AIMC Topic: CRISPR-Cas Systems

Clear Filters Showing 71 to 80 of 115 articles

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...
CRISPR-Cas Systems RNA Gene Editing Humans Deep Learning
View on PubMed DOI

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...
Internet Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Associated Protein 9 Deep Learning Humans CRISPR-Cas Systems Reproducibility of Results Mutation
View on PubMed DOI

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...
CRISPR-Cas Systems Gene Editing Neural Networks, Computer Sequence Deletion RNA, Guide, CRISPR-Cas Systems Deep Learning Bacteria
View on PubMed DOI

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...
Deep Learning CRISPR-Cas Systems Gene Editing Machine Learning Algorithms Sensitivity and Specificity Gene Targeting RNA, Guide, CRISPR-Cas Systems Humans
View on PubMed DOI

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...
Gene Editing Promoter Regions, Genetic Endonucleases INDEL Mutation Humans RNA, Guide, CRISPR-Cas Systems Animals CRISPR-Cas Systems Deep Learning Internet Cell Line, Tumor HEK293 Cells HeLa Cells Mice Base Sequence Clustered Regularly Interspaced Short Palindromic Repeats
View on PubMed DOI

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...
Models, Genetic CRISPR-Cas Systems Mutation Machine Learning Gene Editing DNA Repair DNA End-Joining Repair
View on PubMed DOI

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...
RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Base Sequence Endonucleases Neural Networks, Computer Algorithms Deep Learning
View on PubMed DOI

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 Gene Editing DNA Breaks, Double-Stranded DNA Repair RNA, Guide, CRISPR-Cas Systems Oligodeoxyribonucleotides Mice Mice, Inbred C57BL CRISPR-Cas Systems Machine Learning Animals
View on PubMed DOI

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...
RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Deep Learning Gene Editing Nucleic Acid Conformation Computational Biology Models, Molecular
View on PubMed DOI

Predictable and precise template-free CRISPR editing of pathogenic variants.

Nature Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
Hermanski-Pudlak Syndrome Alleles Base Sequence Humans Menkes Kinky Hair Syndrome HCT116 Cells Reproducibility of Results Machine Learning Gene Editing Templates, Genetic HEK293 Cells Fibroblasts K562 Cells Substrate Specificity CRISPR-Cas Systems DNA Repair CRISPR-Associated Protein 9
View on PubMed DOI
Popular Topics
Recent Journals