ArticleNature biotechnology2023
Predicting prime editing efficiency and product purity by deep learning.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
109 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Prime Editing: An Overview.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Machine-learning in optimization of CRISPR technology.Machine learning. Health · 2026Review
- Article
- Advances in prime editing: Molecular innovations, Large-fragment engineering, and AI-driven design.Biodesign research · 2026Review
- Mechanistic machine learning for prediction of prime editing outcomes.Nature biotechnology · 2026Article
- UNCOVERseq enables sensitive and controlled gene editing off-target nomination across CRISPR-Cas modalities and systems.Nature communications · 2026Article
- Genomic repeats for single-cell molecular recording.bioRxiv : the preprint server for biology · 2026Article
- Prime Editing-Based Functional Characterization Supports a Likely Pathogenic Interpretation ofGenes · 2026Article
- U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations.Nature genetics · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- The Use of Deep Learning in RNA Therapeutic Development.ACS nano · 2026Review
- Uncovering functional variants using a high-efficiency PE3-based screening platform.Science advances · 2026Article
- Adapting prime editing with split prime editors in Escherichia coli and its application to Staphylococcus aureus genome editing.Applied microbiology and biotechnology · 2026Article
- Prime editing: Emerging mechanisms, engineering innovations, and next-generation applications.Biodesign research · 2026Review
- Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates.Nature biotechnology · 2026Article
- Article
- Directed evolution of small RNA-stabilizing motifs that improve prime-editing efficiency.Nature biotechnology · 2026Article
- RNA-LNP-mediated in vivo prime editing corrects disease phenotypes in a mouse model of citrullinemia type I.Science translational medicine · 2026Article
- Prime editing of a pathogenicScience translational medicine · 2026Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Prime editing is a versatile genome editing tool but requires experimental optimization of the prime editing guide RNA (pegRNA) to achieve high editing efficiency. Here we conducted a high-throughput screen to analyze prime editing outcomes of 92,423 pegRNAs on a highly diverse set of 13,349 human pathogenic mutations that include base substitutions, insertions and deletions. Based on this dataset, we identified sequence context features that influence prime editing and trained PRIDICT (prime editing guide prediction), an attention-based bidirectional recurrent neural network. PRIDICT reliably predicts editing rates for all small-sized genetic changes with a Spearman's R of 0.85 and 0.78 for intended and unintended edits, respectively. We validated PRIDICT on endogenous editing sites as well as an external dataset and showed that pegRNAs with high (>70) versus low (<70) PRIDICT scores showed substantially increased prime editing efficiencies in different cell types in vitro (12-fold) and in hepatocytes in vivo (tenfold), highlighting the value of PRIDICT for basic and for translational research applications.
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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.