CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated
protein 9 (Cas9) system has become a successful and promising technology for gene …
protein 9 (Cas9) system has become a successful and promising technology for gene …
[HTML][HTML] Computational approaches for effective CRISPR guide RNA design and evaluation
Abstract The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-
associated (Cas) system has emerged as the main technology for gene editing. Successful …
associated (Cas) system has emerged as the main technology for gene editing. Successful …
[HTML][HTML] Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities
The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference
(CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene …
(CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene …
SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance
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 …
approach based on a human cell library containing single-guide RNA–encoding and target …
Recent advances in machine learning applications in metabolic engineering
Metabolic engineering encompasses several widely-used strategies, which currently hold a
high seat in the field of biotechnology when its potential is manifesting through a plethora of …
high seat in the field of biotechnology when its potential is manifesting through a plethora of …
Sequence-specific prediction of the efficiencies of adenine and cytosine base editors
Base editors, including adenine base editors (ABEs) and cytosine base editors (CBEs),, are
widely used to induce point mutations. However, determining whether a specific nucleotide …
widely used to induce point mutations. However, determining whether a specific nucleotide …
[HTML][HTML] Integration of CRISPR/Cas9 with artificial intelligence for improved cancer therapeutics
Gene editing has great potential in treating diseases caused by well-characterized
molecular alterations. The introduction of clustered regularly interspaced short palindromic …
molecular alterations. The introduction of clustered regularly interspaced short palindromic …
[HTML][HTML] The current state and future of CRISPR-Cas9 gRNA design tools
Recent years have seen the development of computational tools to assist researchers in
performing CRISPR-Cas9 experiment optimally. More specifically, these tools aim to …
performing CRISPR-Cas9 experiment optimally. More specifically, these tools aim to …
An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools
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 …
manipulation applications. Albeit the technology has been broadly adopted by both …
Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on-and off-target activities
G Zhang, Y Luo, X Dai, Z Dai - Briefings in Bioinformatics, 2023 - academic.oup.com
In silico design of single guide RNA (sgRNA) plays a critical role in clustered regularly
interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) …
interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) …