Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering

SaCas9 Requires 5′-NNGRRT-3′ PAM for Sufficient Cleavage and Possesses Higher Cleavage Activity than SpCas9 or FnCpf1 in Human Cells

(2018) Haihua Xie et al.   Biotechnology Journal

Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins

(2018) Zhen Liang et al.   Nature Protocols

The future of CRISPR technologies in agriculture

(2018) Caixia Gao   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Efficient genome editing of wild strawberry genes, vector development and validation

(2018) Junhui Zhou et al.   PLANT BIOTECHNOLOGY JOURNAL

Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention

(2018) Qiang Zhang et al.   PLANT MOLECULAR BIOLOGY

SaCas9 Requires 5′-NNGRRT-3′ PAM for Sufficient Cleavage and Possesses Higher Cleavage Activity than SpCas9 or FnCpf1 in Human Cells

(2018) Haihua Xie et al.   Biotechnology Journal

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1

(2017) Takashi Yamano et al.   MOLECULAR CELL

Generation of targeted mutant rice using a CRISPR-Cpf1 system

(2017) Rongfang Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9

(2017) Javier Gil-Humanes et al.   PLANT JOURNAL

CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing

(2017) Miguel A. Moreno-Mateos et al.   Nature Communications

Mechanisms Used by Plants to Cope with DNA Damage

(2016) Zhubing Hu et al.   Annual Review of Plant Biology

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

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

AnAgrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize

(2016) Si Nian Char et al.   PLANT BIOTECHNOLOGY JOURNAL

A modular toolbox for gRNA–Cas9 genome engineering in plants based on the GoldenBraid standard

(2016) Marta Vazquez-Vilar et al.   Plant Methods

Revolutionizing plant biology: multiple ways of genome engineering by CRISPR/Cas

(2016) Simon Schiml et al.   Plant Methods

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Highly specific targeted mutagenesis in plants using Staphylococcus aureus Cas9

(2016) Hidetaka Kaya et al.   Scientific Reports

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

High-Efficiency Genome Editing in Arabidopsis Using YAO Promoter-Driven CRISPR/Cas9 System

(2015) Liuhua Yan et al.   Molecular Plant

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition

(2015) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

Standards for plant synthetic biology: a common syntax for exchange of DNA parts

(2015) Nicola J. Patron et al.   NEW PHYTOLOGIST

Highly efficient heritable plant genome engineering using Cas9 orthologues fromStreptococcus thermophilusandStaphylococcus aureus

(2015) Jeannette Steinert et al.   PLANT JOURNAL

Cas9-Guide RNA Directed Genome Editing in Soybean

(2015) Zhongsen Li et al.   PLANT PHYSIOLOGY

Rationally engineered Cas9 nucleases with improved specificity

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

Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

(2015) Zhi-Ping Wang et al.   GENOME BIOLOGY

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

(2014) Hui-Li Xing et al.   BMC PLANT BIOLOGY

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

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

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

DNA Replicons for Plant Genome Engineering

(2014) N. J. Baltes et al.   PLANT CELL

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications

(2014) Di Zhang et al.   PLoS One

Targeted Genome Editing of Sweet Orange Using Cas9/sgRNA

(2014) Hongge Jia et al.   PLoS One

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

(2014)   PLoS One

Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice

(2014) Rongfang Xu et al.   Rice

A Golden Gate Modular Cloning Toolbox for Plants

(2014) Carola Engler et al.   ACS Synthetic Biology

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9

(2013) Jian-Feng Li et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One