AIMC Topic: Gene Editing

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Easy-Prime: a machine learning-based prime editor design tool.

Genome biology Aug 19, 2021
Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning-based program traine...
HEK293 Cells Gene Editing RNA, Guide, CRISPR-Cas Systems Machine Learning DNA CRISPR-Cas Systems Humans
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Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods.

Nature communications Aug 12, 2021
Efficient and precise base editors (BEs) for C-to-G transversion are highly desirable. However, the sequence context affecting editing outcome largely remains unclear. Here we report engineered C-to-G BEs of high efficiency and fidelity, with the seq...
CRISPR-Cas Systems HEK293 Cells Uracil-DNA Glycosidase Animals Mice Escherichia coli Female Reproducibility of Results Codon Base Sequence Humans Gene Library Gene Editing Machine Learning Caenorhabditis elegans Binding Sites Cytidine Deaminase
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Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning.

Nature communications May 28, 2021
The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. ...
Humans Software HEK293 Cells Plasmids Gene Editing Lentivirus Deep Learning Computational Biology CRISPR-Cas Systems Genetic Vectors RNA, Guide, CRISPR-Cas Systems
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Deep Learning and Computer Vision Strategies for Automated Gene Editing with a Single-Cell Electroporation Platform.

SLAS technology Jan 15, 2021
Single-cell delivery platforms like microinjection and nanoprobe electroporation enable unparalleled control over cell manipulation tasks but are generally limited in throughput. Here, we present an automated single-cell electroporation system capabl...
Humans Deep Learning Gene Editing Artificial Intelligence Computers Electroporation
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Machine learning based CRISPR gRNA design for therapeutic exon skipping.

PLoS computational biology Jan 8, 2021
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments ...
CRISPR-Cas Systems Gene Editing Genetic Therapy Embryonic Stem Cells RNA, Guide, CRISPR-Cas Systems Humans Cells, Cultured Gene Library Machine Learning Animals Exons Mice
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sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks.

Plant molecular biology Jan 1, 2021
We proposed an ensemble convolutional neural network model to identify sgRNA high on-target activity in four crops and we used one-hot encoding and k-mers for sequence encoding. As an important component of the CRISPR/Cas9 system, single-guide RNA (s...
RNA, Guide, CRISPR-Cas Systems Sorghum Gene Editing Glycine max Triticum Internet HeLa Cells Crops, Agricultural HCT116 Cells HEK293 Cells Computational Biology Zea mays CRISPR-Cas Systems Humans Neural Networks, Computer Algorithms
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Machine learning for metabolic engineering: A review.

Metabolic engineering Nov 19, 2020
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth i...
Gene Editing Metabolic Engineering Machine Learning Algorithms
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Machine-learning approach expands the repertoire of anti-CRISPR protein families.

Nature communications Jul 29, 2020
The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechani...
Host-Parasite Interactions Sequence Homology, Amino Acid Sequence Analysis, Protein Machine Learning CRISPR-Associated Protein 9 Bacteria Computational Biology Bacteriophages Gene Editing CRISPR-Cas Systems Viral Proteins Archaea Datasets as Topic
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Biosystems Design by Machine Learning.

ACS synthetic biology Jun 29, 2020
Biosystems such as enzymes, pathways, and whole cells have been increasingly explored for biotechnological applications. However, the intricate connectivity and resulting complexity of biosystems poses a major hurdle in designing biosystems with desi...
Metabolic Engineering Linear Models Gene Editing Machine Learning Biotechnology Gene Regulatory Networks Proteins
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Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning.

Cell Jun 12, 2020
Although base editors are widely used to install targeted point mutations, the factors that determine base editing outcomes are not well understood. We characterized sequence-activity relationships of 11 cytosine and adenine base editors (CBEs and AB...
Mouse Embryonic Stem Cells Point Mutation Mice RNA, Guide, CRISPR-Cas Systems Humans Machine Learning Gene Editing Animals Gene Library
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