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

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Revisiting the rules of life for viruses of microorganisms

(2021) Adrienne M. S. Correa et al.   NATURE REVIEWS MICROBIOLOGY

A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis

(2021) Ekaterina Kropocheva 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

NgAgo possesses guided DNA nicking activity

(2021) Kok Zhi Lee et al.   NUCLEIC ACIDS RESEARCH

SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation

(2021) Jurre A. Steens et al.   Nature Communications

A Novel NAD Signaling Mechanism in Axon Degeneration and its Relationship to Innate Immunity

(2021) Eleanor L. Hopkins et al.   Frontiers in Molecular Biosciences

Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

(2021) Nitzan Tal et al.   CELL

Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition

(2021) Tatiana Dimitriu et al.   Cell Host & Microbe

Antiviral activity of bacterial TIR domains via immune signalling molecules

(2021) Gal Ofir et al.   NATURE

Are Argonaute-Associated Tiny RNAs Junk, Inferior miRNAs, or a New Type of Functional RNAs?

(2021) Kotaro Nakanishi   Frontiers in Molecular Biosciences

Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease

(2020) Seung-Yoon Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Viral load of SARS-CoV-2 in clinical samples

(2020) Yang Pan et al.   LANCET INFECTIOUS DISEASES

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA targeting and interference by a bacterial Argonaute nuclease

(2020) Anton Kuzmenko et al.   NATURE

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

Thermus thermophilus Argonaute Functions in the Completion of DNA Replication

(2020) Samson M. Jolly et al.   CELL

STING cyclic dinucleotide sensing originated in bacteria

(2020) Benjamin R. Morehouse et al.   NATURE

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

(2020) Linyi Gao 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

The prokaryotic Argonaute proteins enhance homology sequence-directed recombination in bacteria

(2019) Lei Fu et al.   NUCLEIC ACIDS RESEARCH

Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage

(2019) Alexander J. Meeske et al.   NATURE

TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death

(2019) Li Wan et al.   SCIENCE

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

(2019) Shane Horsefield et al.   SCIENCE

HOLMESv2: A CRISPR-Cas12b-Assisted Platform for Nucleic Acid Detection and DNA Methylation Quantitation

(2019) Linxian Li et al.   ACS Synthetic Biology

TIR Domain Proteins Are an Ancient Family of NAD + -Consuming Enzymes

(2018) Kow Essuman et al.   CURRENT BIOLOGY

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA

(2018) Daniel M Dayeh et al.   NUCLEIC ACIDS RESEARCH

Programmable RNA recognition using a CRISPR-associated Argonaute

(2018) Audrone Lapinaite et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

(2018) Jonathan S. Gootenberg et al.   SCIENCE

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

The mitochondrial Nod-like receptor NLRX1 modifies apoptosis through SARM1

(2018) Samuel A. Killackey et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

(2018) Lucas B. Harrington et al.   SCIENCE

The Expanded Universe of Prokaryotic Argonaute Proteins

(2018) Sergei Ryazansky et al.   mBio

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Prokaryotic Argonaute proteins: novel genome-editing tools?

(2017) Jorrit W. Hegge et al.   NATURE REVIEWS MICROBIOLOGY

The SARM1 Toll/Interleukin-1 Receptor Domain Possesses Intrinsic NAD + Cleavage Activity that Promotes Pathological Axonal Degeneration

(2017) Kow Essuman et al.   NEURON

Nucleic acid detection with CRISPR-Cas13a/C2c2

(2017) Jonathan S. Gootenberg et al.   SCIENCE

Guide-independent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii

(2017) Adrian Zander et al.   Nature Microbiology

Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein

(2017) Sarah Willkomm et al.   Nature Microbiology

DNA recognition by an RNA-guided bacterial Argonaute

(2017) Kevin W. Doxzen et al.   PLoS One

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Toxin-antitoxin systems in bacterial growth arrest and persistence

(2016) Rebecca Page et al.   Nature Chemical Biology

Viral Load Kinetics of MERS Coronavirus Infection

(2016) Myoung-don Oh et al.   NEW ENGLAND JOURNAL OF MEDICINE

A bacterial Argonaute with noncanonical guide RNA specificity

(2016) Emine Kaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute

(2016) Tomohiro Miyoshi et al.   Nature Communications

When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins

(2016) Ariel Hecht et al.   ACS Synthetic Biology

Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks

(2016) Natasha Bonilla et al.   PeerJ

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

(2015) Daan C. Swarts et al.   NUCLEIC ACIDS RESEARCH

Metabolic engineering of itaconate production in Escherichia coli

(2014) Kiira S. Vuoristo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

DNA-guided DNA interference by a prokaryotic Argonaute

(2014) Daan C. Swarts et al.   NATURE

The evolutionary journey of Argonaute proteins

(2014) Daan C Swarts et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes

(2013) A Maxwell Burroughs et al.   Biology Direct

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA

(2013) Ivan Olovnikov et al.   MOLECULAR CELL

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma

(2013) Roy L. Maute et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

(2010) Filipp Frank et al.   NATURE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   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

Viral load in patients infected with pandemic H1N1 2009 influenza A virus

(2009) Kelvin K.W. To et al.   JOURNAL OF MEDICAL VIROLOGY

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a PIWI/MID Domain Protein

(2009) James S. Parker et al.   MOLECULAR CELL

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION

Plant ARGONAUTES

(2008) Hervé Vaucheret   TRENDS IN PLANT SCIENCE

Positively regulated bacterial expression systems

(2008) Trygve Brautaset et al.   Microbial Biotechnology