AIMC Topic: Gene Editing

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[Artificial intelligence-assisted design, mining, and modification of CRISPR-Cas systems].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Mar 25, 2025
With the rapid advancement of synthetic biology, CRISPR-Cas systems have emerged as a powerful tool for gene editing, demonstrating significant potential in various fields, including medicine, agriculture, and industrial biotechnology. This review co...
CRISPR-Cas Systems Data Mining Artificial Intelligence Genetic Engineering RNA, Guide, CRISPR-Cas Systems Gene Editing Synthetic Biology
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DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features.

Briefings in functional genomics Jan 15, 2025
The CRISPR/Cas9 system developed from Streptococcus pyogenes (SpCas9) has high potential in gene editing. However, its successful application is hindered by the considerable variability in target efficiencies across different single guide RNAs (sgRNA...
Streptococcus pyogenes CRISPR-Cas Systems RNA, Guide, CRISPR-Cas Systems Gene Editing Neural Networks, Computer Deep Learning
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High throughput variant libraries and machine learning yield design rules for retron gene editors.

Nucleic acids research Jan 11, 2025
The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template fo...
Machine Learning CRISPR-Cas Systems RNA, Untranslated Gene Library Saccharomyces cerevisiae Gene Editing RNA, Guide, CRISPR-Cas Systems
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DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: CRISPR/Cas9 technology has been revolutionizing the field of gene editing. Guide RNAs (gRNAs) enable Cas9 proteins to target specific genomic loci for editing. However, editing efficiency varies between gRNAs and so computational methods ...
RNA, Guide, CRISPR-Cas Systems Computational Biology Gene Editing CRISPR-Cas Systems Machine Learning Deep Learning Humans
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Generating, modeling and evaluating a large-scale set of CRISPR/Cas9 off-target sites with bulges.

Nucleic acids research Jul 8, 2024
The CRISPR/Cas9 system is a highly accurate gene-editing technique, but it can also lead to unintended off-target sites (OTS). Consequently, many high-throughput assays have been developed to measure OTS in a genome-wide manner, and their data was us...
CRISPR-Cas Systems Machine Learning RNA, Guide, CRISPR-Cas Systems Gene Editing Humans
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'ChatGPT for CRISPR' creates new gene-editing tools.

Nature May 1, 2024
Natural Language Processing Humans Gene Editing CRISPR-Cas Systems
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CRISPR-DIPOFF: an interpretable deep learning approach for CRISPR Cas-9 off-target prediction.

Briefings in bioinformatics Jan 22, 2024
CRISPR Cas-9 is a groundbreaking genome-editing tool that harnesses bacterial defense systems to alter DNA sequences accurately. This innovative technology holds vast promise in multiple domains like biotechnology, agriculture and medicine. However, ...
RNA, Guide, CRISPR-Cas Systems Gene Editing Deep Learning CRISPR-Cas Systems Neural Networks, Computer
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Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities.

Briefings in bioinformatics Sep 22, 2023
In silico design of single guide RNA (sgRNA) plays a critical role in clustered regularly interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. Continuous efforts are aimed at improving sgRNA design with efficient o...
Gene Editing CRISPR-Cas Systems RNA, Guide, CRISPR-Cas Systems Deep Learning
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Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review.

Briefings in bioinformatics May 19, 2023
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9) is a popular and effective two-component technology used for targeted genetic manipulation. It is currently the most versatile and accurate method...
CRISPR-Cas Systems Machine Learning Gene Editing Deep Learning
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AcrNET: predicting anti-CRISPR with deep learning.

Bioinformatics (Oxford, England) May 4, 2023
MOTIVATION: As an important group of proteins discovered in phages, anti-CRISPR inhibits the activity of the immune system of bacteria (i.e. CRISPR-Cas), offering promise for gene editing and phage therapy. However, the prediction and discovery of an...
Gene Editing Deep Learning Bacteriophages Proteins Neural Networks, Computer
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