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

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

The magic dance of the alarmones (p)ppGpp

(2016) Wieland Steinchen et al.   MOLECULAR MICROBIOLOGY

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

(2015) Welkin H Pope et al.   eLife

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

DNA-guided DNA interference by a prokaryotic Argonaute

(2014) Daan C. Swarts et al.   NATURE

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

(2014) Pedro H. Oliveira et al.   NUCLEIC ACIDS RESEARCH

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

(2014) T. C. Jordan et al.   mBio

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotypes

(2013) W. H. Pope et al.   JOURNAL OF VIROLOGY

Importance of prophages to evolution and virulence of bacterial pathogens

(2013) Louis-Charles Fortier et al.   Virulence

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The Bacteriophage HK97 gp15 Moron Element Encodes a Novel Superinfection Exclusion Protein

(2012) Nichole Cumby et al.   JOURNAL OF BACTERIOLOGY

Integration-Dependent Bacteriophage Immunity Provides Insights into the Evolution of Genetic Switches

(2012) Gregory W. Broussard et al.   MOLECULAR CELL

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

On the nature of mycobacteriophage diversity and host preference

(2012) Deborah Jacobs-Sera et al.   VIROLOGY

Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

(2012) Tim R. Blower et al.   PLoS Genetics

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

(2011) Steven G Cresawn et al.   BMC 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair

(2009) Peter C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

BRED: A Simple and Powerful Tool for Constructing Mutant and Recombinant Bacteriophage Genomes

(2008) Laura J. Marinelli et al.   PLoS One