Diverse enzymatic activities mediate antiviral immunity in prokaryotes

How a circularized tmRNA moves through the ribosome

(2019) Christopher D. Rae et al.   SCIENCE

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Cyclic GMP–AMP signalling protects bacteria against viral infection

(2019) Daniel Cohen et al.   NATURE

Systematic prediction of functionally linked genes in bacterial and archaeal genomes

(2019) Sergey A. Shmakov et al.   Nature Protocols

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

(2019) Shane Horsefield et al.   SCIENCE

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

Retrons and their applications in genome engineering

(2019) Anna J Simon et al.   NUCLEIC ACIDS RESEARCH

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

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

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

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

(2018) Sergey A. Shmakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site

(2018) Julia Gordeeva 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

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

(2017) Gal Ofir et al.   Nature Microbiology

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling

(2015) A. Maxwell Burroughs et al.   NUCLEIC ACIDS RESEARCH

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

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

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

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

(2014) Nicolás Toro et al.   PLoS One

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Complete genome sequence of 285P, a novel T7-like polyvalent E. coli bacteriophage

(2014) Bin Xu et al.   VIRUS GENES

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

Viruses: unlocking the greatest biodiversity on Earth

(2013) Curtis A. Suttle   GENOME

Revenge of the phages: defeating bacterial defences

(2013) Julie E. Samson et al.   NATURE REVIEWS MICROBIOLOGY

Comparative genomics of defense systems in archaea and bacteria

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

Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

(2012) Vivek Anantharaman et al.   Molecular BioSystems

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

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

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

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

(2009) Kira S Makarova et al.   Biology Direct

Novel Toxin-Antitoxin System Composed of Serine Protease and AAA-ATPase Homologues Determines the High Level of Stability and Incompatibility of the Tumor-Inducing Plasmid pTiC58

(2009) S. Yamamoto et al.   JOURNAL OF BACTERIOLOGY

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

Wheel of Life, Wheel of Death: A Mechanistic Insight into Signaling by STAND Proteins

(2009) Olivier Danot et al.   STRUCTURE

Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture

(2008) K. K. Kojima et al.   MOLECULAR BIOLOGY AND EVOLUTION

A diversity of uncharacterized reverse transcriptases in bacteria

(2008) Dawn M. Simon et al.   NUCLEIC ACIDS RESEARCH