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E. coli K-12 Genome Sequencing and Analysis
Pathogen Genome Sequencing and Analysis
Gene Expression Studies
Methods, Tools, and Strategies
E. coli K-12 Genome Sequencing and Analysis
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M. Riley, 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(1):1-9.
[PMID: 16397293]
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M. B. Lobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny,
H. Lehnherr, M. B. Yarmolinsky, and F. R. Blattner (2004) Genome of bacteriophage
P1. J Bacteriol 186(21):
7032-7068. [PMID: 15489417]
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F. R. Blattner, G. Plunkett III, C. A. Bloch, N. T.
Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K.
Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M.
A. Goeden, D. J. Rose, B. Mau, and Y. Shao (1997) The complete
genome sequence of Escherichia coli K-12. Science
277(5331): 1453-1474. [PMID: 9278503]
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M. Masters and G. Plunkett III (1997) Bacterial
genomes: the Escherichia coli model. pp 715-744, in:
ICRF Handbook of Genome Analysis. N. K. Spurr, B. D. Young,
and S. P. Bryant (eds). Oxford, UK, Blackwell Science Ltd. [ISBN-13: 978-0632037285]
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F. Blattner, G. Plunkett III, G. Mayhew, J. Gregor,
W. Davis, M. Goeden, N. Perna, D. Rose, Y. Shao, H. Kirkpatrick, C.
Bloch, G. Posfai, and C. Rode (1996) E. coli genome
project. Microbial & Comparative Genomics 1(4): 357.
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J. Reizer, A. Reizer, M. J. Merrick, G. Plunkett III,
D. J. Rose, and M. H. Saier, Jr. (1996) Novel phosphotransferase-encoding
genes revealed by analysis of the Escherichia coli genome:
a chimeric gene encoding an Enzyme I homologue that possesses a putative
sensory transduction domain. Gene 181(1-2): 103-108.
[PMID: 8973315]
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V. Burland, G. Plunkett III, H. J. Sofia, D. L. Daniels,
and F. R. Blattner (1995) Analysis of the Escherichia coli
genome VI: DNA sequence of the region from 92.8 through 100 minutes.
Nucleic Acids Res 23(12): 2105-2119. [PMID: 7610040]
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E. M. Lake, H. Jiang, F. R. Blattner, and J. Adler (1995)
Analogue of aspartate and glutamate active at synapses are
attractants for Escherichia coli. Cell Mol Neurobiol
15(2): 283-288. [PMID: 8590457]
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K. E. Rudd, H. J. Sofia, E. V. Koonin, G. Plunkett III,
S. Lazar, and P. E. Rouviere (1995) A new family of peptidyl-prolyl
isomerases. Trends Biochem Sci 20(1): 12-14.
[PMID: 7878731]
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H. J. Sofia, V. Burland, D. L. Daniels, G. Plunkett
III, and F. R. Blattner (1994) Analysis of the Escherichia
coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes.
Nucleic Acids Res 22(13): 2576-2586. [PMID: 8041620]
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S. I. Sukharev, P. Blount, B. Martinac, F. R. Blattner,
and C. Kung (1994) A large-conductance mechanosensitive channel
in E. coli encoded by mscL alone. Nature
368(6468): 265-268. [PMID: 7511799]
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F. R. Blattner, V. Burland, G. Plunkett III, H. J. Sofia,
and D. L. Daniels (1993) Analysis of the Escherichia coli
genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes.
Nucleic Acids Res 21(23): 5408-5417. [PMID: 8265357]
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G. Plunkett III, V. Burland, D. L. Daniels, and F. R.
Blattner (1993) Analysis of the Escherichia coli genome.
III. DNA sequence of the region from 87.2 to 89.2 minutes.
Nucleic Acids Res 21(15): 3391-3398. [PMID: 8346018]
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V. Burland, G. Plunkett III, D. L. Daniels, and F. R.
Blattner (1993) DNA sequence and analysis of 136 kilobases
of the Escherichia coli genome: organizational symmetry around
the origin of replication. Genomics 16(3): 551-561.
[PMID: 7686882]
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S.-E. Chuang, V. Burland, G. Plunkett III, D. L. Daniels,
and F. R. Blattner (1993) Sequence analysis of four new heat-shock
genes constituting the hslTS/ibpAB and hslVU operons
in Escherichia coli. Gene 134(1): 1-6.
[PMID: 8244018]
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S.-E. Chuang and F. R. Blattner (1993) Characterization
of twenty-six new heat shock genes of Escherichia coli.
J Bacteriol 175(16): 5242-5252. [PMID: 8349564]
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F. R. Blattner, D. L. Daniels, V. D. Burland, G. Plunkett
III, and S.-E. Chuang (1992) The E. coli genome project:
towards the first megabase. pp 43-59, in: The Chromosome
(John Innes Symposium, Norwich, England). J. S. Heslop-Harrison
and R. B. Flavell (eds). Oxford, UK, Bios Scientific Publishers. [ISBN-13: 978-1872748320]
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D. L. Daniels, G. Plunkett III, V. Burland, and F. R.
Blattner (1992) Analysis of the Escherichia coli genome:
DNA sequence of the region from 84.5 to 86.5 minutes. Science
257(5071): 771-778. [PMID: 1379743]
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D. L. Daniels and F. R. Blattner (1987) Mapping
using gene encyclopaedias. Nature 325(6107):
831-832. [PMID: 3547141]
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Pathogen Genome Sequencing and Analysis
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C. Brinkley, V. Burland, R. Keller, D. J. Rose, A. T. Boutin,
S. A. Klink, F. R. Blattner, and J. B. Kaper
(2006) Nucleotide sequence analysis of the enteropathogenic Escherichia
coli adherence factor plasmid pMAR7. Infect Immun 74(9): 5408-5413.
[PMID: 16926437]
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Y. Xie, V. Kolisnychenko, M. Paul-Satyaseela, S. Elliott,
G. Parthasarathy, Y. Yao, G. Plunkett III, F. R. Blattner, and K.
S. Kim (2006) Identification and characterization of Escherichia
coli RS218-derived islands in the pathogenesis of E. coli
meningitis. J Infect Dis 194(3): 358-364. Epub
June 30, 2006. [PMID: 16826484]
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S. Zhou, A. Kile, M. Bechner, M. Place, E. Kvikstad,
W. Deng, J. Wei, J. Severin, R. Runnheim, C. Churas, D. Forrest, E.
T. Dimalanta, C. Lamers, V. Burland, F. R. Blattner, and D. C. Schwartz
(2004) Single-molecule approach to bacterial genomic comparisons
via optical mapping. J Bacteriol 186(22): 7773-7782.
[PMID: 15516592]
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E. L. Buckles, F. K. Bahrani-Mougeot, A. Molina, C.
V. Lockatell, D. E. Johnson, C. B. Drachenberg, V. Burland, F. R.
Blattner, and M. S. Donnenberg (2004) Identification and characterization
of a novel uropathogenic Escherichia coli-associated fimbrial
gene cluster. Infect Immun 72(7): 3890-3901.
[PMID: 15213132]
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J. Nishi, J. Sheikh, K. Mizuguchi, B. Luisi, V. Burland,
A. Boutin, D. J. Rose, F. R. Blattner, and J. P. Nataro (2003) The
export of coat protein from enteroaggregative Escherichia coli
by a specific ATP-binding cassette transporter system. J
Biol Chem 278(4): 45680-45689. [PMID: 12933818]
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P. L. Roesch, P. Redford, S. Batchelet, R. L. Moritz,
S. Pellett, B. J. Haugen, F. R. Blattner, and R. A. Welch (2003) Uropathogenic
Escherichia coli use D-serine deaminase to modulate infection
of the murine urinary tract. Mol Microbiol 49(1):
55-67. [PMID: 12823810]
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J. Wei, M. B. Goldberg, V. Burland, M. M. Venkatesan,
W. Deng, G. Fournier, G. F. Mayhew, G. Plunkett III, D. J. Rose, A.
Darling, B. Mau, N. T. Perna, S. M. Payne, L. J. Runyen-Janecky, S.
Zhou, D. C. Schwartz, and F. R. Blattner (2003) Complete Genome
Sequence and Comparative Genomics of Shigella flexneri serotype
2a strain 2457T. Infect Immun 71(5): 2775-2786.
[PMID: 12704152]
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W. Deng, S.-R. Liou, G. Plunkett III, G. F. Mayhew,
D. J. Rose, V. Burland, V. Kodoyianni, D. C. Schwartz, and F. R. Blattner
(2003) Comparative genomics of Salmonella enterica serovar
Typhi strains Ty2 and CT18. J Bacteriol 185(7):
2330-2337. [PMID: 12644504]
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R. A. Welch, V. Burland, G. Plunkett III , P. Redford,
P. Roesch, D. Rasko, E. L. Buckles, S.-R. Liou, A. Boutin, J. Hackett,
D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T.
Perna, H. L. T. Mobley, M. S. Donnenberg, and F. R. Blattner (2002)
Extensive mosiac structure revealed by the complete genome
sequence of uropathogenic Escherichia coli. Proc.
Natl. Acad. Sci. USA 99(26): 17020-17024. [PMID: 12471157]
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S. Zhou, W. Deng, T. S. Anantharaman, A. Lim, E. T.
Dimalanta, J. Wang, T. Wu, T. Chunhong, R. Creighton, A. Kile, E.
Kvikstad, M. Bechner, G. Yen, A. Garic-Stankovic, J. Severin, D. Forrest,
R. Runnheim, C. Churas, C. Lamers, N. T. Perna, V. Burland, F. R.
Blattner, B. Mishra, and D. C. Schwartz (2002) A whole-genome
shotgun optical map of Yersinia pestis strain KIM. Appl
Environ Microbiol 68(12): 6321-6331. [PMID: 12450857]
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A. G. Torres, J. A. Giron, N. T. Perna, V. Burland,
F. R. Blattner, F. Avelino-Flores, and J. B. Kaper (2002) Identification
and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic
Escherichia coli O157:H7. Infect Immun 70(10):
5416-5427. [PMID: 12228266]
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A. G. Torres, N. T. Perna, V. Burland, A. Ruknudin,
F. R. Blattner, and J. B. Kaper (2002) Characterization of
Cah, a calcium-binding and heat-extractable autotransporter protein
of enterohaemorrhagic Escherichia coli . Mol Microbiol
45(4): 951-966. [PMID: 12180916]
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D. E. Taylor, M. Rooker, M. Keelan, L.-K. Ng, I. Martin,
N. T. Perna, V. Burland, and F. R. Blattner (2002) Genomic
variability of O islands encoding tellurite resistance in enterohemorrhagic
Escherichia coli O157:H7 isolates. J Bacteriol
184(17): 4690-4698. [PMID: 12169592]
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N. T. Perna, J. D. Glasner, V. Burland, and G. Plunkett
III (2002) Chapter 1. The Genomes of Escherichia coli
K-12 and Pathogenic E. coli. pp 3-53, in: Escherichia
coli: Virulence Mechanisms of a Versatile Pathogen. M. S. Donnenberg
(ed). Academic Press, San Diego, California, U.S.A. [ISBN-13: 978-0122207518]
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N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J.
D. Glasner, J. Kim, and F. R. Blattner (2002) Comparative Analyses
of Enterobacterial Genomes. pp 296-301, in: Biology of Plant-Microbe
Interactions, Volume 3 [Proceedings of the 10th International
Congress on Molecular Plant-Microbe Interactions Madison, Wisconsin,
U.S.A., July 10-14, 2001]. S. A. Leong, C. Allen, and E. W. Triplett
(eds). International Society for Molecular Plant-Microbe Interactions,
St. Paul, Minnesota, U.S.A. [ISBN-13: 978-0965462525]
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W. Deng, V. Burland, G. Plunkett III, A. Boutin, G.
F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C.
Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano,
S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R.
Blattner, and R. D. Perry (2002) Genome sequence of Yersinia
pestis KIM. J Bacteriol 184(16): 4601-4611.
[PMID: 12142430]
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S. R. Heimer, R. A. Welch, N. T. Perna, G. Posfai, P.
S. Evans, J. B. Kaper, F. R. Blattner, and H. L. Mobley (2002) Urease
of enterohemorrhagic Escherichia coli: evidence for regulation
by fur and a trans-acting factor. Infect
Immun 70(2): 1027-1031. [PMID: 11796646]
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I. T. Kudva, P. S. Evans, N. T. Perna, T. J. Barrett,
G. J. DeCastro, F. M. Ausubel, F. R. Blattner, and S. B. Calderwood
(2002) Polymorphic amplified typing sequences provide a novel
approach to Escherichia coli O157:H7 strain typing.
J Clin Microbiol 40(4): 1152-1159. [PMID: 11923324]
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I. T. Kudva, P. S. Evans, N. T. Perna, T. J. Barrett,
F. M. Ausubel, F. R. Blattner, and S. B. Calderwood (2002) Strains
of Escherichia coli O157:H7 differ primarily by insertions
or deletions, not single-nucleotide polymorphisms. J Bacteriol
184(7): 1873-1879. [PMID: 11889093]
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N. T. Perna, 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 enterohaemorrhagic Escherichia coli O157:H7.
Nature 409(6819): 529-533. [PMID: 11206551]
|
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A. Lim, E. T. Dimalanta, K. D. Potamousis, G. Yen, J.
Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna,
G. Plunkett III, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T.
S. Anantharaman, B. Mishra, and D. C. Schwartz (2001) Shotgun
optical maps of the whole Escherichia coli O157:H7 genome.
Genome Res 11(9): 1584-1593. [PMID: 11544203]
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M. M. Venkatesan, M. B. Goldberg, D. J. Rose, E. J.
Grotbeck, V. Burland, and F. R. Blattner (2001) Complete DNA
sequence and analysis of the large virulence plasmid of Shigella
flexneri. Infect Immun 69(5): 3271-3285.
[PMID: 11292750]
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R. H. Ffrench-Constant, N. Waterfield, V. Burland, N.
T. Perna, P. J. Daborn, D. Bowen, and F. R. Blattner (2000) A
genomic sample sequence of the entomopathogenic bacterium Photorhabdus
luminescens W14: potential implications for virulence.
Appl Environ Microbiol 66(8): 3310-3329. [PMID: 10919786]
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T. D. Lawley, V. Burland, and D. E. Taylor (2000) Analysis
of the complete nucleotide sequence of the tetracycline-resistance
transposon Tn10. Plasmid 43(3): 235-239. [PMID: 10783303]
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C. K. Sherburne, T. D. Lawley, M. W. Gilmour, F. R.
Blattner, V. Burland, E. Grotbeck, D. J. Rose, and D. E. Taylor (2000)
The complete DNA sequence and analysis of R27, a large IncHI
plasmid from Salmonella typhi that is temperature sensitive
for transfer. Nucleic Acids Res 28(10): 2177-2186.
[PMID: 10773089]
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G. Plunkett III, D. J. Rose, T. J. Durfee, and F. R.
Blattner (1999) Sequence of Shiga toxin 2 phage 933W from Escherichia
coli O157:H7: Shiga toxin as a phage late-gene product.
J Bacteriol 181(6): 1767-1778. [PMID: 10074068]
|
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N. T. Perna, G. F. Mayhew, G. Posfai, S. Elliott, M.
S. Donnenberg, J. B. Kaper, and F. R. Blattner (1998) Molecular
evolution of a pathogenicity island from enterohemorrhagic Escherichia
coli O157:H7. Infect Immun 66(8): 3810-3817.
