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Volumn 423, Issue 6937, 2003, Pages 241-254

Sequencing and comparison of yeast species to identify genes and regulatory elements

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; BIOTECHNOLOGY; CELLS; GENES; GENETIC ENGINEERING;

EID: 0038349948     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01644     Document Type: Article
Times cited : (1469)

References (50)
  • 1
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563-567 (1996).
    • (1996) Science , vol.274 , pp. 546
    • Goffeau, A.1
  • 2
    • 0032800891 scopus 로고    scopus 로고
    • Total number of coding open reading frames in the yeast genome
    • Kowalczuk, M., Mackiewicz, P., Gierlik, A., Dudek, M. R. & Cebrat, S. Total number of coding open reading frames in the yeast genome. Yeast 15, 1031-1034 (1999).
    • (1999) Yeast , vol.15 , pp. 1031-1034
    • Kowalczuk, M.1    Mackiewicz, P.2    Gierlik, A.3    Dudek, M.R.4    Cebrat, S.5
  • 3
    • 0036493224 scopus 로고    scopus 로고
    • A question of size: The eukaryotic proteome and the problems in defining it
    • Harrison, P. M., Kumar, A., Lang, N., Snyder, M. & Gerstein, M. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 30, 1083-1090 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1083-1090
    • Harrison, P.M.1    Kumar, A.2    Lang, N.3    Snyder, M.4    Gerstein, M.5
  • 4
    • 0031442518 scopus 로고    scopus 로고
    • Characterization of the yeast transcriptome
    • Velculescu, V. E. et al. Characterization of the yeast transcriptome. Cell 88, 243-251 (1997).
    • (1997) Cell , vol.88 , pp. 243-251
    • Velculescu, V.E.1
  • 5
    • 0034704277 scopus 로고    scopus 로고
    • Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited
    • Blandin, G. et al. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett. 487, 31-36 (2000).
    • (2000) FEBS Lett. , vol.487 , pp. 31-36
    • Blandin, G.1
  • 7
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • International Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
    • (2002) Nature , vol.420 , pp. 520-562
  • 8
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 10
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo, G. D. DNA binding sites: representation and discovery. Bioinformatics 16, 16-23 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 11
    • 0033918228 scopus 로고    scopus 로고
    • Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
    • McGuire, A. M., Hughes, J. D. & Church, G. M. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10, 744-757 (2000).
    • (2000) Genome Res. , vol.10 , pp. 744-757
    • McGuire, A.M.1    Hughes, J.D.2    Church, G.M.3
  • 12
    • 0034616398 scopus 로고    scopus 로고
    • Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
    • Loots, G. G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136-140 (2000).
    • (2000) Science , vol.288 , pp. 136-140
    • Loots, G.G.1
  • 13
    • 0035261381 scopus 로고    scopus 로고
    • Genomic strategies to identify mammalian regulatory sequences
    • Pennacchio, L. A. & Rubin, E. M. Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet. 2, 100-109 (2001).
    • (2001) Nature Rev. Genet. , vol.2 , pp. 100-109
    • Pennacchio, L.A.1    Rubin, E.M.2
  • 14
    • 0030966052 scopus 로고    scopus 로고
    • Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains
    • Oeltjen, J. C. et al. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 7, 315-329 (1997).
    • (1997) Genome Res. , vol.7 , pp. 315-329
    • Oeltjen, J.C.1
  • 15
    • 0034919548 scopus 로고    scopus 로고
    • Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
    • Cliften, P. F. et al. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11, 1175-1186 (2001).
    • (2001) Genome Res. , vol.11 , pp. 1175-1186
    • Cliften, P.F.1
  • 16
    • 0033552961 scopus 로고    scopus 로고
    • Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
    • Alm, R. A. et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176-180 (1999).
    • (1999) Nature , vol.397 , pp. 176-180
    • Alm, R.A.1
  • 17
    • 0037015592 scopus 로고    scopus 로고
    • Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    • Carlton, J. M. et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512-519 (2002).
    • (2002) Nature , vol.419 , pp. 512-519
    • Carlton, J.M.1
  • 18
    • 0036893449 scopus 로고    scopus 로고
    • Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species
    • Perrin, A. et al. Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. Infect. Immun. 70, 7063-7072 (2002).
    • (2002) Infect. Immun. , vol.70 , pp. 7063-7072
    • Perrin, A.1
  • 19
    • 0034671842 scopus 로고    scopus 로고
    • Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi
    • McClelland, M. et al. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 28, 4974-4986 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4974-4986
    • McClelland, M.1
  • 20
    • 0036144823 scopus 로고    scopus 로고
    • ARACHNE: A whole-genome shotgun assembler
    • Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177-189 (2002).
    • (2002) Genome Res. , vol.12 , pp. 177-189
    • Batzoglou, S.1
  • 21
    • 0037015614 scopus 로고    scopus 로고
    • Genome sequence of the human malaria parasite Plasmodium falciparum
    • Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511 (2002).
    • (2002) Nature , vol.419 , pp. 498-511
    • Gardner, M.J.1
  • 23
    • 0037058930 scopus 로고    scopus 로고
    • Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae
    • Dunham, M. J. et al. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 99, 16144-16149 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16144-16149
    • Dunham, M.J.1
  • 24
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739-748 (2002).
    • (2002) Genome Res. , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 25
    • 0035215378 scopus 로고    scopus 로고
    • Evolution of gene order in the genomes of two related yeast species
    • Fischer, G., Neuveglise, C., Durrens, P., Gaillardin, C. & Dujon, B. Evolution of gene order in the genomes of two related yeast species. Genome Res. 11, 2009-2019 (2001).
    • (2001) Genome Res. , vol.11 , pp. 2009-2019
    • Fischer, G.1    Neuveglise, C.2    Durrens, P.3    Gaillardin, C.4    Dujon, B.5
  • 26
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713 (1997).
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 27
    • 0034704326 scopus 로고    scopus 로고
    • Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum
    • Bon, E. et al. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum. FEBS Lett. 487, 37-41 (2000).
    • (2000) FEBS Lett. , vol.487 , pp. 37-41
    • Bon, E.1
  • 28
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
    • (2001) Nature , vol.409 , pp. 860-921
  • 29
    • 0028301199 scopus 로고
    • Complete DNA sequence of yeast chromosome XI
    • Dujon, B. et al. Complete DNA sequence of yeast chromosome XI. Nature 369, 371-378 (1994).
    • (1994) Nature , vol.369 , pp. 371-378
    • Dujon, B.1
  • 30
    • 0023650543 scopus 로고
    • The codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M. & Li, W. H. The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281-1295 (1987).
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 31
    • 0037012922 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA processing in yeast using splicing-specific microarrays
    • Clark, T. A., Sugnet, C. W. & Ares, M. Jr Genome-wide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907-910 (2002).
    • (2002) Science , vol.296 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares Jr., M.3
  • 32
    • 0036720020 scopus 로고    scopus 로고
    • The Ka/Ks ratio: Diagnosing the form of sequence evolution
    • Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18, 486 (2002).
    • (2002) Trends Genet. , vol.18 , pp. 486
    • Hurst, L.D.1
  • 33
    • 0032561246 scopus 로고    scopus 로고
    • The transcriptional program of sporulation in budding yeast
    • Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
    • (1998) Science , vol.282 , pp. 699-705
    • Chu, S.1
  • 34
    • 0034727077 scopus 로고    scopus 로고
    • A yeast prion provides a mechanism for genetic variation and phenotypic diversity
    • True, H. L. & Lindquist, S. L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477-483 (2000).
    • (2000) Nature , vol.407 , pp. 477-483
    • True, H.L.1    Lindquist, S.L.2
  • 35
    • 0036184347 scopus 로고    scopus 로고
    • Adaptation for horizontal transfer in a homing endonuclease
    • Koufopanou, V., Goddard, M. R. & Burt, A. Adaptation for horizontal transfer in a homing endonuclease. Mol. Biol. Evol. 19, 239-246 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 239-246
    • Koufopanou, V.1    Goddard, M.R.2    Burt, A.3
  • 36
    • 0032412476 scopus 로고    scopus 로고
    • Mating-type gene switching in Saccharomyces cerevisiae
    • Haber, J. E. Mating-type gene switching in Saccharomyces cerevisiae. Annu. Rev. Genet. 32, 561-599 (1998).
