AIMC Topic: CRISPR-Cas Systems

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Evaluation of off-targets predicted by sgRNA design tools.

Genomics Apr 27, 2020
The ease of programming CRISPR/Cas9 system for targeting a specific location within the genome has paved way for many clinical and industrial applications. However, its widespread use is still limited owing to its off-target effects. Though this off-...
CRISPR-Cas Systems RNA RNA Editing Machine Learning Algorithms
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Deep learning improves the ability of sgRNA off-target propensity prediction.

BMC bioinformatics Feb 10, 2020
BACKGROUND: CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9...
Deep Learning CRISPR-Cas Systems RNA Humans Gene Editing
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SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.

Science advances Nov 6, 2019
We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-indu...
CRISPR-Associated Protein 9 CRISPR-Cas Systems Humans Gene Editing Reproducibility of Results Internet RNA, Guide, CRISPR-Cas Systems Mutation Deep Learning
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Prediction of sgRNA on-target activity in bacteria by deep learning.

BMC bioinformatics Oct 24, 2019
BACKGROUND: One of the main challenges for the CRISPR-Cas9 system is selecting optimal single-guide RNAs (sgRNAs). Recently, deep learning has enhanced sgRNA prediction in eukaryotes. However, the prokaryotic chromatin structure is different from euk...
Bacteria CRISPR-Cas Systems Gene Editing Neural Networks, Computer Deep Learning RNA, Guide, CRISPR-Cas Systems Sequence Deletion
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An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools.

RNA biology Sep 27, 2019
The CRISPR-Cas9 system has become the most promising and versatile tool for genetic manipulation applications. Albeit the technology has been broadly adopted by both academic and pharmaceutic societies, the activity (on-target) and specificity (off-t...
CRISPR-Cas Systems Gene Editing RNA, Guide, CRISPR-Cas Systems Gene Targeting Algorithms Sensitivity and Specificity Deep Learning Humans Machine Learning
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Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.

Nature communications Sep 19, 2019
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA acti...
Humans Animals Cell Line, Tumor Mice Gene Editing Deep Learning INDEL Mutation CRISPR-Cas Systems HeLa Cells Clustered Regularly Interspaced Short Palindromic Repeats Promoter Regions, Genetic Endonucleases RNA, Guide, CRISPR-Cas Systems HEK293 Cells Internet Base Sequence
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Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing.

Trends in biotechnology Sep 13, 2019
SpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of muta...
Mutation Gene Editing DNA Repair Models, Genetic CRISPR-Cas Systems DNA End-Joining Repair Machine Learning
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Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks.

BMC bioinformatics Jun 13, 2019
BACKGROUND: CRISPR-Cpf1 has recently been reported as another RNA-guided endonuclease of class 2 CRISPR-Cas system, which expands the molecular biology toolkit for genome editing. However, most of the online tools and applications to date have been d...
Base Sequence Endonucleases RNA, Guide, CRISPR-Cas Systems Deep Learning CRISPR-Cas Systems Neural Networks, Computer Algorithms
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Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning.

Scientific reports Feb 26, 2019
Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated "base editing" being limited to certain nucleotide changes, and only achievable within a small window ar...
Mutation Animals Gene Editing Machine Learning Oligodeoxyribonucleotides DNA Breaks, Double-Stranded Mice Mice, Inbred C57BL DNA Repair RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems
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Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network.

Journal of chemical information and modeling Dec 7, 2018
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single-guide RNA (sgRNA) design to improve efficiency of target cl...
Nucleic Acid Conformation RNA, Guide, CRISPR-Cas Systems Models, Molecular Deep Learning CRISPR-Cas Systems Computational Biology Gene Editing
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