    • (2002) Gene , vol.295 , pp. 153-162
    • Bucciarelli, G.1    Bernardi, G.2    Bernardi, G.3
  • 50
    • 21244500957 scopus 로고    scopus 로고
    • Logistic model trees
    • 10.1007/s10994-005-0466-3
    • Landwehr N Hall M Eibe F Logistic model trees. Machine Learning 2005, 95:161-205. 10.1007/s10994-005-0466-3
    • (2005) Machine Learning , vol.95 , pp. 161-205
    • Landwehr, N.1    Hall, M.2    Eibe, F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.