Genomic and Postgenomic Research

  • Vassil St. GeorgievEmail author
Part of the Infectious Disease book series (ID)

The word genomics was first coined by T. Roderick from the Jackson Laboratories in 1986 as the name for the new field of science focused on the analysis and comparison of complete genome sequences of organisms and related high-throughput technologies.


West Nile Virus Complete Genome Sequence Genome Sequencing Project Bacillus Anthracis Pathogenicity Island 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Smith, H. O. (2004) History of microbial genomics. In: Microbial Genomes (Fraser, C. M., Read, T. D., and Nelson, K. E., eds.), Humana Press, Totowa, NJ, pp. 3–16.Google Scholar
  2. 2.
    Salzberg, S. L. and Delcher, A. L. (2004) Tools for gene finding and whole genome comparison. In: Microbial Genomes (Fraser, C. M., Read, T. D., and Nelson, K. E., eds.), Humana Press, Totowa, NJ, pp. 19–31.Google Scholar
  3. 3.
    Salzberg, S. L., Pertea, M., Delcher, A. L., Gardner, M. J., and Tettelin, H. (1999). Interpolated Markov models for eukaryotic gene finding, Genomics, 59, 24–31.PubMedCrossRefGoogle Scholar
  4. 4.
    Pertea, M. and Salzberg, S. L. (2002) Computational gene finding in plants, Plant Mol. Biol., 48, 39–48.PubMedCrossRefGoogle Scholar
  5. 5.
    Parkhill, J. and Thomson, N. R. (2004) The genomes of pathogenic Enterobacteria. In: Microbial Genomes (Fraser, C. M., Read, T. D., and Nelson, K. E., eds.), Humana Press, Totowa, NJ, pp. 269–289.Google Scholar
  6. 6.
    Blattner, F. R., Plunkett, G., Bloch, C. A., et al. (1997) The complete genome sequence of Escherichia coli K-12, Science, 277, 1453–1474.PubMedCrossRefGoogle Scholar
  7. 7.
    Perna, N. T., Plunkett, G., 3rd, Burland, V., et al. (2001) Genome sequence of enterohemorrhagic Escherichia coli O157:H7, Nature, 409, 529–533.Google Scholar
  8. 8.
    Hayashi, T., Makino, K., Ohnishi, M., et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12, DNA Res., 8, 11–22.PubMedCrossRefGoogle Scholar
  9. 9.
    Welch, R. A., Burland, V., Plunkett, G. 3rd, et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. U.S.A., 99, 17020–17024.PubMedCrossRefGoogle Scholar
  10. 10.
    Jin, Q., Yuan, Z., Xu, J., et al. (2002) Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Res., 30, 4432–4441.PubMedCrossRefGoogle Scholar
  11. 11.
    Knapp, S., Hacker, J., Jarchau, T., and Goebel, W. (1986) Large, unstable inserts in the chromosome affect virulence properties of uropathogenic Escherichia coli O6 strain 536, J. Bacteriol., 168, 22–30.PubMedGoogle Scholar
  12. 12.
    Levine, M. M. (1987) Escherichia coli that cause diarrhea: enterotoxigenic, enteropathogenic, enteroinvasive, enterohemorrhagic, and enteroadherent, J. Infect. Dis., 155, 377–389.PubMedGoogle Scholar
  13. 13.
    Hacker, J., Blum-Oehler, G., Muhldorfer, I., and Tschape, H. (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution, Mol. Microbiol., 23, 1089–1097.PubMedCrossRefGoogle Scholar
  14. 14.
    Blum, G., Ott, M., Lischewski, A., et al. (1994) Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen, Infect. Immunol., 62, 606–614.Google Scholar
  15. 15.
    Parkhill, J., Dougan, G., James, K. D., et al. (2001) Complete genome sequence of multiple drug resistant Salmonella enterica serovar Typhi CT18, Nature, 413, 848–852.PubMedCrossRefGoogle Scholar
  16. 16.
    McClelland, M., Sanderson, K. E., Spieth, J., et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2, Nature, 413, 852–856.PubMedCrossRefGoogle Scholar
  17. 17.
    Reeves, P. and Stevenson, G. (1989) Cloning and nucleotide sequence of the Salmonella typhimurium LT2 gnd gene and its homology with the corresponding sequence of Escherichia coli K12, Mol. Gen. Genet., 217, 182–184.PubMedCrossRefGoogle Scholar
  18. 18.
    Mills, D. M., Bajaj, V., and Lee, C. A. (1995) A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K-12 chromosome, Mol. Microbiol. 15, 749–759.PubMedCrossRefGoogle Scholar
  19. 19.
    Galan, J. E. (1996) Molecular genetic bases of Salmonella entry into host cells, Mol. Microbiol., 20, 263–271.PubMedCrossRefGoogle Scholar
  20. 20.
    Shea, J. E., Hensel, M., Gleeson, C., and Holden, D. W. (1996) Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium, Proc. Natl. Acad. Sci. U.S.A., 93, 2593–2597.PubMedCrossRefGoogle Scholar
  21. 21.
    Ochman, H., Soncini, F. C., Solomon, F., and Groisman, E. A. (1996) Identification of a pathogenicity island required for Salmonella survival in host cells, Proc. Natl. Acad. Sci. U.S.A., 93, 7800–7804.PubMedCrossRefGoogle Scholar
  22. 22.
    Kingsley, R. A. and Baumler, A. J. (2002) Pathogenicity islands and host adaptation of Salmonella serovars, Curr. Top. Microbiol. Immunol., 264, 67–87.PubMedGoogle Scholar
  23. 23.
    Blanc-Potard, A. B. and Groisman, E. A. (1997) The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival, EMBO J., 16, 5376–5385.PubMedCrossRefGoogle Scholar
  24. 24.
    Buchrieser, C., Prentice, M., and Carniel, E. (1998) The 102-kb unstable region of Yersinia pestis comprises a high-pathogenicity island linked to a pigmentation segment which undergoes internal rearrangement, J. Bacteriol., 180, 2321–2329.PubMedGoogle Scholar
  25. 25.
    Reiter, W. D., Palm, P., and Yeats, S. (1989) Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements, Nucleic Acid Res., 17, 1907–1914.PubMedCrossRefGoogle Scholar
  26. 26.
    Makino, K., Yokoyama, K., Kubota, Y., et al. (1999) Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak, Genes Genet. Syst., 74, 227–239.PubMedCrossRefGoogle Scholar
  27. 27.
    Mosig, G., Yu, S., Myung, H., et al. (1997) A novel mechanism of virus-virus interactions: bacteriophage P2 Tin protein inhibits phage T4 DNA synthesis by poisoning the T4 single-stranded DNA binding protein, go32, Virology, 230, 72–81.PubMedCrossRefGoogle Scholar
  28. 28.
    Myung, H. and Calendar, R. (1995) The old exonuclease of bacteriophage P2, J. Bacteriol., 177, 497–501.PubMedGoogle Scholar
  29. 29.
    Davis, B. M. and Waldor, M. K. (2003) Filamentous phages linked to virulence of Vibrio cholerae, Curr. Opin. Microbiol., 6, 35–42.PubMedCrossRefGoogle Scholar
  30. 30.
    Donohue-Rolfe, A., Acheson, D. W., and Keusch, G. T. (1999) Shiga toxin: purification, structure, and function, Rev. Infect. Dis., 13(Suppl. 4), S293–S297.Google Scholar
  31. 31.
    Parkhill, J., Wren, B. W., Thomson, N. R., et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague, Nature, 413, 523–527.PubMedCrossRefGoogle Scholar
  32. 32.
    Hansen-Wester, I. and Hensel, M. (2001) Salmonella pathogenicity islands encoding type III secretion systems, Microbes Infect., 3, 549–559.PubMedCrossRefGoogle Scholar
  33. 33.
    Lostroh, C. P. and Lee, C. A. (2001) The Salmonella pathogenicity island-1 type III secretion system, Microbes Infect., 3, 1281–1291.PubMedCrossRefGoogle Scholar
  34. 34.
    Swartley, J. S., Marfin, A. A., Edupuganti, S., et al. (1997) Capsule switching of Neisseria meningitides, Proc. Natl. Acad. Sci. U.S.A., 94, 271–276.PubMedCrossRefGoogle Scholar
  35. 35.
    Dillard, J. P., Caimano, M., Kelly, T., and Yother, J. (1995) Capsules and cassettes: genetic organization of the capsule locus of Streptococcus pneumoniae, Dev. Biol. Stand., 85, 261–265.PubMedGoogle Scholar
  36. 36.
    Dillard, J. P. and Yother, J. (1994) Genetic and molecular characterization of capsular polysaccharide biosynthesis in Streptococcus pneumoniae type 3, Mol. Microbiol., 12, 959–972.PubMedCrossRefGoogle Scholar
  37. 37.
    Cole, S. T., Eiglmeier, K., Parkhill, J., et al. (2001) Massive gene decay in the leprosy bacillus, Nature, 409, 1007–1011.PubMedCrossRefGoogle Scholar
  38. 38.
    Perry, R. D. and Fetherston, J. D. (1997) Yersinia pestis – etiologic agent of plague, Clin. Microbiol. Rev., 10, 35–66.PubMedGoogle Scholar
  39. 39.
    Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A., and Carniel, E. (1999) Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis, Proc. Natl. Acad. Sci. U.S.A., 96, 14043–14048.PubMedCrossRefGoogle Scholar
  40. 40.
    Birkelund, S., Vandahl, B. B., Shaw, A. C., and Christiansen, G. (2004) Microbial proteomics. In: Microbial Genomes (Fraser, C. M., Read, T. D., and Nelson, K. E., eds.), Humana Press, Totowa, NJ, pp. 517–530.Google Scholar
  41. 41.
    Wilkins, M. P., Pasquali, C., Appel, R. D., et al. (1996) From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis, Biotechnology (NY), 14, 61–65.CrossRefGoogle Scholar
  42. 42.
    Santoni, V., Molloy, M., and Rabilloud, T. (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis, 21, 1054–1070.PubMedCrossRefGoogle Scholar
  43. 43.
    Adessi, C., Miege, C., Albrieux, C., and Rabilloud, T. (1997) Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients, Electrophoresis, 18, 127–135.PubMedCrossRefGoogle Scholar
  44. 44.
    Righetti, P. G. and Gianazza, E. (1980) New developments in isoelectric focusing, J. Chromatogr., 184, 415–456.PubMedCrossRefGoogle Scholar
  45. 45.
    Bjellqvist, B., Ek, K., Righetti, P. G., et al. (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications, J. Biochem. Biophys. Methods, 6, 317–339.PubMedCrossRefGoogle Scholar
  46. 46.
    Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons, Analyt. Chem., 60, 2299–2301.CrossRefGoogle Scholar
  47. 47.
    Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules, Science, 246, 64–71.PubMedCrossRefGoogle Scholar
  48. 48.
    Cooks, R. G., Glish, G. L., Kaiser, R. E., and McLuckey, S. A. (1991) Ion trap mass spectrometry, Chem. Eng. News, 69, 26–41.Google Scholar
  49. 49.
    Neuman, B. W., Adair, B. D., Yoshioka, C., Quispe, J. D., Orca, G., Kuhn. P., Milligan, R. A., Yeager, M., and Buchmeier, M. J. (2006) Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy, J. Virol., 80(16),7918–7928.PubMedCrossRefGoogle Scholar
  50. 50.
    Obenauer, J. C., Denson, J., Mehta, P. K., Su, X., Mukatira, S., Finkelstein, D. B., Xu, X., Wang, J., Ma, J., Fan, Y., Rakestraw, K. M., Webster, R. G., Hoffmann, E., Krauss, S., Zheng, J., Zhang, Z., and Naeve, C. W. (2006) Large-scale sequence analysis of avian influenza isolates, Science, 311,1576–1580.PubMedCrossRefGoogle Scholar
  51. 51.
    Ghedin, E., Sengamalay, N. A., Shumway, M., Zaborsky, J., Feldblyum, T., Subbu, V., Spiro, D. J., Sitz, J., Koo, H., Bolotov, P., Dernovoy, D., Tatusova, T., Bao, Y., St. George, K., Taylor, J., Lipman, D. J., Fraser, C.M., Taubenberger, J. K., and Salzberg, S. L. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution, Nature, 437, 1162–1166.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of Health & Human ServicesNational Institutes of HealthBethesdaUSA

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