ArticleBioinformatics (Oxford, England)2022
Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Exploratory Multi-Platform Bioinformatic Analysis of MEAK7 and Its Molecular, Survival, and Immune Associations in Pancreatic Ductal Adenocarcinoma.International journal of molecular sciences · 2026Article
- Establishment of CRISPR/Cas9 Genome Editing inJournal of fungi (Basel, Switzerland) · 2026Article
- Integrative Bioinformatic Characterization of the HDAC6-Driven Cytoskeleton-Wnt Signaling Interface in Hepatocellular Carcinoma: Implications for Immune Modulation and Therapeutic Targeting.International journal of molecular sciences · 2026Article
- Evaluation of computational tools for the prediction of CRISPR/SpCas9 gRNA activity in plants.Plant cell reports · 2026Article
- Article
- Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026Review
- Tiny but powerful: protoplast isolation inFrontiers in plant science · 2026Article
- Immune cell communication networks and memory CD8Frontiers in immunology · 2025Article
- Expanding Horizons of CRISPR/Cas Technology: Clinical Advancements, Therapeutic Applications, and Challenges in Gene Therapy.International journal of molecular sciences · 2024Review
- Article
- High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism,Genome research · 2024Article
- Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells.Nucleic acids research · 2024Article
- Usefulness of current sgRNA design guidelines and in vitro cleavage assays for plant CRISPR/Cas genome editing: a case targeting the polyphenol oxidase gene family in eggplant (Solanum melongena L.).Transgenic research · 2023Article
- Corneal gene therapy: Structural and mechanistic understanding.The ocular surface · 2023Article
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Authors and funding
2 authors.
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Abstract
motivationThe CRISPR/Cas9 system is widely used for genome editing. The editing efficiency of CRISPR/Cas9 is mainly determined by the guide RNA (gRNA). Although many computational algorithms have been developed in recent years, it is still a challenge to select optimal bioinformatics tools for gRNA design in different experimental settings.
resultsWe performed a comprehensive comparison analysis of 15 public algorithms for gRNA design, using 16 experimental gRNA datasets. Based on this analysis, we identified the top-performing algorithms, with which we further implemented various computational strategies to build ensemble models for performance improvement. Validation analysis indicates that the new ensemble model had improved performance over any individual algorithm alone at predicting gRNA efficacy under various experimental conditions. AVAILABILITY AND IMPLEMENTATION: The new sgRNA design tool is freely accessible as a web application via https://crisprdb.org. The source code and stand-alone version is available at Figshare (https://doi.org/10.6084/m9.figshare.21295863) and Github (https://github.com/wang-lab/CRISPRDB). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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