A conserved family of immune effectors cleaves cellular ATP upon viral infection

Bacterial NLR-related proteins protect against phage

(2023) Emily M. Kibby et al.   CELL

The evolutionary success of regulated cell death in bacterial immunity

(2023) François Rousset et al.   CURRENT OPINION IN MICROBIOLOGY

CBASS phage defense and evolution of antiviral nucleotide signaling

(2022) Brianna Duncan-Lowey et al.   CURRENT OPINION IN IMMUNOLOGY

Fungal gasdermin-like proteins are controlled by proteolytic cleavage

(2022) Corinne Clavé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial gasdermins reveal an ancient mechanism of cell death

(2022) Alex G. Johnson et al.   SCIENCE

Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

(2022) Balwina Koopal et al.   CELL

A short prokaryotic Argonaute activates membrane effector to confer antiviral defense

(2022) Zhifeng Zeng et al.   Cell Host & Microbe

Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity

(2022) Samuel J. Hobbs et al.   NATURE

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Control of bacterial immune signaling by a WYL domain transcription factor

(2022) Chelsea L Blankenchip et al.   NUCLEIC ACIDS RESEARCH

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

(2022) Mario Rodríguez Mestre et al.   NUCLEIC ACIDS RESEARCH

Systematic and quantitative view of the antiviral arsenal of prokaryotes

(2022) Florian Tesson et al.   Nature Communications

Cyclic nucleotide-induced helical structure activates a TIR immune effector

(2022) Gaëlle Hogrel et al.   NATURE

Cryo-EM structure of an active bacterial TIR–STING filament complex

(2022) Benjamin R. Morehouse et al.   NATURE

Shared TIR enzymatic functions regulate cell death and immunity across the tree of life

(2022) Kow Essuman et al.   SCIENCE

Prokaryotic innate immunity through pattern recognition of conserved viral proteins

(2022) Linyi Alex Gao et al.   SCIENCE

Bacteria deplete deoxynucleotides to defend against bacteriophage infection

(2022) Nitzan Tal et al.   Nature Microbiology

An expanded arsenal of immune systems that protect bacteria from phages

(2022) Adi Millman et al.   Cell Host & Microbe

Viruses inhibit TIR gcADPR signalling to overcome bacterial defence

(2022) Azita Leavitt et al.   NATURE

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

(2022) Mindaugas Zaremba et al.   Nature Microbiology

Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion

(2022) Jeremy Garb et al.   Nature Microbiology

Calcium-responsive kinase LadS modulates type I–F CRISPR-Cas adaptive immunity

(2021) Chuan-min Zhou et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The purine nucleoside phosphorylase pnp-1 regulates epithelial cell resistance to infection in C. elegans

(2021) Eillen Tecle et al.   PLoS Pathogens

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

(2021) Nitzan Tal et al.   CELL

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

Molecular mechanisms of the CdnG-Cap5 antiphage defense system employing 3′,2′-cGAMP as the second messenger

(2021) Shirin Fatma et al.   Nature Communications

Viral Z-RNA triggers ZBP1-dependent cell death

(2021) Siddharth Balachandran et al.   Current Opinion in Virology

Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity

(2020) Rebecca K. Lau et al.   MOLECULAR CELL

Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets

(2020) Brandon L. Greene et al.   Annual Review of Biochemistry

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

Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation

(2020) Donghyun Ka et al.   Nature Communications

Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy

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

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

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

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 cGAS-like enzymes synthesize diverse nucleotide signals

(2019) Aaron T. Whiteley et al.   NATURE

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

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 discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Cloning and expression of ATP N-glycosidase from the freshwater sponge Ephydatia muelleri

(2018) Tõnu Reintamm et al.   BIOCHIMIE

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Molecular Mechanisms of Two-Component Signal Transduction

(2016) Christopher P. Zschiedrich et al.   JOURNAL OF MOLECULAR BIOLOGY

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

(2016) D. Dar et al.   SCIENCE

Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death

(2015) Jianjin Shi et al.   NATURE

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Diversity and Variability of NOD-Like Receptors in Fungi

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

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

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

DNA-guided DNA interference by a prokaryotic Argonaute

(2014) Daan C. Swarts et al.   NATURE

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

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

Recent advances in understanding and managing adenosine deaminase and purine nucleoside phosphorylase deficiencies

(2013) Eyal Grunebaum et al.   Current Opinion in Allergy and Clinical Immunology

The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals

(2013) Benedict Yuen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA

(2013) Ivan Olovnikov et al.   MOLECULAR CELL

Comparative genomics of defense systems in archaea and bacteria

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

The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations

(2012) Mayuko Hamada et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA Interference in Fungi: Pathways, Functions, and Applications

(2011) Yunkun Dang et al.   EUKARYOTIC CELL

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase

(2011) David C. Goldstone et al.   NATURE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS