Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95

(2019) Steffen L. Jørgensen et al.   mSphere

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

(2019) Nelson Frazão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stratified reconstruction of ancestral Escherichia coli diversification

(2019) José Maria Gonzalez-Alba et al.   BMC GENOMICS

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis

(2018) Alessandro Cassini et al.   LANCET INFECTIOUS DISEASES

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmental Escherichia coli : ecology and public health implications-a review

(2017) J. Jang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination

(2017) Rafał J. Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

(2017) Sabiha Shaik et al.   mBio

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

(2017) Olaya Rendueles et al.   PLoS Pathogens

Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates

(2017) Nancy de Castro Stoppe et al.   Frontiers in Microbiology

Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

(2017) David M. Gordon et al.   mSphere

Genetic Attributes of E. coli Isolates from Chlorinated Drinking Water

(2017) Michaela D. J. Blyton et al.   PLoS One

Diarrheagenic Escherichia coli

(2016) Tânia A.T. Gomes et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

(2016) Claire L O'Brien et al.   GUT

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics

(2016) Tracy H. Hazen et al.   INFECTION AND IMMUNITY

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Evolutionary Ecology of Prokaryotic Immune Mechanisms

(2016) Stineke van Houte et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

(2016) Marguerite Lapierre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

(2016) Nicole Stoesser et al.   mBio

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Two fundamentally different classes of microbial genes

(2016) Yuri I. Wolf et al.   Nature Microbiology

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

(2016) Tess E. Brewer et al.   Nature Microbiology

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

Bacteriophage-mediated spread of bacterial virulence genes

(2015) José R Penadés et al.   CURRENT OPINION IN MICROBIOLOGY

Interactions between genotype and environment drive the metabolic phenotype withinEscherichia coliisolates

(2015) Victor Sabarly et al.   ENVIRONMENTAL MICROBIOLOGY

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Recombinant transfer in the basic genome ofEscherichia coli

(2015) Purushottam D. Dixit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative analysis of commensalEscherichia colipopulations reveals host-specific enterotypes at the intra-species level

(2015) Mounira Smati et al.   MicrobiologyOpen

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Pandemic lineages of extraintestinal pathogenic Escherichia coli

(2014) L.W. Riley   CLINICAL MICROBIOLOGY AND INFECTION

The chromosomal accommodation and domestication of mobile genetic elements

(2014) Marie Touchon et al.   CURRENT OPINION IN MICROBIOLOGY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prospects for Building Large Timetrees Using Molecular Data with Incomplete Gene Coverage among Species

(2014) A. Filipski et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Reductive genome evolution at both ends of the bacterial population size spectrum

(2014) Bérénice Batut et al.   NATURE REVIEWS MICROBIOLOGY

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

(2014) Julien Guglielmini et al.   NUCLEIC ACIDS RESEARCH

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

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

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evidence for Coexistence of Distinct Escherichia coli Populations in Various Aquatic Environments and Their Survival in Estuary Water

(2013) T. Berthe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Horizontal gene transfer in human pathogens

(2013) Mario Juhas   CRITICAL REVIEWS IN MICROBIOLOGY

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenic Escherichia coli Found in Sewage Treatment Plants and Environmental Waters

(2012) E. M. Anastasi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

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

(2012) Rolf S Kaas et al.   BMC GENOMICS

Phylogenetic distribution of traits associated with plant colonization inEscherichia coli

(2012) Guillaume Méric et al.   ENVIRONMENTAL MICROBIOLOGY

The evolution of the Escherichia coli phylogeny

(2012) Roy R. Chaudhuri et al.   INFECTION GENETICS AND EVOLUTION

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Estimating the fitness effect of an insertion sequence

(2012) Manuel Bichsel et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

Core and Panmetabolism in Escherichia coli

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

Population structure and uropathogenic virulence-associated genes of faecal Escherichia coli from healthy young and elderly adults

(2011) T. L. Vollmerhausen et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed

(2010) Mehdy Ratajczak et al.   BMC MICROBIOLOGY

Survival of Escherichia coli in the environment: fundamental and public health aspects

(2010) Jan Dirk van Elsas et al.   ISME Journal

Genome dynamics and its impact on evolution of Escherichia coli

(2010) Ulrich Dobrindt et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

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

Molecular mechanisms of Escherichia coli pathogenicity

(2009) Matthew A. Croxen et al.   NATURE REVIEWS MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Marie Touchon et al.   PLoS Genetics

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Characteristics of human intestinalEscherichia coliwith changing environments

(2008) David Skurnik et al.   ENVIRONMENTAL MICROBIOLOGY

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

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

Escherichia coli in the Environment: Implications for Water Quality and Human Health

(2008) Satoshi Ishii et al.   MICROBES AND ENVIRONMENTS

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology