AIMC Topic: CRISPR-Cas Systems

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CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning.

The CRISPR journal Jul 12, 2023
Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect ma...
Biological Monitoring Deep Learning CRISPR-Cas Systems RNA Gene Editing Artificial Intelligence Ecosystem
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Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning.

Nature biotechnology Jul 3, 2023
Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes i...
Deep Learning CRISPR-Cas Systems Humans Gene Editing RNA, Guide, CRISPR-Cas Systems RNA Clustered Regularly Interspaced Short Palindromic Repeats
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Deep learning models to predict the editing efficiencies and outcomes of diverse base editors.

Nature biotechnology May 15, 2023
Applications of base editing are frequently restricted by the requirement for a protospacer adjacent motif (PAM), and selecting the optimal base editor (BE) and single-guide RNA pair (sgRNA) for a given target can be difficult. To select for BEs and ...
Deep Learning Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Alkanesulfonic Acids CRISPR-Associated Protein 9
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Hybrid Multitask Learning Reveals Sequence Features Driving Specificity in the CRISPR/Cas9 System.

Biomolecules Apr 3, 2023
CRISPR/Cas9 technology is capable of precisely editing genomes and is at the heart of various scientific and medical advances in recent times. The advances in biomedical research are hindered because of the inadvertent burden on the genome when genom...
Genome Machine Learning CRISPR-Cas Systems
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Predicting prime editing efficiency and product purity by deep learning.

Nature biotechnology Jan 16, 2023
Prime editing is a versatile genome editing tool but requires experimental optimization of the prime editing guide RNA (pegRNA) to achieve high editing efficiency. Here we conducted a high-throughput screen to analyze prime editing outcomes of 92,423...
CRISPR-Cas Systems Mutation Hepatocytes Gene Editing Neural Networks, Computer Deep Learning Humans
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Predicting CRISPR/Cas9 Repair Outcomes by Attention-Based Deep Learning Framework.

Cells Jun 5, 2022
As a simple and programmable nuclease-based genome editing tool, the CRISPR/Cas9 system has been widely used in target-gene repair and gene-expression regulation. The DNA mutation generated by CRISPR/Cas9-mediated double-strand breaks determines its ...
CRISPR-Cas Systems Gene Editing Deep Learning Endonucleases Mutation
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Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases.

Molecular cell May 31, 2022
As part of the ongoing bacterial-phage arms race, CRISPR-Cas systems in bacteria clear invading phages whereas anti-CRISPR proteins (Acrs) in phages inhibit CRISPR defenses. Known Acrs have proven extremely diverse, complicating their identification....
Deep Learning Bacteria CRISPR-Cas Systems CRISPR-Associated Protein 9 Bacteriophages Endonucleases
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Deep Learning-Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard-to-Transfect Cells.

Small (Weinheim an der Bergstrasse, Germany) Mar 21, 2022
Genome engineering of cells using CRISPR/Cas systems has opened new avenues for pharmacological screening and investigating the molecular mechanisms of disease. A critical step in many such studies is the intracellular delivery of the gene editing ma...
Humans Induced Pluripotent Stem Cells Deep Learning Gene Editing CRISPR-Cas Systems Electroporation
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A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments.

Nature communications Feb 2, 2022
A genetic knockout can be lethal to one human cell type while increasing growth rate in another. This context specificity confounds genetic analysis and prevents reproducible genome engineering. Genome-wide CRISPR compendia across most common human c...
Clustered Regularly Interspaced Short Palindromic Repeats Humans Cell Line CRISPR-Cas Systems Gene Knockout Techniques Animals Genomics Genetic Engineering Synthetic Lethal Mutations Machine Learning
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AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity.

BMC bioinformatics Dec 13, 2021
BACKGROUND: More and more Cas9 variants with higher specificity are developed to avoid the off-target effect, which brings a significant volume of experimental data. Conventional machine learning performs poorly on these datasets, while the methods b...
CRISPR-Cas Systems Machine Learning RNA, Guide, CRISPR-Cas Systems
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