    • (1998) Annu. Rev. Genet. , vol.32 , pp. 561-599
    • Haber, J.E.1
  • 37
    • 0035999971 scopus 로고    scopus 로고
    • Distribution patterns of over-represented k-mers in non-coding yeast DNA
    • Hampson, S., Kibler, D. & Baldi, P. Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 18, 513-528 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 513-528
    • Hampson, S.1    Kibler, D.2    Baldi, P.3
  • 38
    • 0035253676 scopus 로고    scopus 로고
    • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
    • McCue, L. et al. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29, 774-782 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 774-782
    • McCue, L.1
  • 39
    • 0034141782 scopus 로고    scopus 로고
    • Prediction of transcription regulatory sites in Archaea by a comparative genomic approach
    • Gelfand, M. S., Koonin, E. V. & Mironov, A. A. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res. 28, 695-705 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 695-705
    • Gelfand, M.S.1    Koonin, E.V.2    Mironov, A.A.3
  • 40
    • 0022622235 scopus 로고
    • Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein
    • Keegan, L., Gill, G. & Ptashne, M. Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231, 699-704 (1986).
    • (1986) Science , vol.231 , pp. 699-704
    • Keegan, L.1    Gill, G.2    Ptashne, M.3
  • 41
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: A promoter database of the yeast Saccharomyces cerevisiae
    • Zhu, J. & Zhang, M. Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607-611 (1999).
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2
  • 42
    • 0032893083 scopus 로고    scopus 로고
    • MIPS: A database for genomes and protein sequences
    • Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27, 44-48 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 44-48
    • Mewes, H.W.1
  • 43
    • 0036087548 scopus 로고    scopus 로고
    • Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
    • Dwight, S. S. et al. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69-72 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 69-72
    • Dwight, S.S.1
  • 44
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1
  • 45
    • 0037057374 scopus 로고    scopus 로고
    • Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    • RESEARCH0059
    • Gasch, A. P. & Eisen, M. B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 3 RESEARCH0059 (2002).
    • (2002) Genome Biol. , vol.3
    • Gasch, A.P.1    Eisen, M.B.2
  • 46
    • 0037855780 scopus 로고    scopus 로고
    • Glucose-mediated phosphorylation converts the transcription factor Rgt1 from a repressor to an activator
    • Mosley, A. L., Lakshmanan, J., Aryal, B. K. & Ozcan, S. Glucose-mediated phosphorylation converts the transcription factor Rgt1 from a repressor to an activator. J. Biol. Chem. 278, 10322-10327 (2003).
    • (2003) J. Biol. Chem. , vol.278 , pp. 10322-10327
    • Mosley, A.L.1    Lakshmanan, J.2    Aryal, B.K.3    Ozcan, S.4
  • 47
    • 0034405703 scopus 로고    scopus 로고
    • The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1 transcriptional repressor
    • Lindgren, A. et al. The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1 transcriptional repressor. EMBO J. 19, 6489-6497 (2000).
    • (2000) EMBO J. , vol.19 , pp. 6489-6497
    • Lindgren, A.1
  • 48
    • 0343750650 scopus 로고    scopus 로고
    • Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae
    • Jacobs Anderson, J. S. & Parker, R. Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res. 28, 1604-1617 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1604-1617
    • Jacobs Anderson, J.S.1    Parker, R.2
  • 49
    • 0037722938 scopus 로고    scopus 로고
    • Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
    • Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395-404 (2003).
    • (2003) Cell , vol.113 , pp. 395-404
    • Zeitlinger, J.1
  • 50
    • 0033925018 scopus 로고    scopus 로고
    • Activation of the Kss1 invasive-filamentous growth pathway induces Ty1 transcription and retrotransposition in Saccharomyces cerevisiae
    • Morillon, A., Springer, M. & Lesage, P. Activation of the Kss1 invasive-filamentous growth pathway induces Ty1 transcription and retrotransposition in Saccharomyces cerevisiae. Mol. Cell Biol. 20, 5766-5776 (2000).
    • (2000) Mol. Cell Biol. , vol.20 , pp. 5766-5776
    • Morillon, A.1    Springer, M.2    Lesage, P.3


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