ArticleNucleic acids research2020
PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- AcrSeek: metric learning with hybrid negative mining for anti-CRISPR protein detection under extreme class imbalance.Bioinformatics (Oxford, England) · 2026Article
- Semantic design: Programming functional genes from genomic context.Cell genomics · 2026Article
- Isolation, characterization and genomic analysis of a novel lytic bacteriophage EcoPhCCP1, capable of infecting multiple strains of multidrug-resistantThe Journal of general virology · 2026Article
- TPT: a compact CNN-transformer encoder for efficient microbial small protein modeling.Frontiers in microbiology · 2026Article
- Article
- Artificial Intelligence Applications in Bacteriophage Genomics and Host Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- In silico approaches for discovering microbial antiviral defense systems.Briefings in bioinformatics · 2025Review
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes.Protein science : a publication of the Protein Society · 2025Article
- CombattingAntibiotics (Basel, Switzerland) · 2025Review
- Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome.Frontiers in veterinary science · 2025Article
- Isolation and Characterization of Lytic Bacteriophages Capable of Infecting Diverse Multidrug-Resistant Strains ofPharmaceuticals (Basel, Switzerland) · 2024Article
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- Structure-guided discovery of anti-CRISPR and anti-phage defense proteins.Nature communications · 2024Article
- Current Updates of CRISPR/Cas System and Anti-CRISPR Proteins: Innovative Applications to Improve the Genome Editing Strategies.International journal of nanomedicine · 2024Review
- Comparative Analyses of Bacteriophage Genomes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- TRILL: ORCHESTRATING MODULAR DEEP-LEARNING WORKFLOWS FOR DEMOCRATIZED, SCALABLE PROTEIN ANALYSIS AND ENGINEERING.bioRxiv : the preprint server for biology · 2023Article
- Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR-Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR-Cas machineries for the development of new CRISPR-Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects. PaCRISPR employs different types of feature recognition united within an ensemble framework. Extensive cross-validation and independent tests show that PaCRISPR achieves a significantly more accurate performance compared with homology-based baseline predictors and an existing toolkit. The performance of PaCRISPR was further validated in discovering anti-CRISPRs that were not part of the training for PaCRISPR, but which were recently demonstrated to function as anti-CRISPRs for phage infections. Data visualization on anti-CRISPR relationships, highlighting sequence similarity and phylogenetic considerations, is part of the output from the PaCRISPR toolkit, which is freely available at http://pacrispr.erc.monash.edu/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.