Chapter 1 : Introduction to Pathogenomics

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This chapter provides an introduction to pathogenomics. Any bacterial genome-sequencing project comprises a number of steps and follows the 80:20 principle: that is, 80%, or more, of the work gets done in 20% of the time, while finishing the job consumes a disproportionate amount of effort. The first stage in any bacterial genome project is to choose one or more strains to sequence. The next stage in a genome-sequencing project is to grow enough bacterial cells to yield sufficient genomic DNA for the creation of a random shotgun library in . Shotgun sequencing continues until an acceptable coverage of the genome has been achieved. The final stage in obtaining a bacterial genome sequence is finishing, during which all gaps are closed and all ambiguities resolved. A number of interesting features can be identified rapidly: repetitive sequences and homopolymeric tracts; noncoding RNA genes (tRNAs, rRNAs, small regulatory RNAs); recently acquired DNA; leading and lagging strands and the origin of replication. An interesting sideline will be the metagenomics of the bacteriophage community, given both the numerical preponderance of phages in the biosphere and their well-established role in the evolution and dissemination of bacterial virulence factors.

Citation: Pallen M. 2007. Introduction to Pathogenomics, p 1-20. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch1

Key Concept Ranking

Bacterial Proteins
Bacteria and Archaea
Type III Secretion System
Nuclear Magnetic Resonance Spectroscopy
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1. Achtman, M.,, K. Zurth,, G. Morelli,, G. Torrea,, A. Guiyoule, and, E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:1404314048.
2. Alm, R. A.,, L. S. Ling,, D. T. Moir,, B. L. King,, E. D. Brown,, P. C. Doig,, D. R. Smith,, B. Noonan,, B. C. Guild,, B. L. deJonge,, G. Carmel,, P. J. Tummino,, A. Caruso,, M. Uria-Nickelsen,, D. M. Mills,, C. Ives,, R. Gibson,, D. Merberg,, S. D. Mills,, Q. Jiang,, D. E. Taylor,, G. F. Vovis, and, T. J. Trust. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176180.
3. Alto, N. M.,, F. Shao,, C. S. Lazar,, R. L. Brost,, G. Chua,, S. Mattoo,, S. A. McMahon,, P. Ghosh,, T. R. Hughes,, C. Boone, and, J. E. Dixon. 2006. Identification of a bacterial type III effector family with G protein mimicry functions. Cell 124:133145.
4. Anderson, S.,, A. T. Bankier,, B. G. Barrell,, M. H. de Bruijn,, A. R. Coulson,, J. Drouin,, I. C. Eperon,, D. P. Nierlich,, B. A. Roe,, F. Sanger,, P. H. Schreier,, A. J. Smith,, R. Staden, and, I. G. Young. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457465.
5. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Ponten,, U. C. Als-mark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson,, H. H. Winkler, and, C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.
6. Andries, K.,, P. Verhasselt,, J. Guillemont,, H. W. Gohlmann,, J. M. Neefs,, H. Winkler,, J. Van Gestel,, P. Timmerman,, M. Zhu,, E. Lee,, P. Williams,, D. de Chaffoy,, E. Huitric,, S. Hoffner,, E. Cambau,, C. Truffot-Pernot,, N. Lounis, and, V. Jarlier. 2005. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307:223227.
7. Arcus, V. L.,, J. S. Lott,, J. M. Johnston, and, E. N. Baker. 2006. The potential impact of structural genomics on tuberculosis drug discovery. Drug Discov. Today 11:2834.
8. Baker, M. D.,, P. M. Wolanin, and, J. B. Stock. 2006. Systems biology of bacterial chemotaxis. Curr. Opin. Microbiol. 9:187192.
9. Bartel, P. L.,, J. A. Roecklein,, D. SenGupta, and, S. Fields. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 12:7277.
10. Bentley, S. D.,, M. Maiwald,, L. D. Murphy,, M. J. Pallen,, C. A. Yeats,, L. G. Dover,, H. T. Norbertczak,, G. S. Besra,, M. A. Quail,, D. E. Harris,, A. von Herbay,, A. Goble,, S. Rutter,, R. Squares,, S. Squares,, B. G. Barrell,, J. Parkhill, and, D. A. Relman. 2003. Sequencing and analysis of the genome of the Whipple’s disease bacterium Tropheryma whipplei. Lancet 361:637644.
11. Beres, S. B.,, E. W. Richter,, M. J. Nagiec,, P. Sumby,, S. F. Porcella,, F. R. DeLeo, and, J. M. Musser. 2006. Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus. Proc. Natl. Acad. Sci. USA 103:70597064.
12. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. May-hew,, J. Gregor,, N. W. Davis,, H. A. Kirk-patrick,, M. A. Goeden,, D. J. Rose,, B. Mau, and, Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
13. Bocs, S.,, A. Danchin, and, C. Medigue. 2002. Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes. BMC Bioinformatics 3:5.
14. Burland, V.,, Y. Shao,, N. T. Perna,, G. Plunkett,, H. J. Sofia, and, F. R. Blattner. 1998. The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res. 26:41964204.
15. Burts, M. L.,, W. A. Williams,, K. DeBord, and, D. M. Missiakas. 2005. EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections. Proc. Natl. Acad. Sci. USA 102:11691174.
16. Call, D. R. 2005. Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol. 31:9199.
17. Camus, J. C.,, M. J. Pryor,, C. Medigue, and, S. T. Cole. 2002. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148:29672973.
18. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:277300.
19. Casjens, S. R. 2005. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Microbiol. 8:451458.
20. Chan, K.,, C. C. Kim, and, S. Falkow. 2005. Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. Infect. Immun. 73:54385449.
21. Chance, M. R.,, A. R. Bresnick,, S. K. Burley,, J. S. Jiang,, C. D. Lima,, A. Sali,, S. C. Almo,, J. B. Bonanno,, J. A. Buglino,, S. Boulton,, H. Chen,, N. Eswar,, G. He,, R. Huang,, V. Ilyin,, L. McMahan,, U. Pieper,, S. Ray,, M. Vidal, and, L. K. Wang. 2002. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 11:723738.
22. Chaudhuri, R. R., and, M. J. Pallen. 2006. xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Res. 34:D335D337.
23. Chen, S. L.,, C. S. Hung,, J. Xu,, C. S. Reigstad,, V. Magrini,, A. Sabo,, D. Blasiar,, T. Bieri,, R. R. Meyer,, P. Ozersky,, J. R. Armstrong,, R. S. Fulton,, J. P. Latreille,, J. Spieth,, T. M. Hooton,, E. R. Mardis,, S. J. Hultgren, and, J. I. Gordon. 2006. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103:59775982.
24. Coito, C.,, D. L. Diamond,, P. Neddermann,, M. J. Korth, and, M. G. Katze. 2004. High-throughput screening of the yeast kinome: identification of human serine/threonine protein kinases that phosphorylate the hepatitis C virus NS5A protein. J. Virol. 78:35023513.
25. Cole, S.T.,, R. Brosch,, J. Parkhill,, T. Garnier,, C. Churcher,, D. Harris,, S. V. Gordon,, K. Eiglmeier,, S. Gas,, C. E. Barry III,, F. Tekaia,, K. Badcock,, D. Basham,, D. Brown,, T. Chill-ingworth,, R. Connor,, R. Davies,, K. Devlin,, T. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, A. Krogh,, J. McLean,, S. Moule,, L. Murphy,, K. Oliver,, J. Osborne,, M. A. Quail,, M. A. Rajandream,, J. Rogers,, S. Rutter,, K. Seeger,, J. Skelton,, R. Squares,, S. Squares,, J. E. Sulston,, K. Taylor,, S. Whitehead, and, B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537544.
26. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, N. Honore,, T. Garnier,, C. Churcher,, D. Harris,, K. Mungall,, D. Basham,, D. Brown,, T. Chill-ingworth,, R. Connor,, R. M. Davies,, K. Devlin,, S. Duthoy,, T. Feltwell,, A. Fraser,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, C. Lacroix,, J. Maclean,, S. Moule,, L. Murphy,, K. Oliver,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, S. Rutter,, K. Seeger,, S. Simon,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, K. Taylor,, S. White-head,, J. R. Woodward, and, B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409:10071011.
27. Constantinidou, C.,, J. L. Hobman,, L. Griffiths,, M. D. Patel,, C. W. Penn,, J. A. Cole, and, T. W. Overton. 2006. A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J. Biol. Chem. 281:48024815.
28. Conway, T., and, G. K. Schoolnik. 2003. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47:879889.
29. Creasey, E. A.,, R. M. Delahay,, S. J. Daniell, and, G. Frankel. 2003. Yeast two-hybrid system survey of interactions between LEE-encoded proteins of enteropathogenic Escherichia coli. Microbiology 149:20932106.
30. Dandekar, T.,, M. Huynen,, J. T. Regula,, B. Ueberle,, C. U. Zimmermann,, M. A. Andrade,, T. Doerks,, L. Sanchez-Pulido,, B. Snel,, M. Suyama,, Y. P. Yuan,, R. Herrmann, and, P. Bork. 2000. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res. 28:32783288.
31. Daraselia, N.,, D. Dernovoy,, Y. Tian,, M. Borodovsky,, R. Tatusov, and, T. Tatusova. 2003. Reannotation of Shewanella oneidensis genome. Omics 7:171175.
32. Dharmadi, Y., and, R. Gonzalez. 2004. DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol. Prog. 20:13091324.
33. Edwards, R. A., and, F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504510.
34. Faucher, S. P.,, S. Porwollik,, C. M. Dozois,, M. McClelland, and, F. Daigle. 2006. Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences. Proc. Natl. Acad. Sci. USA 103:19061911.
35. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
36. Forst, C. V. 2006. Host-pathogen systems biology. Drug Discov. Today 11:220227.
37. Fouts, D. E.,, E. F. Mongodin,, R. E. Mandrell,, W. G. Miller,, D. A. Rasko,, J. Ravel,, L. M. Brinkac,, R. T. DeBoy,, C. T. Parker,, S. C. Daugherty,, R. J. Dodson,, A. S. Durkin,, R. Madupu,, S. A. Sullivan,, J. U. Shetty,, M. A. Ayodeji,, A. Shvartsbeyn,, M. C. Schatz,, J. H. Badger,, C. M. Fraser, and, K. E. Nelson. 2005. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 3:e15.
38. Frangeul, L.,, K. E. Nelson,, C. Buchrieser,, A. Danchin,, P. Glaser, and, F. Kunst. 1999. Cloning and assembly strategies in microbial genome projects. Microbiology 145(Pt. 10):26252634.
39. Fraser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, R. D. Fritchman,, J. F. Weidman,, K.V. Small,, M. Sandusky,, J. Fuhrmann,, D. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J. F. Tomb,, B. A. Dougherty,, K. F. Bott,, P. C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. Hutchison III, and, J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397403.
40. Fraser, C. M.,, S. J. Norris,, G. M. Weinstock,, O. White,, G. G. Sutton,, R. Dodson,, M. Gwinn,, E. K. Hickey,, R. Clayton,, K. A. Ketchum,, E. Sodergren,, J. M. Hardham,, M. P. McLeod,, S. Salzberg,, J. Peterson,, H. Khalak,, D. Richardson,, J. K. Howell,, M. Chidambaram,, T. Utterback,, L. McDonald,, P. Artiach,, C. Bowman,, M. D. Cotton,, C. Fujii,, S. Garland,, B. Hatch,, K. Horst,, K. Roberts,, M. Sandusky,, J. Weidman,, H. O. Smith, and, J. C. Venter. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375388.
41. Frishman, D. 2003. What we have learned about prokaryotes from structural genomics. Omics 7:211224.
42. Fux, C. A.,, M. Shirtliff,, P. Stoodley, and, J.W. Costerton. 2005. Can laboratory reference strains mirror “real-world” pathogenesis? Trends Microbiol. 13:5863.
43. Gill, S. R.,, M. Pop,, R. T. Deboy,, P. B. Eckburg,, P. J. Turnbaugh,, B. S. Samuel,, J. I. Gordon,, D. A. Relman,, C. M. Fraser-Liggett, and, K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:13551359.
44. Gohar, M.,, N. Gilois,, R. Graveline,, C. Garreau,, V. Sanchis, and, D. Lereclus. 2005. A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes. Proteomics 5:36963711.
45. Grainger, D. C.,, D. Hurd,, M. Harrison,, J. Holdstock, and, S. J. Busby. 2005. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. USA 102:1769317698.
46. Grainger, D. C.,, T. W. Overton,, N. Reppas,, J. T. Wade,, E. Tamai,, J. L. Hobman,, C. Constantinidou,, K. Struhl,, G. Church, and, S. J. Busby. 2004. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J. Bacteriol. 186:69386943.
47. Gutierrez, M. C.,, S. Brisse,, R. Brosch,, M. Fabre,, B. Omais,, M. Marmiesse,, P. Supply, and, V. Vincent. 2005. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathogens 1:e5.
48. Hallin, P. F., and, D. W. Ussery. 2004. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20:36823686.
49. Hamilton, G. 2006. Virology: the gene weavers. Nature 441:683685.
50. Han, M. J., and, S.Y. Lee. 2006. The Escherichia coli proteome: past, present, and future prospects. Microbiol. Mol. Biol. Rev. 70:362439.
51. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kurokawa,, K. Ishii,, K. Yokoyama,, C. G. Han,, E. Ohtsubo,, K. Nakayama,, T. Murata,, M. Tanaka,, T. Tobe,, T. Iida,, H. Takami,, T. Honda,, C. Sasakawa,, N. Ogasawara,, T. Yasunaga,, S. Kuhara,, T. Shiba,, M. Hattori, and, H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:1122.
52. Hensel, M.,, J. E. Shea,, C. Gleeson,, M. D. Jones,, E. Dalton, and, D.W. Holden. 1995. Simultaneous identification of bacterial virulence genes by negative selection. Science 269:400403.
53. Himmelreich, R.,, H. Hilbert,, H. Plagens,, E. Pirkl,, B. C. Li, and, R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:44204449.
54. Himmelreich, R.,, H. Plagens,, H. Hilbert,, B. Reiner, and, R. Herrmann. 1997. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25:701712.
55. Hinton, J. C.,, I. Hautefort,, S. Eriksson,, A. Thompson, and, M. Rhen. 2004. Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr. Opin. Microbiol. 7:277282.
56. Hitchen, P. G., and, A. Dell. 2006. Bacterial glycoproteomics. Microbiology 152:15751580.
57. Hood, D. W.,, M. E. Deadman,, T. Allen,, H. Masoud,, A. Martin,, J. R. Brisson,, R. Fleisch-mann,, J. C. Venter,, J. C. Richards, and, E. R. Moxon. 1996. Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccharide biosynthesis. Mol. Microbiol. 22:951965.
58. Jones, M. A.,, K. L. Marston,, C. A. Woodall,, D. J. Maskell,, D. Linton,, A. V. Karlyshev,, N. Dorrell,, B. W. Wren, and, P. A. Barrow. 2004. Adaptation of Campylobacter jejuni NCTC11168 to high-level colonization of the avian gastrointestinal tract. Infect. Immun. 72:37693776.
59. Joseph, B.,, K. Przybilla,, C. Stuhler,, K. Schauer,, J. Slaghuis,, T. M. Fuchs, and, W. Goebel. 2006. Identification of Listeria monocyto-genes genes contributing to intracellular replication by expression profiling and mutant screening. J. Bacteriol. 188:556568.
60. Kalir, S., and, U. Alon. 2004. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell 117:713720.
61. Keim, P., and, K. L. Smith. 2002. Bacillus anthracis evolution and epidemiology. Curr. Top. Microbiol. Immunol. 271:2132.
62. Kelly, T. J., Jr., and, H. O. Smith. 1970. A restriction enzyme from Hemophilus influenzae. II. Base sequence of the recognition site. J. Mol. Biol. 51:393409.
63. Kidgell, C.,, U. Reichard,, J. Wain,, B. Linz,, M. Torpdahl,, G. Dougan, and, M. Achtman. 2002. Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect. Genet. Evol. 2:3945.
64. Kim, S. H.,, D. H. Shin,, I. G. Choi,, U. Schulze-Gahmen,, S. Chen, and, R. Kim. 2003. Structure-based functional inference in structural genomics. J. Struct. Funct. Genomics 4:129135.
65. Kim, T. H., and, B. Ren. 2006. Genome-wide analysis of protein-DNA interactions. Annu. Rev. Genomics Hum. Genet. 7:81102.
66. Knutton, S.,, I. Rosenshine,, M. J. Pallen,, I. Nisan,, B. C. Neves,, C. Bain,, C. Wolff,, G. Dougan, and, G. Frankel. 1998. A novel EspA-associated surface organelle of enteropathogenic Escherichia coli involved in protein translocation into epithelial cells. EMBO J. 17:21662176.
67. Koessler, T.,, P. Francois,, Y. Charbonnier,, A. Huyghe,, M. Bento,, S. Dharan,, G. Renzi,, D. Lew,, S. Harbarth,, D. Pittet, and, J. Schrenzel. 2006. Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 44:10401048.
68. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessieres,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Brouillet,, C. V. Bruschi,, B. Caldwell,, V. Capuano,, N. M. Carter,, S. K. Choi,, J. J. Codani,, I. F. Connerton,, A. Danchin, et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249256.
69. Kurian, D.,, K. Phadwal, and, P. Maenpaa. 2006. Proteomic characterization of acid stress response in Synechocystis sp. PCC 6803. Proteomics 6:36143624.
70. Kuroda, M.,, T. Ohta,, I. Uchiyama,, T. Baba,, H. Yuzawa,, I. Kobayashi,, L. Cui,, A. Oguchi,, K. Aoki,, Y. Nagai,, J. Lian,, T. Ito,, M. Kanamori,, H. Matsumaru,, A. Maruyama,, H. Murakami,, A. Hosoyama,, Y. Mizutani-Ui,, N. K. Takahashi,, T. Sawano,, R. Inoue,, C. Kaito,, K. Sekimizu,, H. Hirakawa,, S. Kuhara,, S. Goto,, J. Yabuzaki,, M. Kanehisa,, A. Yamashita,, K. Oshima,, K. Furuya,, C. Yoshino,, T. Shiba,, M. Hattori,, N. Ogasawara,, H. Hayashi, and, K. Hiramatsu. 2001. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357:12251240.
71. Lin, B.,, Z. Wang,, G. J. Vora,, J. A. Thornton,, J. M. Schnur,, D. C. Thach,, K. M. Blaney,, A. G. Ligler,, A. P. Malanoski,, J. Santiago,, E. A. Walter,, B. K. Agan,, D. Metzgar,, D. Seto,, L. T. Daum,, R. Kruzelock,, R. K. Rowley,, E. H. Hanson,, C. Tibbetts, and, D. A. Stenger. 2006. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res. 16:527535.
72. Liolios, K.,, N. Tavernarakis,, P. Hugenholtz, and, N. C. Kyrpides. 2006. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34:D332D334.
73. Lipton, M. S.,, L. Pasa-Tolic,, G. A. Anderson,, D. J. Anderson,, D. L. Auberry,, J. R. Battista,, M. J. Daly,, J. Fredrickson,, K. K. Hixson,, H. Kostandarithes,, C. Masselon,, L. M. Markillie,, R. J. Moore,, M. F. Romine,, Y. Shen,, E. Stritmatter,, N. Tolic,, H. R. Udseth,, A. Venkateswaran,, K. K. Wong,, R. Zhao, and, R. D. Smith. 2002. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. USA 99:1104911054.
74. Manning, G.,, D. B. Whyte,, R. Martinez,, T. Hunter, and, S. Sudarsanam. 2002. The protein kinase complement of the human genome. Science 298:19121934.
75. Margulies, M.,, M. Egholm,, W. E. Altman,, S. Attiya,, J. S. Bader,, L. A. Bemben,, J. Berka,, M. S. Braverman,, Y. J. Chen,, Z. Chen,, S. B. Dewell,, L. Du,, J. M. Fierro,, X. V. Gomes,, B. C. Godwin,, W. He,, S. Helgesen,, C. H. Ho,, G. P. Irzyk,, S. C. Jando,, M. L. Alenquer,, T. P. Jarvie,, K. B. Jirage,, J. B. Kim,, J. R. Knight,, J. R. Lanza,, J. H. Leamon,, S. M. Lefkowitz,, M. Lei,, J. Li,, K. L. Lohman,, H. Lu,, V. B. Makhijani,, K. E. McDade,, M. P. McKenna,, E. W. Myers,, E. Nickerson,, J. R. Nobile,, R. Plant,, B. P. Puc,, M. T. Ronan,, G. T. Roth,, G. J. Sarkis,, J. F. Simons,, J. W. Simpson,, M. Srinivasan,, K. R. Tartaro,, A. Tomasz,, K. A. Vogt,, G. A. Volkmer,, S. H. Wang,, Y. Wang,, M. P. Weiner,, P. Yu,, R. F. Begley, and, J. M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376380.
76. Marshall, E. 2001. Bermuda rules: community spirit, with teeth. Science 291:1192.
77. Marshall, E. 2002. Data sharing. DNA sequencer protests being scooped with his own data. Science 295:12061207.
78. Marykwas, D. L.,, S. A. Schmidt, and, H. C. Berg. 1996. Interacting components of the flagellar motor of Escherichia coli revealed by the two-hybrid system in yeast. J. Mol. Biol. 256:564576.
79. Matte, A.,, J. Sivaraman,, I. Ekiel,, K. Gehring,, Z. Jia, and, M. Cygler. 2003. Contribution of structural genomics to understanding the biology of Escherichia coli. J. Bacteriol. 185:39944002.
80. Mayr, E. 2000. Darwin’s influence on modern thought. Sci. Am. 283:7883.
81. Mazmanian, S. K.,, G. Liu,, H. Ton-That, and, O. Schneewind. 1999. Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. Science 285:760763.
82. Medina, M. 2005. Genomes, phylogeny, and evolutionary systems biology. Proc. Natl. Acad. Sci. USA 102 (Suppl. 1):66306635.
83. Monot, M.,, N. Honore,, T. Garnier,, R. Araoz,, J. Y. Coppee,, C. Lacroix,, S. Sow,, J. S. Spencer,, R. W. Truman,, D. L. Williams,, R. Gelber,, M. Virmond,, B. Flageul,, S. N. Cho,, B. Ji,, A. Paniz-Mondolfi,, J. Convit,, S. Young,, P. E. Fine,, V. Rasolofo,, P. J. Brennan, and, S.T. Cole. 2005. On the origin of leprosy. Science 308:10401042.
84. Mori, H. 2004. From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. J. Biochem. Mol. Biol. 37:8392.
85. Mrazek, J., and, S. Karlin. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95:37203725.
86. Musser, J. M., and, F. R. DeLeo. 2005. Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus. Am. J. Pathol. 167:14611472.
87. Navarre, W. W.,, S. Porwollik,, Y. Wang,, M. Mc-Clelland,, H. Rosen,, S. J. Libby, and, F. C. Fang. 2006. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313:236238.
88. Ohno, T.,, N. Okahashi,, S. Kawai,, T. Kato,, H. Inaba,, Y. Shibata,, I. Morisaki,, Y. Abiko, and, A. Amano. 2006. Proinflammatory gene expression in mouse ST2 cell line in response to infection by Porphyromonas gingivalis. Microbes Infect. 8:10251034.
89. Pallen, M. 2002. From sequence to consequence: in silico hypothesis generation and testing. Meth. Microbiol. 33:2748.
90. Pallen, M. J. 2002. The ESAT-6/WXG100 superfamily—and a new gram-positive secretion system? Trends Microbiol. 10:209212.
91. Pallen, M. J. 1999. Microbial genomes. Mol. Microbiol. 32:907912.
92. Pallen, M. J.,, S. A. Beatson, and, C. M. Bailey. 2005. Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion. BMC Microbiol. 5:9.
93. Pallen, M. J.,, A. C. Lam,, M. Antonio, and, K. Dunbar. 2001. An embarrassment of sortases—a richness of substrates? Trends Microbiol. 9:97102.
94. Pallen, M. J.,, C. W. Penn, and, R. R. Chaudhuri. 2005. Bacterial flagellar diversity in the post-genomic era. Trends Microbiol. 13:143149.
95. Parkhill, J. 2000. In defense of complete genomes. Nat. Biotechnol. 18:493494.
96. Parkhill, J.,, G. Dougan,, K. D. James,, N. R. Thomson,, D. Pickard,, J. Wain,, C. Churcher,, K. L. Mungall,, S. D. Bentley,, M. T. Holden,, M. Sebaihia,, S. Baker,, D. Basham,, K. Brooks,, T. Chillingworth,, P. Connerton,, A. Cronin,, P. Davis,, R. M. Davies,, L. Dowd,, N. White,, J. Farrar,, T. Feltwell,, N. Hamlin,, A. Haque,, T. T. Hien,, S. Holroyd,, K. Jagels,, A. Krogh,, T. S. Larsen,, S. Leather,, S. Moule,, P. O’Gaora,, C. Parry,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead, and, B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848852.
97. Parkhill, J.,, B. W. Wren,, K. Mungall,, J. M. Ketley,, C. Churcher,, D. Basham,, T. Chill-ingworth,, R. M. Davies,, T. Feltwell,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Moule,, M. J. Pallen,, C. W. Penn,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, A. H. van Vliet,, S. Whitehead, and, B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665668.
98. Parkhill, J.,, B. W. Wren,, N. R. Thomson,, R. W. Titball,, M. T. Holden,, M. B. Prentice,, M. Sebaihia,, K. D. James,, C. Churcher,, K. L. Mungall,, S. Baker,, D. Basham,, S. D. Bentley,, K. Brooks,, A. M. Cerdeno-Tarraga,, T. Chillingworth,, A. Cronin,, R. M. Davies,, P. Davis,, G. Dougan,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Leather,, S. Moule,, P. C. Oyston,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead, and, B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523527.
99. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch, and, F. R. Blattner. 2001. Genome sequence of entero-haemorrhagic Escherichia coli O157:H7. Nature 409:529533.
100. Pizza, M.,, V. Scarlato,, V. Masignani,, M. M. Giuliani,, B. Arico,, M. Comanducci,, G. T. Jennings,, L. Baldi,, E. Bartolini,, B. Capecchi,, C. L. Galeotti,, E. Luzzi,, R. Manetti,, E. Marchetti,, M. Mora,, S. Nuti,, G. Ratti,, L. Santini,, S. Savino,, M. Scarselli,, E. Storni,, P. Zuo,, M. Broeker,, E. Hundt,, B. Knapp,, E. Blair,, T. Mason,, H. Tettelin,, D. W. Hood,, A. C. Jeffries,, N. J. Saunders,, D. M. Granoff,, J. C. Venter,, E. R. Moxon,, G. Grandi, and, R. Rappuoli. 2000. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287:18161820.
101. Pop, M., and, D. Kosack. 2004. Using the TIGR assembler in shotgun sequencing projects. Methods Mol. Biol. 255:279294.
102. Powledge, T. 2003. Revisiting Bermuda. Genome Biol. March 11.
103. Rachman, H.,, M. Strong,, T. Ulrichs,, L. Grode,, J. Schuchhardt,, H. Mollenkopf,, G. A. Kosmiadi,, D. Eisenberg, and, S. H. Kaufmann. 2006. Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect. Immun. 74:12331242.
104. Rain, J. C.,, L. Selig,, H. De Reuse,, V. Battaglia,, C. Reverdy,, S. Simon,, G. Lenzen,, F. Petel,, J. Wojcik,, V. Schachter,, Y. Chemama,, A. Labigne, and, P. Legrain. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409:211215.
105. Raoult, D.,, S. Audic,, C. Robert,, C. Abergel,, P. Renesto,, H. Ogata,, B. La Scola,, M. Suzan, and, J. M. Claverie. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306:13441350.
106. Raoult, D.,, H. Ogata,, S. Audic,, C. Robert,, K. Suhre,, M. Drancourt, and, J. M. Claverie. 2003. Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. Genome Res. 13:18001809.
107. Rappuoli, R. 2000. Reverse vaccinology. Curr. Opin. Microbiol. 3:445450.
108. Read, T. D.,, S. L. Salzberg,, M. Pop,, M. Shumway,, L. Umayam,, L. Jiang,, E. Holtzapple,, J. D. Busch,, K. L. Smith,, J. M. Schupp,, D. Solomon,, P. Keim, and, C. M. Fraser. 2002. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296:20282033.
109. Ren, C. P.,, S. A. Beatson,, J. Parkhill, and, M. J. Pallen. 2005. The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli. J. Bacteriol. 187:14301440.
110. Ren, C. P.,, R. R. Chaudhuri,, A. Fivian,, C. M. Bailey,, M. Antonio,, W. M. Barnes, and, M. J. Pallen. 2004. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J. Bacteriol. 186:35473560.
111. Renesto, P.,, N. Crapoulet,, H. Ogata,, B. La Scola,, G. Vestris,, J. M. Claverie, and, D. Raoult. 2003. Genome-based design of a cell-free culture medium for Tropheryma whipplei. Lancet 362:447449.
112. Riley, M.,, T. Abe,, M. B. Arnaud,, M. K. Berlyn,, F. R. Blattner,, R. R. Chaudhuri,, J. D. Glasner,, T. Horiuchi,, I. M. Keseler,, T. Kosuge,, H. Mori,, N. T. Perna,, G. Plunkett III,, K. E. Rudd,, M. H. Serres,, G. H. Thomas,, N. R. Thomson,, D. Wishart, and, B. L. Wanner. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot— 2005. Nucleic Acids Res. 34:19.
