To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

(2021) Jorge A Moura de Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

(2021) Eugen Pfeifer et al.   NUCLEIC ACIDS RESEARCH

Structure of the Capsid Size-Determining Scaffold of “Satellite” Bacteriophage P4

(2020) James L. Kizziah et al.   Viruses-Basel

Viral Satellites Exploit Phage Proteins to Escape Degradation of the Bacterial Host Chromosome

(2019) Amelia C. McKitterick et al.   Cell Host & Microbe

Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements

(2019) Terje Dokland   Viruses-Basel

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe

(2018) Alfred Fillol-Salom et al.   ISME Journal

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome

(2017) Brendan J. O’Hara et al.   PLoS Genetics

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

(2016) Sherwood R. Casjens et al.   VIROLOGY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites

(2015) José R. Penadés et al.   Annual Review of Virology

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

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

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

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

(2013) Kimberley D. Seed et al.   NATURE

Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits

(2013) Renata C. Matos et al.   PLoS Genetics

The First Structure of Polarity Suppression Protein, Psu from Enterobacteria Phage P4, Reveals a Novel Fold and a Knotted Dimer

(2012) Ramanuj Banerjee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pirates of the Caudovirales

(2012) Gail E. Christie et al.   VIROLOGY

The ClermontEscherichia coliphylo-typing method revisited: improvement of specificity and detection of new phylo-groups

(2012) Olivier Clermont et al.   Environmental Microbiology Reports

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Defective Prophage Pool of Escherichia coli O157: Prophage–Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants

(2009) Md Asadulghani et al.   PLoS Pathogens

Noisy: Identification of problematic columns in multiple sequence alignments

(2008) Andreas WM Dress et al.   Algorithms for Molecular Biology

The virophage as a unique parasite of the giant mimivirus

(2008) Bernard La Scola et al.   NATURE

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH