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Items: 1 to 20 of 119

1.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

Kaas RS, Friis C, Ussery DW, Aarestrup FM.

BMC Genomics. 2012 Oct 31;13:577. doi: 10.1186/1471-2164-13-577.

3.

Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments.

Sahl JW, Matalka MN, Rasko DA.

Appl Environ Microbiol. 2012 Jul;78(14):4884-92. doi: 10.1128/AEM.00929-12. Epub 2012 May 11.

4.

Genomic variation in Salmonella enterica core genes for epidemiological typing.

Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW.

BMC Genomics. 2012 Mar 12;13:88. doi: 10.1186/1471-2164-13-88.

5.

Comparison of 61 sequenced Escherichia coli genomes.

Lukjancenko O, Wassenaar TM, Ussery DW.

Microb Ecol. 2010 Nov;60(4):708-20. doi: 10.1007/s00248-010-9717-3. Epub 2010 Jul 11. Review.

6.

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.

Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP.

BMC Bioinformatics. 2010 Sep 15;11:461. doi: 10.1186/1471-2105-11-461.

7.

A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation.

Sahl JW, Steinsland H, Redman JC, Angiuoli SV, Nataro JP, Sommerfelt H, Rasko DA.

Infect Immun. 2011 Feb;79(2):950-60. doi: 10.1128/IAI.00932-10. Epub 2010 Nov 15.

8.

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.

Chattaway MA, Schaefer U, Tewolde R, Dallman TJ, Jenkins C.

J Clin Microbiol. 2017 Feb;55(2):616-623. doi: 10.1128/JCM.01790-16. Epub 2016 Dec 14.

9.
10.

Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci.

Diamant E, Palti Y, Gur-Arie R, Cohen H, Hallerman EM, Kashi Y.

Appl Environ Microbiol. 2004 Apr;70(4):2464-73.

11.

Phylogenetic incongruence in E. coli O104: understanding the evolutionary relationships of emerging pathogens in the face of homologous recombination.

Hao W, Allen VG, Jamieson FB, Low DE, Alexander DC.

PLoS One. 2012;7(4):e33971. doi: 10.1371/journal.pone.0033971. Epub 2012 Apr 6.

12.

Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray.

Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW.

Genome Biol. 2007;8(12):R267.

13.
14.

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica.

Gordienko EN, Kazanov MD, Gelfand MS.

J Bacteriol. 2013 Jun;195(12):2786-92. doi: 10.1128/JB.02285-12. Epub 2013 Apr 12.

15.

CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection.

Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C.

J Bacteriol. 2011 May;193(10):2460-7. doi: 10.1128/JB.01307-10. Epub 2011 Mar 18.

16.

Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing.

Ferdous M, Friedrich AW, Grundmann H, de Boer RF, Croughs PD, Islam MA, Kluytmans-van den Bergh MF, Kooistra-Smid AM, Rossen JW.

Clin Microbiol Infect. 2016 Jul;22(7):642.e1-9. doi: 10.1016/j.cmi.2016.03.028. Epub 2016 Apr 4.

17.

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E.

PLoS Genet. 2009 Jan;5(1):e1000344. doi: 10.1371/journal.pgen.1000344. Epub 2009 Jan 23.

18.

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

Mau B, Glasner JD, Darling AE, Perna NT.

Genome Biol. 2006;7(5):R44. Epub 2006 May 31.

19.

A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data.

Carrillo CD, Kruczkiewicz P, Mutschall S, Tudor A, Clark C, Taboada EN.

Front Cell Infect Microbiol. 2012 May 1;2:57. doi: 10.3389/fcimb.2012.00057. eCollection 2012.

20.

Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.

Hall BG, Cardenas H, Barlow M.

PLoS One. 2013 Jul 23;8(7):e68901. doi: 10.1371/journal.pone.0068901. Print 2013.

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