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Planetary-scale metagenomic search reveals new patterns of CRISPR targeting
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.cell.2022.08.023openalex-snapshot
Expansion of the global RNA virome reveals diverse clades of bacteriophages
inferredcites →https://doi.org/10.1016/j.chom.2019.01.017openalex-snapshot
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
inferredcites →https://doi.org/10.1016/j.chom.2021.03.018openalex-snapshot
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages
inferredcites →https://doi.org/10.1016/j.chom.2021.09.001openalex-snapshot
Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations
inferredcites →https://doi.org/10.1016/j.copbio.2020.09.008openalex-snapshot
Conquering CRISPR: how phages overcome bacterial adaptive immunity
inferredcites →https://doi.org/10.1016/j.cub.2023.06.033openalex-snapshot
Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales
inferredcites →https://doi.org/10.1016/j.jmb.2023.168036openalex-snapshot
In Silico Approaches for Prediction of Anti-CRISPR Proteins
inferredcites →https://doi.org/10.1016/j.mib.2022.102152openalex-snapshot
Ecological dynamics of plasmid transfer and persistence in microbial communities
inferredcites →https://doi.org/10.1016/j.molcel.2016.02.031openalex-snapshot
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
inferredcites →https://doi.org/10.1016/j.xgen.2024.100725openalex-snapshot
CRISPR-Cas spacer acquisition is a rare event in human gut microbiome
inferredcites →https://doi.org/10.1038/ismej.2015.162openalex-snapshot
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories
inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
inferredcites →https://doi.org/10.1038/ncomms10476openalex-snapshot
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
inferredcites →https://doi.org/10.1038/ncomms10613openalex-snapshot
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
inferredcites →https://doi.org/10.1038/nm.4517openalex-snapshot
Current understanding of the human microbiome
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmicrobiol.2017.92openalex-snapshot
A decade of discovery: CRISPR functions and applications
inferredcites →https://doi.org/10.1038/nrmicro.2015.14openalex-snapshot
CRISPR–Cas adaptation: insights into the mechanism of action
inferredcites →https://doi.org/10.1038/nrmicro.2017.120openalex-snapshot
Anti-CRISPR: discovery, mechanism and function
inferredcites →https://doi.org/10.1038/s41467-020-20241-wopenalex-snapshot
Perineuronal nets stabilize the grid cell network
inferredcites →https://doi.org/10.1038/s41564-017-0096-0openalex-snapshot
Stability of the human faecal microbiome in a cohort of adult men
inferredcites →https://doi.org/10.1038/s41564-018-0166-yopenalex-snapshot
Phage puppet masters of the marine microbial realm
inferredcites →https://doi.org/10.1038/s41564-018-0190-yopenalex-snapshot
Host-linked soil viral ecology along a permafrost thaw gradient
inferredcites →https://doi.org/10.1038/s41564-018-0302-8openalex-snapshot
Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation
inferredcites →https://doi.org/10.1038/s41564-018-0312-6openalex-snapshot
Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
inferredcites →https://doi.org/10.1038/s41564-019-0510-xopenalex-snapshot
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
inferredcites →https://doi.org/10.1038/s41564-021-00928-6openalex-snapshot
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
inferredcites →https://doi.org/10.1038/s41564-022-01203-yopenalex-snapshot
Wildfire-dependent changes in soil microbiome diversity and function
inferredcites →https://doi.org/10.1038/s41564-023-01347-5openalex-snapshot
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats
inferredcites →https://doi.org/10.1038/s41579-019-0299-xopenalex-snapshot
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
inferredcites →https://doi.org/10.1038/s41586-024-07994-wopenalex-snapshot
Diverse anti-defence systems are encoded in the leading region of plasmids
inferredcites →https://doi.org/10.1038/s41592-025-02701-7openalex-snapshot
Ultrafast and accurate sequence alignment and clustering of viral genomes
inferredcites →https://doi.org/10.1038/s41598-023-32078-6openalex-snapshot
CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts
inferredcites →https://doi.org/10.1080/15476286.2018.1509662openalex-snapshot
Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems
inferredcites →https://doi.org/10.1089/crispr.2020.0059openalex-snapshot
CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btw456openalex-snapshot
Assemble CRISPRs from metagenomic sequencing data
inferredcites →https://doi.org/10.1093/ismejo/wrae134openalex-snapshot
Dynamics of CRISPR-mediated virus–host interactions in the human gut microbiome
inferredcites →https://doi.org/10.1093/nar/gkaa967openalex-snapshot
The international nucleotide sequence database collaboration
inferredcites →https://doi.org/10.1093/nar/gkac1037openalex-snapshot
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
inferredcites →https://doi.org/10.1093/nar/gkac1080openalex-snapshot
MGnify: the microbiome sequence data analysis resource in 2023
inferredcites →https://doi.org/10.1093/nar/gkac142openalex-snapshot
Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences
inferredcites →https://doi.org/10.1093/nar/gkac163openalex-snapshot
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
inferredcites →https://doi.org/10.1093/nar/gkac974openalex-snapshot
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9
inferredcites →https://doi.org/10.1093/nar/gkac976openalex-snapshot
The IMG/M data management and analysis system v.7: content updates and new features
inferredcites →https://doi.org/10.1093/nar/gkad932openalex-snapshot
dbAPIS: a database of anti-prokaryotic immune system genes
inferredcites →https://doi.org/10.1093/nar/gkad964openalex-snapshot
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
inferredcites →https://doi.org/10.1093/nar/gkae772openalex-snapshot
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gkt183openalex-snapshot
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
inferredcites →https://doi.org/10.1093/nargab/lqaa063openalex-snapshot
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nargab/lqab067openalex-snapshot
PHROG: families of prokaryotic virus proteins clustered using remote homology
inferredcites →https://doi.org/10.1098/rstb.2012.0383openalex-snapshot
Energy, ecology and the distribution of microbial life
inferredcites →https://doi.org/10.1111/j.1462-2920.2012.02879.xopenalex-snapshot
Phage mutations in response to CRISPR diversification in a bacterial population
inferredcites →https://doi.org/10.1126/science.1138140openalex-snapshot
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
inferredcites →https://doi.org/10.1126/science.1153213openalex-snapshot
The Microbial Engines That Drive Earth's Biogeochemical Cycles
inferredcites →https://doi.org/10.1126/science.1157358openalex-snapshot
Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities
inferredcites →https://doi.org/10.1126/science.1258096openalex-snapshot
The new frontier of genome engineering with CRISPR-Cas9
inferredcites →https://doi.org/10.1126/science.add8643openalex-snapshot
CRISPR technology: A decade of genome editing is only the beginning
inferredcites →https://doi.org/10.1128/aem.00177-23openalex-snapshot
Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in “Pink Berry” Marine Microbial Aggregates
inferredcites →https://doi.org/10.1128/mbio.00897-17openalex-snapshot
On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
inferredcites →https://doi.org/10.1128/msystems.00075-18openalex-snapshot
Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses
inferredcites →https://doi.org/10.1128/msystems.00284-23openalex-snapshot
Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation
inferredcites →https://doi.org/10.1146/annurev-ecolsys-121415-032428openalex-snapshot
Evolution and Ecology of CRISPR
inferredcites →https://doi.org/10.1146/annurev-micro-030322-040423openalex-snapshot
Accelerated Evolution by Diversity-Generating Retroelements
inferredcites →https://doi.org/10.1146/annurev-virology-100120-011239openalex-snapshot
Microviruses: A World Beyond phiX174
inferredcites →https://doi.org/10.1146/annurev-virology-101416-041639openalex-snapshot
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
inferredcites →https://doi.org/10.1146/annurev.ecolsys.38.091206.095740openalex-snapshot
The Social Lives of Microbes
inferredcites →https://doi.org/10.1146/annurev.micro.112408.134123openalex-snapshot
CRISPR/Cas System and Its Role in Phage-Bacteria Interactions
inferredcites →https://doi.org/10.1155/2013/370871openalex-snapshot
Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-8-209openalex-snapshot
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.12688/f1000research.4492.2openalex-snapshot
Cytoscape: the network visualization tool for GenomeSpace workflows
inferredcites →https://doi.org/10.1371/journal.pbio.3002638openalex-snapshot
Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.3389/fmicb.2021.664299openalex-snapshot
Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array
inferredcites →https://doi.org/10.5281/zenodo.10525085openalex-snapshot
Kingfisher: A utility for procurement of public sequencing data
inferredcites →https://doi.org/10.5281/zenodo.7517352openalex-snapshot
Host Translation Machinery is not a Barrier to Phages that Infect CPR and non-CPR Bacteria
inferredcites →https://doi.org/10.7717/peerj.3788openalex-snapshot
MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41467-026-71096-6openalex-snapshot
Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag244openalex-snapshot
Sassy: fuzzy searching DNA sequences using SIMD
inferred← citeshttps://doi.org/10.1093/ismejo/wrag172openalex-snapshot
Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions
inferred← citeshttps://doi.org/10.1101/2025.09.09.675206openalex-snapshot
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
inferred← citeshttps://doi.org/10.1101/2025.09.30.679422openalex-snapshot
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae
inferred← citeshttps://doi.org/10.52843/cassyni.rndrq2openalex-snapshot
Beyond microbes: multiomics reveals the influence of viruses on microbiomes
inferred← citeshttps://doi.org/10.64898/2026.05.01.722327openalex-snapshot
The Updateable Human Virome Database and toolkit: A novel framework for human virome analysis
inferred← citeshttps://doi.org/10.64898/2026.09.22.753571openalex-snapshot
Self-organized division of labor and selection for long-term antiviral defense in CRISPR arrays
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