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The complete genome sequence of Escherichia coli K-12.
TLDR
The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. Expand
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TLDR
This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution. Expand
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
TLDR
It is found that lateral gene transfer is far more extensive than previously anticipated and 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7, including candidate virulence factors, alternative metabolic capacities, several prophages and other new functions—all of which could be targets for surveillance. Expand
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
TLDR
The complete genome sequence of uropathogenic Escherichia coli, strain CFT073 is presented and Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. Expand
On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data
TLDR
This work considers the problem of inferring fold changes in gene expression from cDNA microarray data and derives estimates of gene expression changes within a simple hierarchical model that accounts for measurement error and fluctuations in absolute gene expression levels. Expand
Emergent Properties of Reduced-Genome Escherichia coli
TLDR
Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties and led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Expand
Molecular Evolution of a Pathogenicity Island from Enterohemorrhagic Escherichia coli O157:H7
TLDR
The complete 43,359-bp sequence of the locus of enterocyte effacement (LEE) from EDL933 is reported, which suggests recombinational divergence coupled with natural selection and has implications for the understanding of the interaction of both pathogens with their host, for the emergence of O157:H7, and for the evolutionary history of pathogens in general. Expand
Functional Genomics: Expression Analysis ofEscherichia coli Growing on Minimal and Rich Media
TLDR
This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest. Expand
Comparative Genomics of Salmonellaenterica Serovar Typhi Strains Ty2 and CT18
TLDR
The 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain Ty2 is presented, a human-specific pathogen causing typhoid fever, and a half-genome interreplichore inversion in Ty2 relative to CT18 was confirmed. Expand
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005
TLDR
A snapshot analysis based on the most recent genome sequences of two E.coli K-12 strains allows comparison of their genotypes and mutant status of alleles. Expand
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