Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages

(2020) Aurélie Mathieu et al.   Nature Communications

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

(2020) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

(2019) Rene S. Hendriksen et al.   Nature Communications

Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy

(2019) Korf et al.   Viruses-Basel

Two Phages of the Genera Felixounavirus Subjected to 12 Hour Challenge on Salmonella Infantis Showed Distinct Genotypic and Phenotypic Changes

(2019) Rivera et al.   Viruses-Basel

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

(2018) Pakorn Aiewsakun et al.   JOURNAL OF GENERAL VIROLOGY

The Odd “RB” Phage—Identification of Arabinosylation as a New Epigenetic Modification of DNA in T4-Like Phage RB69

(2018) Julie Thomas et al.   Viruses-Basel

Complete genome sequence of C130_2, a novel myovirus infecting pathogenic Escherichia coli and Shigella strains

(2018) Domonkos Sváb et al.   ARCHIVES OF VIROLOGY

Characterization of the Escherichia coli Virulent Myophage ST32

(2018) Honghui Liu et al.   Viruses-Basel

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki

(2017) Dann Turner et al.   PLoS One

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

Prophage-mediated defence against viral attack and viral counter-defence

(2017) Rebekah M. Dedrick et al.   Nature Microbiology

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

The microviridae: Diversity, assembly, and experimental evolution

(2016) Sarah M. Doore et al.   VIROLOGY

The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

(2016) Lisa T. Crummett et al.   VIROLOGY

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Isolation and molecular characterisation of Achromobacter phage phiAxp-3, an N4-like bacteriophage

(2016) Yanyan Ma et al.   Scientific Reports

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Biodiversity of bacteriophages: morphological and biological properties of a large group of phages isolated from urban sewage

(2016) Agata Jurczak-Kurek et al.   Scientific Reports

Genomic Diversity of Phages Infecting Probiotic Strains of Lactobacillus paracasei

(2015) Diego J. Mercanti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d’Ivoire

(2015) Christiane Essoh et al.   PLoS One

Structure and biochemical characterization of bacteriophage phi92 endosialidase

(2015) David Schwarzer et al.   VIROLOGY

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

A New Microviridae Phage Isolated from a Failed Biotechnological Process Driven by Escherichia coli

(2014) Simon J. Labrie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread

(2014) Victoriya V. Volkova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of the morphology and genome of an Escherichia coli podovirus

(2014) Yuhui Hua et al.   ARCHIVES OF VIROLOGY

Automated classification of tailed bacteriophages according to their neck organization

(2014) Anne Lopes et al.   BMC GENOMICS

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

(2014) Julianne H. Grose et al.   VIROLOGY

Mycobacteriophages: Windows into Tuberculosis

(2014) Graham F. Hatfull   PLoS Pathogens

The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella

(2014) Bradley L. Bearson et al.   Frontiers in Microbiology

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

DPS – A rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque

(2013) Witold Kot et al.   JOURNAL OF VIROLOGICAL METHODS

Characterization and complete genome sequence of the Shigella bacteriophage pSf-1

(2013) Jin Woo Jun et al.   RESEARCH IN MICROBIOLOGY

Importance of prophages to evolution and virulence of bacterial pathogens

(2013) Louis-Charles Fortier et al.   Virulence

Identification of acquired antimicrobial resistance genes

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8

(2012) J. Tsonos et al.   JOURNAL OF VIROLOGY

A Multivalent Adsorption Apparatus Explains the Broad Host Range of Phage phi92: a Comprehensive Genomic and Structural Analysis

(2012) D. Schwarzer et al.   JOURNAL OF VIROLOGY

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

On the nature of mycobacteriophage diversity and host preference

(2012) Deborah Jacobs-Sera et al.   VIROLOGY

Easyfig: a genome comparison visualizer

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size

(2010) Graham F. Hatfull et al.   JOURNAL OF MOLECULAR BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools

(2008) Rob Lavigne et al.   RESEARCH IN MICROBIOLOGY