113. Rupp, B. 2003. High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. Acc. Chem. Res. 36:173181.
114. Rutherford, K.,, J. Parkhill,, J. Crook,, T. Horsnell,, P. Rice,, M. A. Rajandream, and, B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944945.
115. Salzberg, S. L.,, A. L. Delcher,, S. Kasif, and, O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544548.
116. Sanger, F.,, G. M. Air,, B. G. Barrell,, N. L. Brown,, A. R. Coulson,, C. A. Fiddes,, C. A. Hutchison,, P. M. Slocombe, and, M. Smith. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687695.
117. Sanger, F.,, A. R. Coulson,, G. F. Hong,, D. F. Hill, and, G. B. Petersen. 1982. Nucleotide sequence of bacteriophage lambda DNA. J. Mol. Biol. 162:729773.
118. Sanger, F.,, S. Nicklen, and, A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:54635467.
119. Schmid, M. B. 2002. Structural proteomics: the potential of high-throughput structure determination. Trends Microbiol. 10:S27S31.
120. Schoolnik, G. K. 2002. Microarray analysis of bacterial pathogenicity. Adv. Microb. Physiol. 46:145.
121. Serruto, D., and, R. Rappuoli. 2006. Post-genomic vaccine development. FEBS Lett. 580:29852992.
122. Service, R. F. 2006. Gene sequencing. The race for the $1000 genome. Science 311:15441546.
123. Silva, N. A.,, J. McCluskey,, J. M. Jefferies,, J. Hinds,, A. Smith,, S. C. Clarke,, T. J. Mitchell, and, G. K. Paterson. 2006. Genomic diversity between strains of the same serotype and multi-locus sequence type among pneumococcal clinical isolates. Infect. Immun. 74:35133518.
124. Sitkiewicz, I., and, J. M. Musser. 2006. Expression microarray and mouse virulence analysis of four conserved two-component gene regulatory systems in group a streptococcus. Infect. Immun. 74:13391351.
125. Smith, H. O., and, K. W. Wilcox. 1970. A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J. Mol. Biol. 51:379391.
126. Smith, L. M.,, J. Z. Sanders,, R. J. Kaiser,, P. Hughes,, C. Dodd,, C. R. Connell,, C. Heiner,, S. B. Kent, and, L. E. Hood. 1986. Fluorescence detection in automated DNA sequence analysis. Nature 321:674679.
127. Spratt, B. G. 2004. Exploring the concept of clonality in bacteria. Methods Mol. Biol. 266:323352.
128. Sreevatsan, S.,, X. Pan,, K. E. Stockbauer,, N. D. Connell,, B. N. Kreiswirth,, T. S. Whit-tam, and, J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:98699874.
129. Sumby, P.,, A. R. Whitney,, E. A. Graviss,, F. R. DeLeo, and, J. M. Musser. 2006. Genome-wide analysis of group a streptococci reveals a mutation that modulates global pheno-type and disease specificity. PLoS Pathog. 2:e5.
130. Terwilliger, T. C.,, M. S. Park,, G. S. Waldo,, J. Berendzen,, L. W. Hung,, C. Y. Kim,, C. V. Smith,, J. C. Sacchettini,, M. Bellinzoni,, R. Bossi,, E. De Rossi,, A. Mattevi,, A. Milano,, G. Riccardi,, M. Rizzi,, M. M. Roberts,, A. R. Coker,, G. Fossati,, P. Mascagni,, A. R. Coates,, S. P. Wood,, C. W. Goulding,, M. I. Apostol,, D. H. Anderson,, H. S. Gill,, D. S. Eisenberg,, B. Taneja,, S. Mande,, E. Pohl,, V. Lamzin,, P. Tucker,, M. Wilmanns,, C. Colovos,, W. Meyer-Klaucke,, A. W. Munro,, K. J. McLean,, K. R. Marshall,, D. Leys,, J. K. Yang,, H. J. Yoon,, B. I. Lee,, M. G. Lee,, J. E. Kwak,, B. W. Han,, J. Y. Lee,, S. H. Baek,, S. W. Suh,, M. M. Komen,, V. L. Arcus,, E. N. Baker,, J. S. Lott,, W. Jacobs, Jr.,, T. Alber, and, B. Rupp. 2003. The TB Structural Genomics Consortium: a resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb.) 83:223249.
131. Tettelin, H.,, V. Masignani,, M. J. Cieslewicz,, C. Donati,, D. Medini,, N. L. Ward,, S. V. Angiuoli,, J. Crabtree,, A. L. Jones,, A. S. Durkin,, R. T. Deboy,, T. M. Davidsen,, M. Mora,, M. Scarselli,, I. Margarit y Ros,, J. D. Peterson,, C. R. Hauser,, J. P. Sundaram,, W. C. Nelson,, R. Madupu,, L. M. Brinkac,, R. J. Dodson,, M. J. Rosovitz,, S. A. Sullivan,, S. C. Daugherty,, D. H. Haft,, J. Selengut,, M. L. Gwinn,, L. Zhou,, N. Zafar,, H. Khouri,, D. Radune,, G. Dimitrov,, K. Watkins,, K. J. O’Connor,, S. Smith,, T. R. Utterback,, O. White,, C. E. Rubens,, G. Grandi,, L. C. Madoff,, D. L. Kasper,, J. L. Telford,, M. R. Wessels,, R. Rappuoli, and, C. M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc. Natl. Acad. Sci. USA 102:1395013955.
132. Tjalsma, H.,, H. Antelmann,, J. D. Jong-bloed,, P. G. Braun,, E. Darmon,, R. Dorenbos,, J. Y. Dubois,, H. Westers,, G. Zanen,, W. J. Quax,, O. P. Kuipers,, S. Bron,, M. Hecker, and, J. M. van Dijl. 2004. Proteomics of protein secretion by Bacillus subtilis: separating the “secrets” of the secretome. Microbiol. Mol. Biol. Rev. 68:207233.
133. Venkatasubbarao, S. 2004. Microarrays—status and prospects. Trends Biotechnol. 22:630637.
134. Venter, J. C.,, M. D. Adams,, E. W. Myers,, P. W. Li,, R. J. Mural,, G. G. Sutton,, H. O. Smith,, M. Yandell,, C. A. Evans,, R. A. Holt,, J. D. Gocayne,, P. Amanatides,, R. M. Ballew,, D. H. Huson,, J. R. Wortman,, Q. Zhang,, C. D. Kodira,, X. H. Zheng,, L. Chen,, M. Skupski,, G. Subramanian,, P. D. Thomas,, J. Zhang,, G. L. Gabor Miklos,, C. Nelson,, S. Broder,, A. G. Clark,, J. Nadeau,, V. A. McKu-sick,, N. Zinder,, A. J. Levine,, R. J. Roberts,, M. Simon,, C. Slayman,, M. Hunkapiller,, R. Bolanos,, A. Delcher,, I. Dew,, D. Fasulo,, M. Flanigan,, L. Florea,, A. Halpern,, S. Hannen-halli,, S. Kravitz,, S. Levy,, C. Mobarry,, K. Reinert,, K. Remington,, J. Abu-Threideh,, E. Beasley,, K. Biddick,, V. Bonazzi,, R. Brandon,, M. Cargill,, I. Chandramouliswaran,, R. Charlab,, K. Chaturvedi,, Z. Deng,, V. Di Francesco,, P. Dunn,, K. Eilbeck,, C. Evange-lista,, A. E. Gabrielian,, W. Gan,, W. Ge,, F. Gong,, Z. Gu,, P. Guan,, T. J. Heiman,, M. E. Higgins,, R. R. Ji,, Z. Ke,, K. A. Ketchum,, Z. Lai,, Y. Lei,, Z. Li,, J. Li,, Y. Liang,, X. Lin,, F. Lu,, G. V. Merkulov,, N. Milshina,, H. M. Moore,, A. K. Naik,, V. A. Narayan,, B. Neelam,, D. Nusskern,, D. B. Rusch,, S. Salzberg,, W. Shao,, B. Shue,, J. Sun,, Z. Wang,, A. Wang,, X. Wang,, J. Wang,, M. Wei,, R. Wides,, C. Xiao,, C. Yan, et al. 2001. The sequence of the human genome. Science 291:13041351.
135. Venter, J. C.,, M. D. Adams,, G. G. Sutton,, A. R. Kerlavage,, H. O. Smith, and, M. Hunkapiller. 1998. Shotgun sequencing of the human genome. Science 280:15401542.
136. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
137. Venter, J. C.,, H. O. Smith, and, L. Hood. 1996. A new strategy for genome sequencing. Nature 381:364366.
138. Wilmes-Riesenberg, M. R.,, J.W. Foster, and, R. Curtiss III. 1997. An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2. Infect. Immun. 65:203210.
139. Wren, B. W. 2000. Microbial genome analysis: insights into virulence, host adaptation and evolution. Nat. Rev. Genet. 1:3039.
140. Wren, B. W.,, D. Linton,, N. Dorrell, and, A.V. Karlyshev. 2001. Post genome analysis of Campylobacter jejuni. Symp. Ser. Soc. Appl. Microbiol. 30:36S44S.
141. Zhang, W.,, W. Qi,, T. J. Albert,, A. S. Motiwala,, D. Alland,, E. K. Hyytia-Trees,, E. M. Ribot,, P. I. Fields,, T. S. Whittam, and, B. Swaminathan. 2006. Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Res. 16:757767.


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Milestones in bacterial genomics

Citation: Pallen M. 2007. Introduction to Pathogenomics, p 1-20. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch1
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Bacterial genome sequencing centers and other resources

Citation: Pallen M. 2007. Introduction to Pathogenomics, p 1-20. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch1
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Recent applications of microarrays in bacterial pathogenomics

Citation: Pallen M. 2007. Introduction to Pathogenomics, p 1-20. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch1
Generic image for table

Sequencing of multiple strains from the same species

Citation: Pallen M. 2007. Introduction to Pathogenomics, p 1-20. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch1

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