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

Characterization of the cryptic Escherichia lineages: rapid identification and prevalence

(2011) Olivier Clermont et al.   ENVIRONMENTAL MICROBIOLOGY

Core and Panmetabolism in Escherichia coli

(2011) G. Vieira et al.   JOURNAL OF BACTERIOLOGY

Real-time sequencing

(2011) Thomas D. Otto   NATURE REVIEWS MICROBIOLOGY

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

(2011) C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic anatomy of Escherichia coli O157:H7 outbreaks

(2011) M. Eppinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

Cryptic Lineages of the Genus Escherichia

(2009) S. T. Walk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial comparative pan-genomics using binomial mixture models

(2009) Lars Snipen et al.   BMC GENOMICS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

(2009) S. Chattopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Classification of Bacteria and Archaea: Past, present and future

(2009) Karl Heinz Schleifer   SYSTEMATIC AND APPLIED MICROBIOLOGY

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

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

(2009) Marie Touchon et al.   PLoS Genetics

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

(2008) Françoise Jaureguy et al.   BMC GENOMICS

Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method

(2008) David M. Gordon et al.   ENVIRONMENTAL MICROBIOLOGY

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY