A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome

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

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

Phages and their satellites encode hotspots of antiviral systems

(2022) François Rousset et al.   Cell Host & Microbe

Systematic and quantitative view of the antiviral arsenal of prokaryotes

(2022) Florian Tesson et al.   Nature Communications

The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA

(2022) Michele LeRoux et al.   Nature Microbiology

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

(2021) Cameron L M Gilchrist et al.   BIOINFORMATICS

TaxonKit: A practical and efficient NCBI taxonomy toolkit

(2021) Wei Shen et al.   Journal of Genetics and Genomics

New technologies for developing phage-based tools to manipulate the human microbiome

(2021) Mohammadali Khan Mirzaei et al.   TRENDS IN MICROBIOLOGY

A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence-specific immunity against subviral parasites

(2021) Zachary K Barth et al.   eLife

Intestinal Bacteriophage Therapy: Looking for Optimal Efficacy

(2021) François Javaudin et al.   CLINICAL MICROBIOLOGY REVIEWS

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

(2021) Fatima Aysha Hussain et al.   SCIENCE

Are there 1031 virus particles on Earth, or more, or less?

(2020) A.R. Mushegian   JOURNAL OF BACTERIOLOGY

HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity

(2020) Qiaozhen Ye et al.   MOLECULAR CELL

DNA Features Viewer: a sequence annotation formatting and plotting library for Python

(2020) Valentin Zulkower et al.   BIOINFORMATICS

Identification of uncharacterized components of prokaryotic immune systems and their diverse eukaryotic reformulations

(2020) A. Maxwell Burroughs et al.   JOURNAL OF BACTERIOLOGY

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

(2020) Linyi Gao et al.   SCIENCE

Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms

(2020) Andrea Garretto et al.   Frontiers in Microbiology

(Ph)ighting Phages: How Bacteria Resist Their Parasites

(2019) Jakob T. Rostøl et al.   Cell Host & Microbe

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Phage Therapy in the Twenty-First Century: Facing the Decline of The Antibiotic Era; Is it Finally Time for The Age of the Phage?

(2019) Shayla Hesse et al.   Annual Review of Microbiology

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

(2019) Bryan B. Hsu et al.   Cell Host & Microbe

Cyclic GMP–AMP signalling protects bacteria against viral infection

(2019) Daniel Cohen et al.   NATURE

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

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

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

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

TADB 2.0: an updated database of bacterial type II toxin–antitoxin loci

(2017) Yingzhou Xie et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

Chaperone addiction of toxin–antitoxin systems

(2016) Patricia Bordes et al.   Nature Communications

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

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

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

The other face of restriction: modification-dependent enzymes

(2013) Wil A. M. Loenen et al.   NUCLEIC ACIDS RESEARCH

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

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

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

The many blades of the β-propeller proteins: conserved but versatile

(2011) Cammy K.-M. Chen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Toxin–antitoxin systems: why so many, what for?

(2010) Laurence Van Melderen   CURRENT OPINION IN MICROBIOLOGY

Escherichia coli rnlA and rnlB Compose a Novel Toxin-Antitoxin System

(2010) M. Koga et al.   GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH