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

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

(2018) Hui Peng et al.   BIOINFORMATICS

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Target-Specific Precision of CRISPR-Mediated Genome Editing

(2018) Anob M. Chakrabarti et al.   MOLECULAR CELL

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

(2017) Fadi J Najm et al.   NATURE BIOTECHNOLOGY

GUIDES: sgRNA design for loss-of-function screens

(2017) Joshua A Meier et al.   NATURE METHODS

Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions

(2017) John Paul Shen et al.   NATURE METHODS

Genetic interaction mapping in mammalian cells using CRISPR interference

(2017) Dan Du et al.   NATURE METHODS

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

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Raj Chari et al.   ACS Synthetic Biology

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

In vivo high-throughput profiling of CRISPR–Cpf1 activity

(2016) Hui K Kim et al.   NATURE METHODS

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

(2016) Alan S. L. Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Traver Hart et al.   CELL

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9

(2015) Gaurav K. Varshney et al.   GENOME RESEARCH

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

Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries

(2015) Joana A. Vidigal et al.   Nature Communications

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

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

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

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

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY