The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

Global dissemination of a multidrug resistant Escherichia coli clone

(2014) N. K. Petty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A FimH Inhibitor Prevents Acute Bladder Infection and Treats Chronic Cystitis Caused by Multidrug-Resistant Uropathogenic Escherichia coli ST131

(2013) Makrina Totsika et al.   JOURNAL OF INFECTIOUS DISEASES

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Control of Directionality in Streptomyces Phage φBT1 Integrase-Mediated Site-Specific Recombination

(2013) Lin Zhang et al.   PLoS One

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

(2013) Shea N. Gardner et al.   PLoS One

The Epidemic of Extended-Spectrum- -Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx

(2013) L. B. Price et al.   mBio

The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone

(2013) Minh-Duy Phan et al.   PLoS Genetics

The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

(2012) N. Ricker et al.   GENOMICS

Role of Homologous Recombination in Adaptive Diversification of Extraintestinal Escherichia coli

(2012) Sandip Paul et al.   JOURNAL OF BACTERIOLOGY

Escherichia coli-Mediated Impairment of Ureteric Contractility Is Uropathogenic E. coli Specific

(2012) R. V. Floyd et al.   JOURNAL OF INFECTIOUS DISEASES

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India

(2011) T. S. Avasthi et al.   JOURNAL OF BACTERIOLOGY

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms

(2011) Makrina Totsika et al.   PLoS One

Assembly complexity of prokaryotic genomes using short reads

(2010) Carl Kingsford et al.   BMC BIOINFORMATICS

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

(2010) Niranjan Nagarajan et al.   BMC GENOMICS

Escherichia coliSequence Type ST131 as the Major Cause of Serious Multidrug‐ResistantE. coliInfections in the United States

(2010) James R. Johnson et al.   CLINICAL INFECTIOUS DISEASES

Molecular epidemiology of Escherichia coli producing CTX-M β-lactamases: the worldwide emergence of clone ST131 O25:H4

(2010) Gisele Peirano et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Genetics and Virulence Association of the Shigella flexneri Sit Iron Transport System

(2009) C. R. Fisher et al.   INFECTION AND IMMUNITY

Genomic Sequencing Reveals Regulatory Mutations and Recombinational Events in the Widely Used MC4100 Lineage of Escherichia coli K-12

(2009) T. Ferenci et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence of the Wild-Type Commensal Escherichia coli Strain SE15, Belonging to Phylogenetic Group B2

(2009) H. Toh et al.   JOURNAL OF BACTERIOLOGY

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

(2008) K. Oshima et al.   DNA RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

UK epidemic Escherichia coli strains A-E, with CTX-M-15  -lactamase, all belong to the international O25:H4-ST131 clone

(2008) S. H. Lau et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Major Uropathogenic Escherichia coli Strain Isolated in the Northwest of England Identified by Multilocus Sequence Typing

(2008) S. H. Lau et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY