ArticleBioinformatics (Oxford, England)2020
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 67 citations in OpenAlex.
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- SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.Briefings in bioinformatics · 2026Article
- The genome takes the wheel: CAR T with built-in circuits.Immuno-oncology technology · 2026Article
- Advances in CRISPR-Cas for Diagnosis and Treatment ofPathogens (Basel, Switzerland) · 2026Review
- Sassy: fuzzy searching DNA sequences using SIMD.Bioinformatics (Oxford, England) · 2026Article
- Deep learning-driven prediction of on-target activity, off-target risk, and repair outcomes in CRISPR/Cas9: current landscape and multi-scale perspectives.Journal of translational medicine · 2026Review
- PCdb: A comprehensive plant genome-editing database integrating sgRNA efficiency, off-target predictions, and epigenomic landscapes.Plant communications · 2026Article
- Targeting redundant gene families: A multiplexed, tissue-specific CRISPR toolbox for Arabidopsis genetic screens.Cell reports · 2026Article
- CRISPR-GPT for agentic automation of gene-editing experiments.Nature biomedical engineering · 2026Article
- A precision gene-engineered B cell medicine producing sustained levels of active factor IX for hemophilia B therapy.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- An overview of CRISPR-artificial intelligence theranostics: Current and emerging applications.Biomaterials translational · 2026Review
- CRISPR-HAWK: Haplotype- and Variant-aware guide design toolkit for CRISPR-Cas.bioRxiv : the preprint server for biology · 2025Article
- Targeted inhibition ofMolecular therapy. Methods & clinical development · 2025Article
- Cell line-matched reference enables high-precision functional genomics.Nature communications · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications.Nucleic acids research · 2025Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- Current trends in gene therapy to treat inherited disorders of the brain.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2.Genome biology · 2025Article
- A bioinformatic analysis of gene editing off-target loci altered by common polymorphisms, using 'PopOff'.Journal of the Royal Society of New Zealand · 2025Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationClustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects.
resultsTo overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project). AVAILABILITY AND IMPLEMENTATION: The software is freely available at: https://github.com/pinellolab/CRISPRitzhttps://github.com/InfOmics/CRISPRitz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.