Design of Guide RNA for CRISPR/Cas Plant Genome Editing

CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity

(2019) Houxiang Zhu et al.   BIOINFORMATICS

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

(2019) Robin Graf et al.   Cell Reports

Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning

(2019) Aidan R. O’Brien et al.   Scientific Reports

GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes

(2019) Brian B. Merritt et al.   BMC BIOINFORMATICS

Plant breeding at the speed of light: the power of CRISPR/Cas to generate directed genetic diversity at multiple sites

(2019) Felix Wolter et al.   BMC PLANT BIOLOGY

beditor: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing

(2019) Rohan Dandage et al.   GENETICS

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

CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications

(2019) Kutubuddin A. Molla et al.   TRENDS IN BIOTECHNOLOGY

A Review of CRISPR-Based Genome Editing: Survival, Evolution and Challenges

(2018) Hafiz Ishfaq Ahmad et al.   CURRENT ISSUES IN MOLECULAR BIOLOGY

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

(2018) Jean-Paul Concordet et al.   NUCLEIC ACIDS RESEARCH

Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery

(2018) Mariette Andersson et al.   PHYSIOLOGIA PLANTARUM

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing

(2018) Daan C. Swarts et al.   Wiley Interdisciplinary Reviews-RNA

Review of CRISPR/Cas9 sgRNA Design Tools

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

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

(2018) Jennifer Listgarten et al.   Nature Biomedical Engineering

Synergizing CRISPR/Cas9 off-target predictions for ensemble insights and practical applications

(2018) Shixiong Zhang et al.   BIOINFORMATICS

Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a

(2018) Isabel Strohkendl et al.   MOLECULAR CELL

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

CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes

(2018) Jiamin Sun et al.   BIOINFORMATICS

Web-based design and analysis tools for CRISPR base editing

(2018) Gue-Ho Hwang et al.   BMC BIOINFORMATICS

Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network

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

CRISPR-PLANT v2: an online resource for highly specific guide RNA spacers based on improved off-target analysis

(2018) Bastian Minkenberg et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR/Cas precision: do we need to worry about off-targeting in plants?

(2018) Florian Hahn et al.   PLANT CELL REPORTS

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

(2017) Kristopher Torp Jensen et al.   FEBS LETTERS

CRISPR/Cas9: An RNA-guided highly precise synthetic tool for plant genome editing

(2017) Yeliz Demirci et al.   JOURNAL OF CELLULAR PHYSIOLOGY

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

CRISPR-GE: A Convenient Software Toolkit for CRISPR-Based Genome Editing

(2017) Xianrong Xie et al.   Molecular Plant

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

(2017) Maurice Labuhn et al.   NUCLEIC ACIDS RESEARCH

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

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

Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes

(2017) Zhen Liang et al.   Nature Communications

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-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9

(2016) Jeongbin Park et al.   BIOINFORMATICS

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

(2016) Achal Rastogi et al.   BMC BIOINFORMATICS

A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases

(2016) Vinita Periwal   BRIEFINGS IN BIOINFORMATICS

Versatility of chemically synthesized guide RNAs for CRISPR-Cas9 genome editing

(2016) Melissa L. Kelley et al.   JOURNAL OF BIOTECHNOLOGY

Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System

(2016) Chao Feng et al.   Journal of Genetics and Genomics

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes

(2016) Juan C. Oliveros 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

Fine-Tuning Next-Generation Genome Editing Tools

(2016) Chidananda Nagamangala Kanchiswamy et al.   TRENDS IN BIOTECHNOLOGY

Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes

(2016) Sergei Svitashev et al.   Nature Communications

CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

(2016) Houxiang Zhu et al.   Scientific Reports

Achieving Plant CRISPR Targeting that Limits Off-Target Effects

(2016) Jeffrey D. Wolt et al.   Plant Genome

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

(2015) Jeongbin Park et al.   BIOINFORMATICS

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.

(2015) Honglei Liu et al.   BIOINFORMATICS

CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system

(2015) Meng Yan et al.   Journal of Integrative Plant Biology

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

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

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

A quick guide to CRISPR sgRNA design tools

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

CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

(2015) Sergey V. Prykhozhij et al.   PLoS One

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

(2015) Manuel Stemmer et al.   PLoS One

Correction: CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

(2015) Sergey V. Prykhozhij et al.   PLoS One

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

GT-Scan: identifying unique genomic targets

(2014) A. O'Brien 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

Genome-Wide Prediction of Highly Specific Guide RNA Spacers for CRISPR–Cas9-Mediated Genome Editing in Model Plants and Major Crops

(2014) Kabin Xie et al.   Molecular Plant

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

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

(2014) John G Doench 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

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

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

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE