Computational Tools and Resources Supporting CRISPR-Cas Experiments

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

(2019) Robin Graf et al.   Cell Reports

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design

(2019) Dong Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery of CRISPR/Cas9 for therapeutic genome editing

(2019) Xiaojie Xu et al.   JOURNAL OF GENE MEDICINE

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

(2019) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Methods of Evaluating the Efficiency of CRISPR/Cas Genome Editing

(2019) N. A. Lomov et al.   MOLECULAR BIOLOGY

SNP-CRISPR: A Web Tool for SNP-Specific Genome Editing

(2019) Chiao-Lin Chen et al.   G3-Genes Genomes Genetics

Delivering CRISPR: a review of the challenges and approaches

(2018) Christopher A. Lino et al.   DRUG DELIVERY

How cells ensure correct repair of DNA double-strand breaks

(2018) Joonyoung Her et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kinetics and Fidelity of the Repair of Cas9-Induced Double-Strand DNA Breaks

(2018) Eva K. Brinkman et al.   MOLECULAR CELL

qEva-CRISPR: a method for quantitative evaluation of CRISPR/Cas-mediated genome editing in target and off-target sites

(2018) Magdalena Dabrowska et al.   NUCLEIC ACIDS RESEARCH

Easy quantification of template-directed CRISPR/Cas9 editing

(2018) Eva K Brinkman et al.   NUCLEIC ACIDS RESEARCH

Decoding non-random mutational signatures at Cas9 targeted sites

(2018) Amir Taheri-Ghahfarokhi et al.   NUCLEIC ACIDS RESEARCH

Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)

(2018) Meri I. E. Uusi-Mäkelä et al.   PLoS One

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles

(2018) Brenda R. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparison of Techniques to Evaluate the Effectiveness of Genome Editing

(2018) Diego Germini et al.   TRENDS IN BIOTECHNOLOGY

A Survey of Validation Strategies for CRISPR-Cas9 Editing

(2018) Monica F. Sentmanat et al.   Scientific Reports

Review of CRISPR/Cas9 sgRNA Design Tools

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

The Current State and Future of CRISPR-Cas9 gRNA Design Tools

(2018) Laurence O. W. Wilson et al.   Frontiers in Pharmacology

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

(2018) Jennifer Listgarten et al.   Nature Biomedical Engineering

A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells

(2018) Christopher A. Vakulskas et al.   NATURE MEDICINE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo

(2018) Robert M. Yarrington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target-Specific Precision of CRISPR-Mediated Genome Editing

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

Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements

(2018) Annalisa Lattanzi et al.   MOLECULAR THERAPY

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

A Single H1 Promoter Can Drive Both Guide RNA and Endonuclease Expression in the CRISPR-Cas9 System

(2018) Zongliang Gao et al.   Molecular Therapy-Nucleic Acids

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

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

Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency

(2017) Kristopher Torp Jensen et al.   FEBS LETTERS

Regulation of repair pathway choice at two-ended DNA double-strand breaks

(2017) Atsushi Shibata   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Implications of human genetic variation in CRISPR-based therapeutic genome editing

(2017) David A Scott et al.   NATURE MEDICINE

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

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

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci

(2017) Samuel Lessard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

(2017) Philipp N. Spahn et al.   Scientific Reports

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action

(2017) Shiran Abadi et al.   PLoS Computational Biology

Cas-analyzer: an online tool for assessing genome editing results using NGS data

(2016) Jeongbin Park et al.   BIOINFORMATICS

BAGEL: a computational framework for identifying essential genes from pooled library screens

(2016) Traver Hart et al.   BMC BIOINFORMATICS

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

A Self-restricted CRISPR System to Reduce Off-target Effects

(2016) Yanhao Chen et al.   MOLECULAR THERAPY

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

CrispRVariants charts the mutation spectrum of genome engineering experiments

(2016) Helen Lindsay et al.   NATURE BIOTECHNOLOGY

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello 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

A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing

(2016) Kaiwen Ivy Liu et al.   Nature Chemical Biology

Probing the impact of chromatin conformation on genome editing tools

(2016) Xiaoyu Chen et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

(2016) René M. Daer et al.   ACS Synthetic Biology

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia

(2016) Konstantinos Tzelepis et al.   Cell Reports

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

(2016) R Stefan Isaac et al.   eLife

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells

(2016) Scott D. Findlay et al.   PLoS One

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

Fast and sensitive detection of indels induced by precise gene targeting

(2015) Zhang Yang et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

CRISPRz: a database of zebrafish validated sgRNAs

(2015) Gaurav K. Varshney et al.   NUCLEIC ACIDS RESEARCH

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases

(2015) Léna Vouillot et al.   G3-Genes Genomes Genetics

A quick guide to CRISPR sgRNA design tools

(2015) Vincent A Brazelton et al.   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)

(2014) M. Guell et al.   BIOINFORMATICS

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

A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing

(2014) Charles C Bell et al.   BMC GENOMICS

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

(2014) John A Zuris et al.   NATURE BIOTECHNOLOGY

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

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

Microhomology-based choice of Cas9 nuclease target sites

(2014) Sangsu Bae et al.   NATURE METHODS

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

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

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

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

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

(2013) Nicola Crosetto et al.   NATURE METHODS

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

(2013) Thomas J. Cradick et al.   NUCLEIC ACIDS RESEARCH

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

(2013) Ines Fonfara et al.   NUCLEIC ACIDS RESEARCH

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

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

(2012) M. Jinek et al.   SCIENCE