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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...–1247. Buckles EL, Bahrani-Mougeot FK, Molina A, Lockatell CV, Johnson DE, Drachenberg CB, Burland V, Blattner FR, Donnenberg MS. 2004. Identification and characterization of a novel uropathogenic Escherichia coli-associated fimbrial gene cluster. Infect Immun 72: 3890–3901. Carlos C, Pires MM, Stoppe NC...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...Large-scale analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains Yoko Arimizu1,2, Yumi Kirino3, Mitsuhiko P. Sato1, Koichi Uno4, Toshio Sato4, Yasuhiro Gotoh1, Frédéric...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
...for each transgene are used for readability and are defined in Supplemental Table S1.In our initial analysis, we identified several cases where mapped sequences were fused to unknown sequences. Further analysis revealed that some of these fusions were with the Escherichia coli and not vector sequences...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...2 0QQ, United Kingdom; 6Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; 7British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom; 8London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom Escherichia coli...
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Methods: Large-scale analysis of gene clustering in bacteria
- Qingwu Yang and
- Sing-Hoi Sze
Genome Res. June 2008 18: 949-956; Published in Advance April 4, 2008, doi:10.1101/gr.072322.107
...a given query cluster. We use this algorithm to study gene clustering in 400 bacterial genomes by starting from a well-characterized list of operons in Escherichia coli K12 and perform comparative analysis of operon occurrences, gene orientations, and rearrangements both within and across clusters. We...
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Methods: High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12
- Christiane Honisch,
- Anu Raghunathan,
- Charles R. Cantor,
- Bernhard Ø. Palsson,
- and Dirk van den Boom
Genome Res. December 2004 14: 2495-2502; doi:10.1101/gr.2977704
...High-throughput mutation detection underlying adaptive evolution of Escherichia coli -K12 Christiane Honisch 1 , 3 , Anu Raghunathan 2 , Charles R. Cantor 1 , Bernhard Ø. Palsson 2 , and Dirk van den Boom 1 1 Sequenom, Inc...
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LETTER: Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
- Rosa María Gutiérrez-Ríos,
- David A. Rosenblueth,
- José Antonio Loza,
- Araceli M. Huerta,
- Jeremy D. Glasner,
- Fred R. Blattner,
- and Julio Collado-Vides
Genome Res. November 2003 13: 2435-2443; doi:10.1101/gr.1387003
....J., Ziegelhoffer, E.C., Kiley, P.J., and Stewart, V. 1998 . Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J. Bacteriol. 180 : 4192 -4198. ↵ Dombrecht, B., Marchal, K., Vanderleyden, J., and Michiels, J. 2002 . Prediction and overview...
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LETTER: Comparison of the Small Molecule Metabolic Enzymes of Escherichia coli and Saccharomyces cerevisiae
- Oliver Jardine,
- Julian Gough,
- Cyrus Chothia,
- and Sarah A. Teichmann
Genome Res. June 1, 2002 12: 916-929; doi:10.1101/gr.228002
...Comparison of the Small Molecule Metabolic Enzymes of Escherichia coli and Saccharomyces cerevisiae Oliver Jardine 1 , Julian Gough 2 , Cyrus Chothia 2 , and Sarah A. Teichmann 3 , 4 , 5 1Department of Crystallography, Birkbeck...
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Letter: Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
- Tadasuke Ooka,
- Yoshitoshi Ogura,
- Md Asadulghani,
- Makoto Ohnishi,
- Keisuke Nakayama,
- Jun Terajima,
- Haruo Watanabe,
- and Tetsuya Hayashi
Genome Res. October 2009 19: 1809-1816; Published in Advance June 29, 2009, doi:10.1101/gr.089615.108
...horizontal transfer of virulence determinants. PLoS Pathog 5: e1000408. doi: 10.1371/journal. ppat.1000408. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, RileyM, ColladoVides J, Glasner JD, Rode CK, Mayhew GF, et al. 1997. The complete sequence of Escherichia coli K-12. Science 277: 1453...
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METHODS: Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome
- Alex Lim,
- Eileen T. Dimalanta,
- Konstantinos D. Potamousis,
- Galex Yen,
- Jennifer Apodoca,
- Chunhong Tao,
- Jieyi Lin,
- Rong Qi,
- John Skiadas,
- Arvind Ramanathan,
- Nicole T. Perna,
- Guy Plunkett III,
- Valerie Burland,
- Bob Mau,
- Jeremiah Hackett,
- Frederick R. Blattner,
- Thomas S. Anantharaman,
- Bhubaneswar Mishra,
- and David C. Schwartz
Genome Res. September 1, 2001 11: 1584-1593; Published in Advance August 16, 2001, doi:10.1101/gr.172101
.... ( 1997 ) The complete sequence of Escherichia coli K-12. Science 277 : 1453 – 1462 . ↵ Cai W. , Jing J. , Irvin B. , Ohler L. , Rose E. , Shizuya H. , Kim U. , Simon M. , Anantharaman T. , Mishra B. , et al. ( 1998 ) High-resolution restriction maps of bacterial artificial chromosomes constructed...

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