Phages and their satellites encode hotspots of antiviral systems

Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

(2022) Eduardo P. C. Rocha et al.   PLOS BIOLOGY

clinker & clustermap.js: automatic generation of gene cluster comparison figures

(2021) Cameron L M Gilchrist et al.   BIOINFORMATICS

The impact of genetic diversity on gene essentiality within the Escherichia coli species

(2021) François Rousset et al.   Nature Microbiology

A nucleotide-sensing endonuclease from the Gabija bacterial defense system

(2021) Rui Cheng et al.   NUCLEIC ACIDS RESEARCH

Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts

(2021) Kristen N. LeGault et al.   SCIENCE

Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

(2021) Nitzan Tal et al.   CELL

Prophages encode phage-defense systems with cognate self-immunity

(2021) Siân V. Owen et al.   Cell Host & Microbe

Effector-mediated membrane disruption controls cell death in CBASS antiphage defense

(2021) Brianna Duncan-Lowey et al.   MOLECULAR CELL

Antiviral activity of bacterial TIR domains via immune signalling molecules

(2021) Gal Ofir et al.   NATURE

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

(2021) Jorge A. Moura de Sousa et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages

(2021) Fatima Aysha Hussain et al.   SCIENCE

The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases

(2020) Carl J Schiltz et al.   NUCLEIC ACIDS RESEARCH

On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria

(2020) Alicia Calvo-Villamañán et al.   NUCLEIC ACIDS RESEARCH

Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence

(2020) Artem Isaev et al.   NUCLEIC ACIDS RESEARCH

SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities

(2020) Xiaolin Xiong et al.   Nature Microbiology

Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation

(2020) Alfred Fillol-Salom et al.   CURRENT OPINION IN MICROBIOLOGY

DNA targeting and interference by a bacterial Argonaute nuclease

(2020) Anton Kuzmenko et al.   NATURE

Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy

(2020) Anna Lopatina et al.   Annual Review of Virology

STING cyclic dinucleotide sensing originated in bacteria

(2020) Benjamin R. Morehouse et al.   NATURE

Prokaryotic viperins produce diverse antiviral molecules

(2020) Aude Bernheim et al.   NATURE

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

(2020) Linyi Gao et al.   SCIENCE

Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems

(2020) Adi Millman et al.   Nature Microbiology

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems

(2020) Mario Rodríguez Mestre et al.   NUCLEIC ACIDS RESEARCH

Yet More Evidence of Collusion: a New Viral Defense System Encoded by Gordonia Phage CarolAnn

(2019) Matthew T. Montgomery et al.   mBio

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Cyclic GMP–AMP signalling protects bacteria against viral infection

(2019) Daniel Cohen et al.   NATURE

Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage

(2019) Carl J Schiltz et al.   NUCLEIC ACIDS RESEARCH

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

(2019) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

(2018) Lun Cui et al.   Nature Communications

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

A chemical defence against phage infection

(2018) Sarah Kronheim et al.   NATURE

The Pfam protein families database in 2019

(2018) Sara El-Gebali 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

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

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

DISARM is a widespread bacterial defence system with broad anti-phage activities

(2017) Gal Ofir et al.   Nature Microbiology

A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages

(2016) Florence Depardieu et al.   Cell Host & Microbe

Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition

(2016) Matthieu Galtier et al.   ENVIRONMENTAL MICROBIOLOGY

Prophages mediate defense against phage infection through diverse mechanisms

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

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

The Extraintestinal Pathogenic Escherichia coli Factor RqlI Constrains the Genotoxic Effects of the RecQ-Like Helicase RqlH

(2015) Colin W. Russell et al.   PLoS Pathogens

The chromosomal accommodation and domestication of mobile genetic elements

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

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

The T4 Phage DNA Mimic Protein Arn Inhibits the DNA Binding Activity of the Bacterial Histone-like Protein H-NS

(2014) Chun-Han Ho et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antirestriction activity of the monomeric and dimeric forms of T7 Ocr

(2014) G. B. Zavilgelsky et al.   MOLECULAR BIOLOGY

A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism

(2014) Ron L. Dy et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

(2014) Nicolás Toro et al.   PLoS One

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

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

A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa

(2014) A. Pawluk et al.   mBio

Sirtuins Are Evolutionarily Conserved Viral Restriction Factors

(2014) Emre Koyuncu et al.   mBio

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

(2014) Kira S. Makarova et al.   Frontiers in Genetics

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

(2013) Vivek Anantharaman et al.   Biology Direct

Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

(2013) Hila Sberro et al.   MOLECULAR CELL

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

A vast collection of microbial genes that are toxic to bacteria

(2012) A. Kimelman et al.   GENOME RESEARCH

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

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

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice

(2011) Damien Maura et al.   ENVIRONMENTAL MICROBIOLOGY

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

(2011) K. S. Makarova et al.   JOURNAL OF BACTERIOLOGY

Activation of a prophage-encoded tyrosine kinase by a heterologous infecting phage results in a self-inflicted abortive infection

(2011) David I. Friedman et al.   MOLECULAR MICROBIOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Temperate bacteriophage ΦO18P from an Aeromonas media isolate: Characterization and complete genome sequence

(2007) Frauke Beilstein et al.   VIROLOGY