Prokaryotic innate immunity through pattern recognition of conserved viral proteins

Shutoff of host transcription triggers a toxin-antitoxin system to cleave phage RNA and abort infection

(2021) Chantal K. Guegler et al.   MOLECULAR CELL

A nucleotide-sensing endonuclease from the Gabija bacterial defense system

(2021) Rui Cheng et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans

(2021) Gurmeet Kaur et al.   eLife

New tools for automated cryo-EM single-particle analysis in RELION-4.0

(2021) Dari Kimanius et al.   BIOCHEMICAL JOURNAL

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The arms race between bacteria and their phage foes

(2020) Hannah G. Hampton et al.   NATURE

Comparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7

(2020) Aurelija M. Grigonyte et al.   Viruses-Basel

Highly-regulated, diversifying NTP-based biological conflict systems with implications for emergence of multicellularity

(2020) Gurmeet Kaur et al.   eLife

CBASS Immunity Uses CARF-Related Effectors to Sense 3′–5′- and 2′–5′-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection

(2020) Brianna Lowey et al.   CELL

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense

(2020) Kira S Makarova et al.   NUCLEIC ACIDS RESEARCH

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

Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

(2020) Nikoline S. Olsen et al.   Viruses-Basel

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Human NLRP1 is a sensor for double-stranded RNA

(2020) Stefan Bauernfried et al.   SCIENCE

Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme

(2020) Shoucai Ma et al.   SCIENCE

Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ

(2020) Raoul Martin et al.   SCIENCE

Reconstitution and structure of a plant NLR resistosome conferring immunity

(2019) Jizong Wang et al.   SCIENCE

Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses

(2019) Corynne L. Dedeo et al.   Annual Review of Virology

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

(2019) Anna-Lena Van de Weyer et al.   CELL

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

(2019) Tristan Bepler et al.   NATURE METHODS

Current Developments in Coot for Macromolecular Model Building of Electron Cryo‐microscopy and Crystallographic Data

(2019) Ana Casañal et al.   PROTEIN SCIENCE

Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism

(2019) Ana Cuervo et al.   Nature Communications

Translational coupling via termination-reinitiation in archaea and bacteria

(2019) Madeleine Huber et al.   Nature Communications

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova 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

NLR surveillance of essential SEC-9 SNARE proteins induces programmed cell death upon allorecognition in filamentous fungi

(2018) Jens Heller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

A chemical defence against phage infection

(2018) Sarah Kronheim et al.   NATURE

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Anti-CRISPR: discovery, mechanism and function

(2017) April Pawluk et al.   NATURE REVIEWS MICROBIOLOGY

The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion

(2017) Jeannette L. Tenthorey et al.   SCIENCE

Intracellular innate immune surveillance devices in plants and animals

(2016) J. D. G. Jones et al.   SCIENCE

Atomic structure of the apoptosome: mechanism of cytochromec- and dATP-mediated activation of Apaf-1

(2015) Mengying Zhou et al.   GENES & DEVELOPMENT

Structure of the apoptosome: mechanistic insights into activation of an initiator caspase fromDrosophila

(2015) Yuxuan Pang et al.   GENES & DEVELOPMENT

Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization

(2015) L. Zhang et al.   SCIENCE

Diversity and Variability of NOD-Like Receptors in Fungi

(2014) Witold Dyrka et al.   Genome Biology and Evolution

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

NOD1 and NOD2: Signaling, Host Defense, and Inflammatory Disease

(2014) Roberta Caruso et al.   IMMUNITY

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

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

Synergy as a rationale for phage therapy using phage cocktails

(2014) Matthew Schmerer et al.   PeerJ

Revenge of the phages: defeating bacterial defences

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

A DNA break inducer activates the anticodon nuclease RloC and the adaptive immunity in Acinetobacter baylyi ADP1

(2013) Daniel Klaiman et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

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

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

(2012) Kamil Steczkiewicz et al.   NUCLEIC ACIDS RESEARCH

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

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

The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus

(2011) Yue Zhao et al.   NATURE

Innate immune recognition of bacterial ligands by NAIPs determines inflammasome specificity

(2011) Eric M. Kofoed et al.   NATURE

The DNA-packaging nanomotor of tailed bacteriophages

(2011) Sherwood R. Casjens   NATURE REVIEWS MICROBIOLOGY

Bacteriophages and their genomes

(2011) Graham F Hatfull et al.   Current Opinion in Virology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Structures of restriction endonucleaseHindIII in complex with its cognate DNA and divalent cations

(2009) Nobuhisa Watanabe et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2009) Olivier Danot et al.   STRUCTURE

The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces

(2008) Siyang Sun et al.   CELL

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH