AIMC Topic: RNA, Guide, CRISPR-Cas Systems

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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 Genetic Engineering Synthetic Biology RNA, Guide, CRISPR-Cas Systems Artificial Intelligence Gene Editing
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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...
RNA, Guide, CRISPR-Cas Systems Deep Learning CRISPR-Cas Systems Streptococcus pyogenes Gene Editing Neural Networks, Computer
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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 Saccharomyces cerevisiae RNA, Untranslated CRISPR-Cas Systems Gene Editing Gene Library 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 CRISPR-Cas Systems Gene Editing Humans Machine Learning Deep Learning Computational Biology
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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...
Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Humans Machine Learning
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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, ...
Neural Networks, Computer Deep Learning CRISPR-Cas Systems Gene Editing RNA, Guide, CRISPR-Cas Systems
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SLKB: synthetic lethality knowledge base.

Nucleic acids research Jan 5, 2024
Emerging CRISPR-Cas9 technology permits synthetic lethality (SL) screening of large number of gene pairs from gene combination double knockout (CDKO) experiments. However, the poor integration and annotation of CDKO SL data in current SL databases li...
Synthetic Lethal Mutations Internet Use Knowledge Bases Humans RNA, Guide, CRISPR-Cas Systems
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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 RNA, Guide, CRISPR-Cas Systems Deep Learning CRISPR-Cas Systems
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CRISPR-Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning.

Nucleic acids research Apr 22, 2022
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become a successful and promising technology for gene-editing. To facilitate its effective application, various computational tools ha...
Deep Learning RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Gene Editing
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Uncertainty-aware and interpretable evaluation of Cas9-gRNA and Cas12a-gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning.

Nucleic acids research Jan 25, 2022
The choice of guide RNA (gRNA) for CRISPR-based gene targeting is an essential step in gene editing applications, but the prediction of gRNA specificity remains challenging. Lack of transparency and focus on point estimates of efficiency disregarding...
RNA, Guide, CRISPR-Cas Systems Reproducibility of Results Deep Learning Gene Editing Gene Targeting Genomics CRISPR-Cas Systems Neural Networks, Computer Algorithms Humans
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