AIMC Topic: 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...
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...
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...
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...
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...
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...
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...
Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations.
ACS synthetic biology
Feb 25, 2025
CRISPR-Cas technology has revolutionized biology by enabling precise DNA and RNA edits with ease. However, significant challenges remain for translating this technology into clinical applications. Traditional protein engineering methods, such as rati...
Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.
Scientific reports
Feb 13, 2025
Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocy...
Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.
Journal of translational medicine
Feb 4, 2025
The revolutionary CRISPR-Cas9 system leverages a programmable guide RNA (gRNA) and Cas9 proteins to precisely cleave problematic regions within DNA sequences. This groundbreaking technology holds immense potential for the development of targeted ther...
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