AIMC Topic: CRISPR-Cas Systems
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Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights.
BioEssays : news and reviews in molecular, cellular and developmental biology
May 8, 2024
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type diffe...
DNA shape features improve prediction of CRISPR/Cas9 activity.
Methods (San Diego, Calif.)
Apr 17, 2024
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine ...
CrnnCrispr: An Interpretable Deep Learning Method for CRISPR/Cas9 sgRNA On-Target Activity Prediction.
International journal of molecular sciences
Apr 17, 2024
CRISPR/Cas9 is a powerful genome-editing tool in biology, but its wide applications are challenged by a lack of knowledge governing single-guide RNA (sgRNA) activity. Several deep-learning-based methods have been developed for the prediction of on-ta...
CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network.
PLoS computational biology
Mar 14, 2024
Using the CRISPR-Cas9 system to perform base substitutions at the target site is a typical technique for genome editing with the potential for applications in gene therapy and agricultural productivity. When the CRISPR-Cas9 system uses guide RNA to d...
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d.
BioTechniques
Feb 29, 2024
In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail () gene as...
DNA Robots for CRISPR/Cas12a Activity Management and Universal Platforms for Biosensing.
Analytical chemistry
Jan 13, 2024
The CRISPR/Cas12a system is a revolutionary genome editing technique that is widely employed in biosensing and molecular diagnostics. However, there are few reports on precisely managing the -cleavage activity of Cas12a by simple modification since t...
Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions.
Nature computational science
Dec 14, 2023
Finely tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Developing predictive and interpretable models for these pathways is challenging because of the complexity of the pathways and of the cellular an...
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting.
Cell systems
Dec 12, 2023
Effective and precise mammalian transcriptome engineering technologies are needed to accelerate biological discovery and RNA therapeutics. Despite the promise of programmable CRISPR-Cas13 ribonucleases, their utility has been hampered by an incomplet...
Enhanced detection of Listeria monocytogenes using tetraethylenepentamine-functionalized magnetic nanoparticles and LAMP-CRISPR/Cas12a-based biosensor.
Analytica chimica acta
Oct 11, 2023
BACKGROUND: Listeria monocytogenes is a pathogenic bacterium that can lead to severe illnesses, especially among vulnerable populations. Therefore, the development of rapid and sensitive detection methods is vital to prevent and manage foodborne dise...
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