Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

Mechanisms That Shape Microbial Pangenomes

(2021) Maria Rosa Domingo-Sananes et al.   TRENDS IN MICROBIOLOGY

Evidence for selection in the abundant accessory gene content of a prokaryote pangenome

(2021) Fiona J Whelan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28

(2020) Keiji Nakamura et al.   Microbial Genomics

Coinfinder: detecting significant associations and dissociations in pangenomes

(2020) Fiona Jane Whelan et al.   Microbial Genomics

The population genetics of pathogenic Escherichia coli

(2020) Erick Denamur et al.   NATURE REVIEWS MICROBIOLOGY

Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat

(2020) Michael E. Hibbing et al.   mBio

Genus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens

(2019) Qun-Feng Lu et al.   International Journal of Genomics

Model selection may not be a mandatory step for phylogeny reconstruction

(2019) Shiran Abadi et al.   Nature Communications

Genomic and functional analysis of emerging virulent and multi-drug resistant E. coli lineage ST648

(2019) Katharina Schaufler et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

(2019) Alan McNally et al.   mBio

Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

(2019) Amee R. Manges et al.   CLINICAL MICROBIOLOGY REVIEWS

The Ecology and Evolution of Pangenomes

(2019) Michael A. Brockhurst et al.   CURRENT BIOLOGY

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

(2019) Arun Gonzales Decano et al.   Scientific Reports

The Essential Genome of Escherichia coli K-12

(2018) Emily C. A. Goodall et al.   mBio

The Two-Component System ZraPSR Is a Novel ESR that Contributes to Intrinsic Antibiotic Tolerance in Escherichia coli

(2018) Kévin Rome et al.   JOURNAL OF MOLECULAR BIOLOGY

Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment

(2018) Tin Yau Pang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function-related replacement of bacterial siderophore pathways

(2017) Hilke Bruns et al.   ISME Journal

Prokaryote genome fluidity is dependent on effective population size

(2017) Nadia Andrea Andreani et al.   ISME Journal

The population genetics of pangenomes

(2017) B. Jesse Shapiro   Nature Microbiology

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Separate F-Type Plasmids Have Shaped the Evolution of the H 30 Subclone of Escherichia coli Sequence Type 131

(2016) Timothy J. Johnson et al.   mSphere

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

(2013) Carsten Kuenne et al.   BMC GENOMICS

First identification of coexistence of blaNDM-1 and blaCMY-42 among Escherichia coli ST167 clinical isolates

(2013) Xueqing Zhang et al.   BMC MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Virulence Plasmid Harbored by Uropathogenic Escherichia coli Functions in Acute Stages of Pathogenesis

(2010) C. K. Cusumano et al.   INFECTION AND IMMUNITY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DsbA directs efficient expression of outer membrane secretin EscC of the enteropathogenic Escherichia coli type III secretion apparatus

(2007) Tsuyoshi Miki et al.   MICROBIAL PATHOGENESIS