Genome editing: A perspective on the application of CRISPR/Cas9 to study human diseases

DR Rodríguez-Rodríguez… - International …, 2019 - spandidos-publications.com
Genome editing reemerged in 2012 with the development of CRISPR/Cas9 technology,
which is a genetic manipulation tool derived from the defense system of certain bacteria …

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) …

sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks

M Niu, Y Lin, Q Zou - Plant molecular biology, 2021 - Springer
Key message 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 …

An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools

J Wang, X Zhang, L Cheng, Y Luo - RNA biology, 2020 - Taylor & Francis
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 …

Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta

DS Booth, N King - Elife, 2020 - elifesciences.org
In a previous study, we established a forward genetic screen to identify genes required for
multicellular development in the choanoflagellate, Salpingoeca rosetta (Levin et al., 2014) …

Efficient genome engineering of a virulent Klebsiella bacteriophage using CRISPR-Cas9

J Shen, J Zhou, GQ Chen, ZL Xiu - Journal of Virology, 2018 - Am Soc Microbiol
Klebsiella pneumoniae is one of the most common nosocomial opportunistic pathogens and
usually exhibits multiple-drug resistance. Phage therapy, a potential therapeutic to replace …

CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling

H Peng, Y Zheng, M Blumenstein, D Tao, J Li - Bioinformatics, 2018 - academic.oup.com
Motivation CRISPR/Cas9 system is a widely used genome editing tool. A prediction problem
of great interests for this system is: how to select optimal single-guide RNAs (sgRNAs), such …

[HTML][HTML] Genome editing using engineered nucleases and their use in genomic screening

JR Costa, BE Bejcek, JE McGee, AI Fogel… - Assay Guidance …, 2017 - ncbi.nlm.nih.gov
Understanding gene function is critical for developing therapeutic strategies to target
disease. Common approaches to understanding gene function in a systematic and unbiased …

Understanding rice blast: investigating biotechnological methods to speed up the development of robust rice cultivars

N Rajput, MU Younas, M Qasim, SP Memon… - Genetic Resources and …, 2024 - Springer
The fungus Magnaporthe oryzae is responsible for causing rice blast, which is a significant
threat to rice production worldwide. Cultivating resistant cultivars is a crucial and long-lasting …

Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection

Y Chen, X Wang - Bioinformatics, 2022 - academic.oup.com
Abstract Motivation The CRISPR/Cas9 system is widely used for genome editing. The
editing efficiency of CRISPR/Cas9 is mainly determined by the guide RNA (gRNA). Although …