Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs

Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity

(2017) Ciaran M. Lee et al.   EXPERIMENTAL PHYSIOLOGY

Mapping the genomic landscape of CRISPR–Cas9 cleavage

(2017) Peter Cameron et al.   NATURE METHODS

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets

(2017) Shengdar Q Tsai et al.   NATURE METHODS

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

(2017) David W. Morgens et al.   Nature Communications

CRISPR-DO for genome-wide CRISPR design and optimization

(2016) Jian Ma et al.   BIOINFORMATICS

Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

(2016) Daesik Kim et al.   GENOME RESEARCH

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

(2016) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim 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

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

(2016) D. M. Munoz et al.   Cancer Discovery

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

(2015) Xiaoling Wang 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

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi

(2015) Benjamin E. Housden et al.   Science Signaling

Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi

(2015) Benjamin E. Housden et al.   Science Signaling

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

(2015) Manuel Stemmer et al.   PLoS One

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

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

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

(2014) Y. Lin et al.   NUCLEIC ACIDS RESEARCH

COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

(2014) Thomas J Cradick et al.   Molecular Therapy-Nucleic Acids

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH