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

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. [PubMed] [full text] [abstract]
    Supplemental material: Tables 1 - 6 and explanatory notes
 
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. [PubMed] [full text] [abstract]
    Supplemental material: Table S1 (ASM)
 
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. [PubMed] [Science Online]
 
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. [publisher's description]
 
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.
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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.
 
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. [PubMed]
 
D. L. Daniels and F. R. Blattner (1987) “Mapping using gene encyclopaedias.” Nature 325(6107): 831-832. [PubMed]
 

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Pathogen Genome Sequencing and Analysis

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. [PubMed] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [abstract]
 
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. [PubMed] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [PDF] [abstract]
 
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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 
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. [publisher's description]
 
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. [publisher's description]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [Nature Online]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed] [full text]
 
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. [PubMed] [full text]
 
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. [PubMed] [full text]
 
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. [PubMed]
 
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. [PubMed]
 
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.
 
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. [PubMed] [full text]
 
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. [PubMed]
 

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Gene Expression Studies

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. [PubMed] [abstract]
 
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. [PubMed]
    Supplemental material: (Publisher's site)
 
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. [PubMed] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
    Supplemental material: Table 1 (JBC Online) Movies (local)
 
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. [PubMed] [full text] [abstract]
    Supplemental material: Table S2 and Normalized array data (ASM)
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 

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. [PubMed] [abstract]
 
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. [PubMed]
 

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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 

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Methods, Tools, and Strategies

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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
 
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. [PubMed] [full text] [abstract]
    Supplemental material: Table S1 (ASM) (local)
 
C. D. Herring and F. R. Blattner (2004) “Conditional lethal amber mutations in essential Escherichia coli genes.” J Bacteriol 186(9): 2673-2681. [PubMed] [full text] [abstract]
 
A. E. Darling, B. Mau, F. R. Blattner, and N. T. Perna (2004) “GRIL: genome rearrangement and inversion locator.” Bioinformatics 20(1): 122-124. [PubMed]
 
J. Bockhorst, M. Craven, D. Page, J. Shavlik, and J. Glasner (2003) “A Bayesian network approach to operon prediction.” Bioinformatics 19(10): 1227-1235. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed] [full text] [abstract]
 
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. [SummaryPlus]
 
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. [PubMed] [full text] [abstract]
 
Y. Dong, J. D. Glasner, F. R. Blattner, and E. W. Triplett (2001) “Genomic interspecies microarray hybridization: rapid 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. [PubMed] [full text] [abstract]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 
S.-E. Chuang and F. R. Blattner (1994) “Ultrafast DNA recovery from agarose by centrifugation through a paper slurry.” Biotechniques 17(4): 634, 636. [PubMed]
 
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. [PubMed]
 
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. [PubMed]
 

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