CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

(2021) Xi Xiang et al.   Nature Communications

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency

(2020) Kasidet Hiranniramol et al.   BIOINFORMATICS

A Novel Hybrid CNN-SVR for CRISPR/Cas9 Guide RNA Activity Prediction

(2020) Guishan Zhang et al.   Frontiers in Genetics

sgRNA Sequence Motifs Blocking Efficient CRISPR/Cas9-Mediated Gene Editing

(2019) Robin Graf et al.   Cell Reports

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

(2019) Jun Wang et al.   RNA Biology

A benchmark of computational CRISPR-Cas9 guide design methods

(2019) Jacob Bradford et al.   PLoS Computational Biology

Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning

(2019) Daqi Wang et al.   Nature Communications

SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance

(2019) Hui Kwon Kim et al.   Science Advances

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Correlation Coefficients

(2018) Patrick Schober et al.   ANESTHESIA AND ANALGESIA

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

(2018) Hui Peng et al.   BIOINFORMATICS

Review of CRISPR/Cas9 sgRNA Design Tools

(2018) Yingbo Cui et al.   Interdisciplinary Sciences-Computational Life Sciences

Deep learning for biology

(2018) Sarah Webb   NATURE

Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network

(2018) Li Xue et al.   Journal of Chemical Information and Modeling

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas9 gene repair of hematopoietic stem cells from patients with X-linked chronic granulomatous disease

(2017) Suk See De Ravin et al.   Science Translational Medicine

In Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design

(2017) Guo-hui Chuai et al.   TRENDS IN BIOTECHNOLOGY

Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice

(2017) Wenhan Yu et al.   Nature Communications

sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity

(2017) Raj Chari et al.   ACS Synthetic Biology

CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems

(2017) Md. Khaledur Rahman et al.   PLoS One

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

(2016) Prarthana Mohanraju et al.   SCIENCE

Internal guide RNA interactions interfere with Cas9-mediated cleavage

(2016) Summer B. Thyme et al.   Nature Communications

Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system

(2016) Xiaoxi Liu et al.   Scientific Reports

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

(2015) Raj Chari et al.   NATURE METHODS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing

(2015) Abba Malina et al.   Nature Communications

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity

(2014) Rodolphe Barrangou et al.   MOLECULAR CELL

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

A guide to genome engineering with programmable nucleases

(2014) Hyongbum Kim et al.   NATURE REVIEWS GENETICS

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

(2014) James A. Gagnon et al.   PLoS One

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

To acquire or resist: the complex biological effects of CRISPR–Cas systems

(2014) Joseph Bondy-Denomy et al.   TRENDS IN MICROBIOLOGY

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Mechanism of Eukaryotic RNA Polymerase III Transcription Termination

(2013) S. Nielsen et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Double-Strand Break End Resection and Repair Pathway Choice

(2011) Lorraine S. Symington et al.   Annual Review of Genetics

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage

(2011) Ruiying Wang et al.   STRUCTURE

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM