ArticleNucleic acids research2023
Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
5 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design.Nucleic acids research · 2026Article
- Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.Nucleic acids research · 2026Article
- Application of functional genomics for domestication of novel non-model microbes.Journal of industrial microbiology & biotechnology · 2024Review
- Research Hotspots and Trends of NK Cell Immunotherapy for Acute Myeloid Leukemia: A Bibliometric Analysis From 2000 to 2023.Cancer control : journal of the Moffitt Cancer CenterReview
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.
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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.