AIMC Topic: Clustered Regularly Interspaced Short Palindromic Repeats

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Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity.

ACS synthetic biology Nov 4, 2024
CRISPR-Cas systems have transformed the field of synthetic biology by providing a versatile method for genome editing. The efficiency of CRISPR systems is largely dependent on the sequence of the constituent sgRNA, necessitating the development of co...
Gene Editing Neural Networks, Computer RNA, Guide, CRISPR-Cas Systems Deep Learning CRISPR-Cas Systems Yarrowia Clustered Regularly Interspaced Short Palindromic Repeats
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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...
RNA, Guide, CRISPR-Cas Systems RNA Humans Clustered Regularly Interspaced Short Palindromic Repeats Deep Learning Gene Editing CRISPR-Cas Systems
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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...
Humans Machine Learning Animals Clustered Regularly Interspaced Short Palindromic Repeats Gene Knockout Techniques Genetic Engineering Synthetic Lethal Mutations Genomics Cell Line CRISPR-Cas Systems
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Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework.

PLoS computational biology Dec 29, 2021
Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by sp...
Pest Control, Biological Gene Drive Technology Population Control Models, Genetic Population Dynamics Supervised Machine Learning Biodiversity Clustered Regularly Interspaced Short Palindromic Repeats Introduced Species Animals Male Rats Female
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Ultrasound Elastography under Deep Learning Algorithm to Analyze the Therapeutic Effect of Clustered Regularly Interspaced Short Palindromic Repeats Short Hairpin Ribonucleic Acid Nanoparticles on Cervical Cancer.

Journal of healthcare engineering Nov 29, 2021
This study aimed to analyze the effect of the deep learning algorithm on ultrasound elastography on the treatment of cervical cancer with clustered regularly interspaced short palindromic repeats (CRISPR) short hairpin ribonucleic acid (shRNA) nanopa...
Clustered Regularly Interspaced Short Palindromic Repeats Elasticity Imaging Techniques Humans Algorithms Female Nanoparticles Uterine Cervical Neoplasms RNA Deep 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...
Mice CRISPR-Cas Systems Internet HeLa Cells HEK293 Cells Base Sequence Animals Deep Learning Cell Line, Tumor Humans Endonucleases INDEL Mutation Clustered Regularly Interspaced Short Palindromic Repeats RNA, Guide, CRISPR-Cas Systems Gene Editing Promoter Regions, Genetic
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Opportunities and Challenges in Phenotypic Screening for Neurodegenerative Disease Research.

Journal of medicinal chemistry Jul 18, 2019
Toxic misfolded proteins potentially underly many neurodegenerative diseases, but individual targets which regulate these proteins and their downstream detrimental effects are often unknown. Phenotypic screening is an unbiased method to screen for no...
Clustered Regularly Interspaced Short Palindromic Repeats Cell Line, Transformed Biomedical Research Animals Neurodegenerative Diseases Humans High-Throughput Screening Assays Machine Learning Phenotype
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GuideScan software for improved single and paired CRISPR guide RNA design.

Nature biotechnology Mar 6, 2017
We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We a...
Clustered Regularly Interspaced Short Palindromic Repeats Sequence Analysis, RNA Machine Learning Chromosome Mapping CRISPR-Cas Systems Software Gene Silencing RNA, Small Interfering Algorithms
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Prediction of potent shRNAs with a sequential classification algorithm.

Nature biotechnology Mar 6, 2017
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a give...
Clustered Regularly Interspaced Short Palindromic Repeats Machine Learning Chromosome Mapping Software Gene Silencing Sequence Analysis, RNA Algorithms CRISPR-Cas Systems RNA, Small Interfering
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Deep Learning-Enhanced Hand-Driven Microfluidic Chip for Multiplexed Nucleic Acid Detection Based on RPA/CRISPR.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jun 1, 2025
The early detection of high-risk human papillomavirus (HR-HPV) is crucial for the assessment and improvement of prognosis in cervical cancer. However, existing PCR-based screening methods suffer from inadequate accessibility, which dampens the enthus...
Female Uterine Cervical Neoplasms Deep Learning Humans Clustered Regularly Interspaced Short Palindromic Repeats Lab-On-A-Chip Devices Human papillomavirus 16 Human papillomavirus 18 Papillomavirus Infections Early Detection of Cancer Nucleic Acid Amplification Techniques
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