ArticleBMC bioinformatics2017
A systematic evaluation of nucleotide properties for CRISPR sgRNA design.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools.RNA biology · 2020Pooled it
- Minimizing Off-Target Effects of CRISPR-Cas9 With Optimized sgRNA: Evaluation of Efficiency and Specificity in the Tumor Protein 53 (TP53) Region.Biotechnology and bioengineering · 2026Article
- Impact of predictive selection of LbCas12a CRISPR RNAs upon on- and off-target editing rates in soybean.Plant direct · 2024Article
- Computational Tools and Resources for CRISPR/Cas Genome Editing.Genomics, proteomics & bioinformatics · 2023Review
- Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?Nano today · 2022Article
- Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection.Bioinformatics (Oxford, England) · 2022Article
- Sequence-specific prediction of the efficiencies of adenine and cytosine base editors.Nature biotechnology · 2020Article
- Deep learning improves the ability of sgRNA off-target propensity prediction.BMC bioinformatics · 2020Article
- Computational approaches for effective CRISPR guide RNA design and evaluation.Computational and structural biotechnology journal · 2020Review
- SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.Science advances · 2019Article
- An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants.3 Biotech · 2019Article
- GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes.BMC bioinformatics · 2019Article
- Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity.International journal of biological sciences · 2019Article
- Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities.Nature communications · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the success of CRISPR screens.
resultsBy borrowing knowledge from oligonucleotide design and nucleosome occupancy models, we systematically evaluated candidate features computed from a number of nucleic acid, thermodynamic and secondary structure models on real CRISPR datasets. Our results showed that taking into account position-dependent dinucleotide features improved the design of effective sgRNAs with area under the receiver operating characteristic curve (AUC) >0.8, and the inclusion of additional features offered marginal improvement (∼2% increase in AUC).
conclusionUsing a machine-learning approach, we proposed an accurate prediction model for sgRNA design efficiency. An R package predictSGRNA implementing the predictive model is available at http://www.ams.sunysb.edu/~pfkuan/softwares.html#predictsgrna .
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