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 …
CRISPR technologies and the search for the PAM-free nuclease
D Collias, CL Beisel - Nature communications, 2021 - nature.com
The ever-expanding set of CRISPR technologies and their programmable RNA-guided
nucleases exhibit remarkable flexibility in DNA targeting. However, this flexibility comes with …
nucleases exhibit remarkable flexibility in DNA targeting. However, this flexibility comes with …
Multiplexed CRISPR technologies for gene editing and transcriptional regulation
NS McCarty, AE Graham, L Studená… - Nature …, 2020 - nature.com
Multiplexed CRISPR technologies, in which numerous gRNAs or Cas enzymes are
expressed at once, have facilitated powerful biological engineering applications, vastly …
expressed at once, have facilitated powerful biological engineering applications, vastly …
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 …
Base-resolution models of transcription-factor binding reveal soft motif syntax
Ž Avsec, M Weilert, A Shrikumar, S Krueger… - Nature …, 2021 - nature.com
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
DeepCRISPR: optimized CRISPR guide RNA design by deep learning
A major challenge for effective application of CRISPR systems is to accurately predict the
single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would …
single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would …
Computational tools and resources for CRISPR/Cas genome editing
The past decade has witnessed a rapid evolution in identifying more versatile clustered
regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) …
regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) …
Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs)
Prime editors (PEs), which can install desired base edits without donor DNA or double-
strand breaks, have been used in plants and can, in principle, accelerate crop improvement …
strand breaks, have been used in plants and can, in principle, accelerate crop improvement …
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 …
Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning
X Xiang, GI Corsi, C Anthon, K Qu, X Pan… - Nature …, 2021 - nature.com
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 …
demand high-quality gRNA activity data and efficient modeling. To advance, we here report …