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CRISPR-Cas Systems

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Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations.

ACS synthetic biology
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
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
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...

CRISPR-MFH: A Lightweight Hybrid Deep Learning Framework with Multi-Feature Encoding for Improved CRISPR-Cas9 Off-Target Prediction.

Genes
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...

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

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
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...

Machine learning and statistical classification in CRISPR-Cas12a diagnostic assays.

Biosensors & bioelectronics
CRISPR-based diagnostics have gained increasing attention as biosensing tools able to address limitations in contemporary molecular diagnostic tests. To maximize the performance of CRISPR-based assays, much effort has focused on optimizing the chemis...

CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network.

International journal of biological macromolecules
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
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...

A new strategy for Cas protein recognition based on graph neural networks and SMILES encoding.

Scientific reports
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...

Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.

ACS synthetic biology
With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown si...