[PMID: 9673266]
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R. D. Perry, S. C. Straley, J. D. Fetherston, D. J.
Rose, J. Gregor, and F. R. Blattner (1998) DNA sequencing and
analysis of the low-Ca2+-response plasmid pCD1 of Yersinia pestis
KIM5. Infect Immun 66(10): 4611-4623. [PMID: 9746557]
|
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V. Burland, Y. Shao, N. T. Perna, G. Plunkett III, 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(18): 4196-4204.
[PMID: 9722640]
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A. M. Gehring, E. DeMoll, J. D. Fetherston, I. Mori,
G. F. Mayhew, F. R. Blattner, C. T. Walsh, and R. D. Perry (1998)
Iron acquisition in plague: modular logic in enzymatic biogenesis
of yersiniabactin by Yersinia pestis. Chem Biol
5(10): 573-586. [PMID: 9818149]
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J. B. Kaper, S. Elliott, V. Sperandio, N. T. Perna,
G. F. Mayhew, and F. R. Blattner (1998) Attaching-and-effacing
intestinal histopathology and the locus of enterocyte effacement.
pp 163-182, in: Escherichia coli O157:H7 and other Shiga Toxin-producing
E. coli strains. J. B. Kaper and A. D. O'Brien (eds). Washington,
DC, ASM Press. [ISBN-13: 978-1555811297]
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L. E. Lindler, G. V. Plano, V. Burland, G. F. Mayhew,
and F. R. Blattner (1998) Complete DNA sequence and detailed
analysis of the Yersinia pestis KIM5 plasmid encoding murine
toxin and capsular antigen. Infect Immun 66(12):
5731-5742. [PMID: 9826348]
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M. Hensel, J. E. Shea, A. J. Baumler, C. Gleeson, F.
Blattner, and D. W. Holden (1997) Analysis of the boundaries
of Salmonella pathogenicity island 2 and the corresponding
chromosomal region of Escherichia coli K-12. J Bacteriol
179(4): 1105-1111. [PMID: 9023191]
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Gene Expression Studies
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J. L. Giel, D. Rodionov, M. Liu, F. R. Blattner, and
P. J. Kiley (2006) IscR-dependent gene expression links iron-sulphur
cluster assembly to the control of O-regulated genes in Escherichia
coli. Mol Microbiol 60(4): 1058-1075. [PMID: 16677314]
|
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S.S. Fong, A. P. Burgard, C. D. Herring, E. M. Knight,
F. R. Blattner, C. D. Maranas, and B. O. Palsson (2005) In
silico design and adaptive evolution of Escherichia coli for
production of lactic acid. Biotechnol Bioeng 91(5):
643-648. Epub June 16, 2005. [PMID: 15962337]
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A. M. Hansen, Y. Qiu, N. Yeh, F. R. Blattner, T. Durfee,
and D. J. Jin (2005) SspA is required for acid resistance in
stationary phase by downregulation of H-NS in Escherichia coli.
Mol Microbiol 56(3): 719-734. [PMID: 15819627]
|
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K. Zhao, M. Liu, and R. R. Burgess (2005) The global transcriptional response
of Escherichia coli to induced sigma protein involves sigma regulon activation followed by
inactivation and degradation of sigma in vivo.
J Biol Chem 280(18): 17758-17768. Epub March 9, 2005.
[PMID: 15757896]
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M. Liu, T. Durfee, J. E. Cabrera, K. Zhao, D. J. Jin,
and F. R. Blattner (2005) Global transcriptional programs reveal
a carbon source foraging strategy by Escherichia coli.
J Biol Chem 280(16): 15921-15927. Epub February 10, 2005.
[PMID: 15705577]
[CEL files] [Movies]
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Y. Kang, K. D. Weber, Y. Qiu, P. J. Kiley, and F. R. Blattner (2005)
Genome-wide expression analysis indicates that FNR of Escherichia coli
K-12 regulates a large number of genes of unknown function.
J Bacteriol 187(3): 1135-1160. [PMID: 15659690]
[CEL files]
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C. D. Herring and F. R. Blattner (2004) Global transcriptional
effects of a suppressor tRNA and the inactivation of the regulator frmR.
J Bacteriol 186(20): 6714-6720. [PMID: 15466022]
[CEL files]
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T. E. Allen, M. J. Herrgard, M. Liu, Y. Qiu, J. D. Glasner,
F. R. Blattner, and B. O. Palsson (2003) Genome-Scale analysis
of the uses of the Escherichia coli genome: Model-driven analysis
of heterogeneous data sets.J Bacteriol 185(21):
6392-6399. [PMID: 14563874]
[CEL files]
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R. M. Gutierrez-Rios, D. A. Rosenblueth, J. A. Loza,
A. M. Huerta, J. D. Glasner, F. R. Blattner, and J. Collado-Vides
(2003) Regulatory network of Escherichia coli: consistency
between literature knowledge and microarray profiles. Genome
Res 13(11): 2435-2443. [PMID: 14597655]
|
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E. F. Nuwaysir, W. Huang, T. J. Albert, J. Singh, K.
Nuwaysir, A. Pitas, T. Richmond, T. Gorski, J. P. Berg, J. Ballin,
M. McCormick, J. Norton, T. Pollock, T. Sumwalt, L. Butcher, D. Porter,
M. Molla, C. Hall, F. Blattner, M. R. Sussman, R. L. Wallace, F. Cerrina,
and R. D. Green (2002) Gene expression analysis using oligonucleotide
arrays produced by maskless photolithography.Genome Res
12(11): 1749-1755. [PMID: 12421762]
|
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I. M. Ong, J. D. Glasner, and D. Page (2002) Modelling
regulatory pathways in E. coli from time series expression profiles.
Bioinformatics 18(Suppl 1): S241-S248. [PMID: 12169553]
|
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M. A. Newton, C. M. Kendziorski, C. S. Richmond, F.
R. Blattner, and K. W. Tsui (2001) On differential variability
of expression ratios: improving statistical inference about gene expression
changes from microarray data. J Comput Biol 8(1):
37-52. [PMID: 11339905]
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Y. Wei, J. M. Lee, C. Richmond, F. R. Blattner, J. A.
Rafalski, and R. A. LaRossa (2001) High-density microarray-mediated
gene expression profiling of Escherichia coli. J
Bacteriol 183(2): 545-556. [PMID: 11133948]
|
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D. W. Selinger, K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond,
F. R. Blattner, D. J. Lockhart, and G. M. Church (2000) RNA
expression analysis using a 30 base pair resolution Escherichia
coli genome array. Nat Biotechnol 18(12):
1262-1268. [PMID: 11101804]
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S.-E. Chuang and F. R. Blattner (1999) Identification
of phosphate-regulated genes by differential expression in the UV-irradiated
host system. J Microbiol Methods 37(1): 93-96.
[PMID: 10395468]
|
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C. S. Richmond, J. D. Glasner, R. Mau, H. Jin, and F. R. Blattner
(1999) Genome-wide expression profiling in Escherichia coli
K-12. Nucleic Acids Res 27(19): 3821-3835. [PMID: 10481021]
|
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H. Tao, C. Bausch, C. Richmond, F. R. Blattner, and
T. Conway (1999) Functional genomics: expression analysis of
Escherichia coli growing on minimal and rich media.
J Bacteriol 181(20): 6425-6440. [PMID: 10515934]
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S.-E. Chuang, D. L. Daniels, and F. R. Blattner (1993)
Global regulation of gene expression in Escherichia coli.
J Bacteriol 175(7): 2026-2036. [PMID: 8458845]
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Methods, Tools, and Strategies
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G. Posfai, G. Plunkett III, T. Feher, D. Frisch, G.
M. Keil, K. Umenhoffer, V. Kolisnychenko, B. Stahl, S. S. Sharma,
M. de Arruda, V. Burland, S. W. Harcum, and F. R. Blattner (2006)
Emergent properties of reduced-genome Escherichia coli.
Science 312(5776): 1044-1046. Epub April 27, 2006. [16645050]
|
|
B. H. Sung, C. H. Lee, B. J. Yu, J. H. Lee, J. Y. Lee,
M. S. Kim, F. R. Blattner, and S. C. Kim (2006) Development
of a biofilm production-deficient Escherichia coli strain as
a host for biotechnological applications. Appl Environ Microbiol
72(5): 3336-3342. [16672475]
|
|
J. D. Glasner, M. Rusch, P. Liss, G. Plunkett III, E.
L. Cabot, A. Darling, B. D. Anderson, P. Infield-Harm, M. C. Gilson,
and N. T. Perna (2006) ASAP: a resource for annotating, curating,
comparing, and disseminating genomic data. Nucleic Acids
Res 34(Database issue): D41-D45. [16381899]
|
|
A. C. E. Darling, B. Mau, F. R. Blattner, and N. T.
Perna (2004) Mauve: Multiple alignment of conserved genomic
sequence with rearrangements. Genome Res 14(7):
1394-1403. [PMID: 15231754]
|
|
Y. Kang, T. Durfee, J. D. Glasner, Y. Qiu, D. Frisch,
K. M. Winterberg, and F. R. Blattner (2004) Systematic mutagenesis
of the Escherichia coli genome. J Bacteriol 186(15):
4921-4930. [PMID: 15262929]
Supplemental material: Table S1 (local)
|
|
C. D. Herring and F. R. Blattner (2004) Conditional
lethal amber mutations in essential Escherichia coli genes.
J Bacteriol 186(9): 2673-2681. [PMID: 15090508]
|
|
A. E. Darling, B. Mau, F. R. Blattner, and N. T. Perna
(2004) GRIL: genome rearrangement and inversion locator.
Bioinformatics 20(1): 122-124. [PMID: 14693819]
|
|
J. Bockhorst, M. Craven, D. Page, J. Shavlik, and J.
Glasner (2003) A Bayesian network approach to operon prediction.
Bioinformatics 19(10): 1227-1235. [PMID: 12835266]
|
|
J. Bockhorst, Y. Qiu, J. Glasner, M. Liu, F. Blattner,
and M. Craven (2003) Predicting bacterial transcription units
using sequence and expression data. Bioinformatics 19(Suppl
1): I34-I43. [PMID: 12855435]
|
|
C. D. Herring, J. D. Glasner, and F. R. Blattner (2003)
Gene replacement without selection: regulated suppression of
amber mutations in Escherichia coli. Gene 311:
153-163. [PMID: 12853150]
|
|
J. D. Glasner, P. Liss, G. Plunkett III, A. Darling,
T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner,
and N. T. Perna (2003) ASAP, a systematic annotation package
for community analysis of genomes. Nucleic Acids Res
31(1): 147-151. [PMID: 12519969]
|
|
M. Molla, P. Andrae, J. Glasner, F. Blattner, and J.
Shavlik (2002) Interpreting microarray expression data using
text annotating the genes. Information Sciences 146(1-4):
75-88. (also appears in Proceedings of the 4th Conference on Computational
Biology and Genome Informatics, Durham, NC) [abstract]
|
|
A. M. Huerta, J. D. Glasner, R. M. Gutierrez-Rios, F.
R. Blattner, and J. Collado-Vides (2002) GETools: gene expression
tool for analysis of transcriptome experiments in E. coli.
Trends Genet 18(4): 217-218. [DOI: https://doi.org/10.1016/S0168-9525(01)02620-8]
|
|
V. Kolisnychenko, G. Plunkett III, C. D. Herring, T.
Feher, J. Posfai, F. R. Blattner, and G. Posfai (2002) Engineering
a reduced Escherichia coli genome. Genome Res
12(4): 640-647. [PMID: 11932248]
|
|
Y. Dong, J. D. Glasner, F. R. Blattner, and E. W. Triplett
(2001) Genomic interspecies microarray hybridization: rapiod
discovery of three thousand genes in the maize endophyte, Klebsiella
pneumoniae 342, by microarray hybridization with Escherichia
coli K-12 open reading frames. Appl Environ Microbiol
67(4): 1911-1921. [PMID: 11282649]
|
|
M. Craven, D. Page, J. Shavlik, J. Bockhorst, and J.
Glasner (2000) A probabilistic learning approach to whole-genome
operon prediction. Proc Int Conf Intell Syst Mol Biol
8: 116-127. [PMID: 10977072]
|
|
H. Salgado, A. Santos-Zavaleta, S. Gama-Castro, D. Millan-Zarate,
F. R. Blattner, and J. Collado-Vides (2000) RegulonDB (version
3.0): transcriptional regulation and operon organization in Escherichia
coli K-12. Nucleic Acids Res 28(1): 65-67.
[PMID: 10592182]
|
|
C. F. Allex, J. W. Shavlik, and F. R. Blattner (1999)
Neural network input representations that produce accurate
consensus sequences from DNA fragment assemblies. Bioinformatics
15(9): 723-728. [PMID: 10498772]
|
|
G. Posfai, V. Kolisnychenko, Z. Bereczki, and F. R.
Blattner (1999) Markerless gene replacement in Escherichia
coli stimulated by a double-strand break in the chromosome.
Nucleic Acids Res 27(22): 4409-4415. [PMID: 10536150]
|
|
S. Singh-Gasson, R. D. Green, Y. Yue, C. Nelson, F.
Blattner, M. R. Sussman, and F. Cerrina (1999) Maskless fabrication
of light-directed oligonucleotide microarrays using a digital micromirror
array. Nat Biotechnol 17(10): 974-978. [PMID: 10504697]
|
|
J. Mahillon, H. A. Kirkpatrick, H. L. Kijenski, C. A.
Bloch, C. K. Rode, G. F. Mayhew, D. J. Rose, G. Plunkett III, V. Burland,
and F. R. Blattner (1998) Subdivision of the Escherichia
coli K-12 genome for sequencing: manipulation and DNA sequence
of transposable elements introducing unique restriction sites.
Gene 223(1-2): 47-54. [PMID: 9858680]
|
|
C. F. Allex, S. F. Baldwin, J. W. Shavlik, and F. R.
Blattner (1997) Increasing consensus accuracy in DNA fragment
assemblies by incorporating fluorescent trace representations.
Proc Int Conf Intell Syst Mol Biol 5: 3-14. [PMID: 9322009]
|
|
G. Posfai, M. D. Koob, H. A. Kirkpatrick, and F. R.
Blattner (1997) Versatile insertion plasmids for targeted genome
manipulations in bacteria: isolation, deletion, and rescue of the
pathogenicity island LEE of the Escherichia coli O157:H7 genome.
J Bacteriol 179(13): 4426-4428. [PMID: 9209066]
|
|
C. F. Allex, S. F. Baldwin, J. W. Shavlik, and F. R.
Blattner (1996) Improving the quality of automatic DNA sequence
assembly using fluorescent trace-data classifications. Proc
Int Conf Intell Syst Mol Biol 4: 3-14. [PMID: 8877499]
|
|
S.-E. Chuang and F. R. Blattner (1994) Ultrafast
DNA recovery from agarose by centrifugation through a paper slurry.
Biotechniques 17(4): 634, 636. [PMID: 7833013]
|
|
V. Burland, D. L. Daniels, G. Plunkett III, and F. R.
Blattner (1993) Genome sequencing on both strands: the Janus
strategy. Nucleic Acids Res 21(15): 3385-3390.
[PMID: 8346017]
|
|
D. L. Daniels, C. H. Olson, R. Brumley, and F. R. Blattner
(1990) Field inversion gel electrophoresis applied to the rapid,
multi-enzyme restriction mapping of phage lambda clones. Nucleic
Acids Res 18(5): 1312. [PMID: 2138731]
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