ArticleNature communications2023
Prediction of base editor off-targets by deep learning.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Transgene-free genome editing in plants.aBIOTECH · 2026Review
- Cytosine base editing of LPA in transgenic mice averts large deletions.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Base Editors for Engineering Industrial Microorganisms: Types, Applications, and Future Perspectives.Biotechnology journal · 2026Review
- Review
- Decoding the role of chromatin context in the off-target effects of CRISPR gene editing with EGOLD.Cell discovery · 2026Article
- Genetic recording and in situ readout of single-cell signaling memory.Nature chemical biology · 2026Article
- Non-clinical safety considerations on genome editing using the CRISPR/Cas system.Genes & diseases · 2026Review
- CasMiner: a deep-learning tool for high-throughput mining and rational design of efficient Cas9.National science review · 2026Article
- Harnessing artificial intelligence to advance CRISPR-based genome editing technologies.Nature reviews. Genetics · 2026Review
- An overview of CRISPR-artificial intelligence theranostics: Current and emerging applications.Biomaterials translational · 2026Review
- Pharmacovigilance in Cell and Gene Therapy: Evolving Challenges in Risk Management and Long-Term Follow-Up.Drug safety · 2026Review
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- From Code to Life: The AI-Driven Revolution in Genome Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Revolutionizing CRISPR technology with artificial intelligence.Experimental & molecular medicine · 2025Review
- Deep Learning Based Models for CRISPR/Cas Off-Target Prediction.Small methods · 2025Review
- Article
- Preclinical evaluation of AGT mRNA replacement therapy for primary hyperoxaluria type I disease.Science advances · 2025Article
- The Interface of Gene Editing with Regenerative Medicine.Engineering (Beijing, China) · 2025Article
- The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells.Genome biology · 2024Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to the tolerance of mismatches between gRNA and targeting sequence, base editors frequently induce unwanted Cas9-dependent off-target mutations. Here, to develop models to predict such off-targets, we design gRNA-off- target pairs for adenine base editors (ABEs) and cytosine base editors (CBEs) and stably integrate them into the human cells. After five days of editing, we obtain valid efficiency datasets of 54,663 and 55,727 off-targets for ABEs and CBEs, respectively. We use the datasets to train deep learning models, resulting in ABEdeepoff and CBEdeepoff, which can predict off-target sites. We use these tools to predict off-targets for a panel of endogenous loci and achieve Spearman correlation values varying from 0.710 to 0.859. Finally, we develop an integrated tool that is freely accessible via an online web server http://www.deephf.com/#/bedeep/bedeepoff . These tools could facilitate minimizing the off-target effects of base editing.
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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.