AIMC Topic: CRISPR-Cas Systems

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Integrating AI and CRISPR Cas13a for rapid detection of tomato brown rugose fruit virus.

Scientific reports Jul 14, 2025
The Tomato Brown Rugose Fruit Virus (ToBRFV) has recently emerged as a serious threat to global tomato production, underscoring the need for rapid and sensitive diagnostic tools. Here, we present an AI-driven CRISPR-Cas13a pipeline for designing crRN...
Computational Biology RNA, Viral Plant Diseases Plant Viruses CRISPR-Cas Systems Solanum lycopersicum
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Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design.

Nature communications Jul 10, 2025
DNA is a promising medium for digital data storage due to its exceptional data density and longevity. Practical DNA-based storage systems require selective data retrieval to minimize decoding time and costs. In this work, we introduce CRISPR-Cas9 as ...
CRISPR-Associated Protein 9 Information Storage and Retrieval Semantics DNA Sequence Analysis, DNA Machine Learning CRISPR-Cas Systems
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CRISPR/Cas-Based Biosensing Strategies for Non-Nucleic Acid Contaminants in Food Safety: Status, Challenges, and Perspectives.

Journal of agricultural and food chemistry Jul 9, 2025
Non-nucleic acid targets (non-NATs), such as heavy metals, toxins, and pesticide residues, pose critical threats to food safety. Although CRISPR/Cas systems were initially developed for nucleic acid detection, recent advances have enabled their adapt...
Biosensing Techniques Metals, Heavy Nucleic Acids Food Safety Food Contamination CRISPR-Cas Systems
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Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.

Nature communications Jul 1, 2025
Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Fluorescent Timer protein, the Timer-of-cell-kinetics-and-activity system enables analysis of transcrip...
Transcription, Genetic Enhancer Elements, Genetic Genes, Reporter Gene Expression Regulation Spleen Forkhead Transcription Factors T-Lymphocytes, Regulatory Single-Cell Analysis Mice CRISPR-Cas Systems Machine Learning Flow Cytometry Animals Neural Networks, Computer Mice, Inbred C57BL
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Split DNA Tetrahedron-Mediated Spatiotemporal-Hierarchy CRISPR Cascade Integrated with Au@Pt Nanolabels and Artificial Intelligence for a Cervical Cancer MicroRNA Bioassay.

ACS nano Jun 11, 2025
The screening and monitoring of microRNAs as cancer molecular biomarkers is clinically significant, but traditional methods lack sufficient sensitivity, accuracy, and convenience. The CRISPR-colorimetric lateral flow assay (CLFA) integration offers a...
MicroRNAs DNA Female Uterine Cervical Neoplasms CRISPR-Cas Systems Platinum Gold Metal Nanoparticles Humans Artificial Intelligence
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Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity.

Nature communications Jun 3, 2025
Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA ed...
Artificial Intelligence CRISPR-Cas Systems Gene Editing RNA, Guide, CRISPR-Cas Systems HEK293 Cells CRISPR-Associated Protein 9 Humans
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A new strategy for Cas protein recognition based on graph neural networks and SMILES encoding.

Scientific reports Apr 30, 2025
The CRISPR-Cas system, an adaptive immune mechanism found in bacteria and archaea, has evolved into a promising genomic editing tool, with various types of Cas proteins playing a crucial role. In this study, we developed a set of strategies for minin...
Graph Neural Networks Neural Networks, Computer Computational Biology CRISPR-Cas Systems Databases, Protein CRISPR-Associated Proteins
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CRISPR-MFH: A Lightweight Hybrid Deep Learning Framework with Multi-Feature Encoding for Improved CRISPR-Cas9 Off-Target Prediction.

Genes Mar 28, 2025
BACKGROUND: The CRISPR-Cas9 system has emerged as one of the most promising gene-editing technologies in biology. However, off-target effects remain a significant challenge. While recent advances in deep learning have led to the development of models...
RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Humans Gene Editing Deep Learning
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CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network.

International journal of biological macromolecules Mar 22, 2025
Cas proteins (CRISPR-associated protein) are the core components of the CRISPR-Cas system, playing critical roles in defending against foreign DNA and RNA invasions. Identifying Cas proteins can provide deeper insights into the immune mechanisms of t...
CRISPR-Cas Systems Neural Networks, Computer Convolutional Neural Networks CRISPR-Associated Proteins Software Computational Biology
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Accurate Prediction of CRISPR/Cas13a Guide Activity Using Feature Selection and Deep Learning.

Journal of chemical information and modeling Mar 17, 2025
CRISPR/Cas13a serves as a key tool for nucleic acid tests; therefore, accurate prediction of its activity is essential for creating robust and sensitive diagnosis. In this study, we create a dual-branch neural network model that achieves high predict...
Neural Networks, Computer Deep Learning CRISPR-Cas Systems RNA, Guide, CRISPR-Cas Systems
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