Sequencing and comparison of yeast species to identify genes and regulatory elements (original) (raw)

• Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563–567 (1996)
  ADS CAS PubMed Google Scholar
• 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)
  Article CAS PubMed Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• Velculescu, V. E. et al. Characterization of the yeast transcriptome. Cell 88, 243–251 (1997)
  Article CAS PubMed Google Scholar
• Blandin, G. et al. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett. 487, 31–36 (2000)
  Article CAS PubMed Google Scholar
• Wood, V., Rutherford, K. M., Ivens, A., Rajandream, M.-A. & Barrell, B. A Re-annotation of the Saccaromyces cerevisiae genome. Comp. Funct. Genomics 2, 143–154 (2001)
  Article CAS PubMed PubMed Central Google Scholar
• International Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
  Article Google Scholar
• 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)
  CAS PubMed Google Scholar
• Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. & Church, G. M. Systematic determination of genetic network architecture. Nature Genet. 22, 281–285 (1999)
  Article CAS PubMed Google Scholar
• Stormo, G. D. DNA binding sites: representation and discovery. Bioinformatics 16, 16–23 (2000)
  Article CAS PubMed Google Scholar
• 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)
  Article CAS PubMed Google Scholar
• 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)
  Article ADS CAS PubMed Google Scholar
• Pennacchio, L. A. & Rubin, E. M. Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet. 2, 100–109 (2001)
  Article CAS PubMed Google Scholar
• 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)
  Article CAS PubMed Google Scholar
• Cliften, P. F. et al. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11, 1175–1186 (2001)
  Article CAS PubMed Google Scholar
• Alm, R. A. et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180 (1999)
  Article ADS PubMed Google Scholar
• Carlton, J. M. et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512–519 (2002)
  Article ADS CAS PubMed Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177–189 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002)
  Article ADS CAS PubMed Google Scholar
• Fischer, G., James, S. A., Roberts, I. N., Oliver, S. G. & Louis, E. J. Chromosomal evolution in Saccharomyces. Nature 405, 451–454 (2000)
  Article ADS CAS PubMed Google Scholar
• Dunham, M. J. et al. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 99, 16144–16149 (2002)
  Article ADS CAS PubMed PubMed Central Google Scholar
• Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739–748 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article CAS PubMed Google Scholar
• Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708–713 (1997)
  Article ADS CAS PubMed Google Scholar
• Bon, E. et al. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum. FEBS Lett. 487, 37–41 (2000)
  Article ADS CAS PubMed Google Scholar
• International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
  Article Google Scholar
• Dujon, B. et al. Complete DNA sequence of yeast chromosome XI. Nature 369, 371–378 (1994)
  Article ADS CAS PubMed Google Scholar
• 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)
  Article ADS CAS PubMed PubMed Central Google Scholar
• 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)
  Article ADS CAS PubMed Google Scholar
• Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18, 486 (2002)
  Article PubMed Google Scholar
• Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699–705 (1998)
  Article ADS CAS PubMed Google Scholar
• True, H. L. & Lindquist, S. L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477–483 (2000)
  Article ADS CAS PubMed Google Scholar
• Koufopanou, V., Goddard, M. R. & Burt, A. Adaptation for horizontal transfer in a homing endonuclease. Mol. Biol. Evol. 19, 239–246 (2002)
  Article CAS PubMed Google Scholar
• Haber, J. E. Mating-type gene switching in Saccharomyces cerevisiae. Annu. Rev. Genet. 32, 561–599 (1998)
  Article CAS PubMed Google Scholar
• Hampson, S., Kibler, D. & Baldi, P. Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 18, 513–528 (2002)
  Article CAS PubMed Google Scholar
• McCue, L. et al. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29, 774–782 (2001)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article ADS CAS PubMed Google Scholar
• Zhu, J. & Zhang, M. Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607–611 (1999)
  Article CAS PubMed Google Scholar
• Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27, 44–48 (1999)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002)
  Article ADS CAS PubMed Google Scholar
• Gasch, A. P. & Eisen, M. B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 3 RESEARCH0059 (2002)
• 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)
  Article CAS PubMed Google Scholar
• Lindgren, A. et al. The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1 transcriptional repressor. EMBO J. 19, 6489–6497 (2000)
  Article CAS PubMed PubMed Central Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar
• Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395–404 (2003)
  Article CAS PubMed Google Scholar
• 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)
  Article CAS PubMed PubMed Central Google Scholar