CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement

Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks

(2018) Ryan Clarke et al.   MOLECULAR CELL

High-efficiency genome editing using a dmc1 promoter-controlled CRISPR/Cas9 system in maize

(2018) Chao Feng et al.   PLANT BIOTECHNOLOGY JOURNAL

Blocking amino acid transporter OsAAP3 improves grain yield by promoting outgrowth buds and increasing tiller number in rice

(2018) Kai Lu et al.   PLANT BIOTECHNOLOGY JOURNAL

Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize

(2018) Keunsub Lee et al.   PLANT BIOTECHNOLOGY JOURNAL

Physiological status of plant tissue affects the frequency and types of mutations induced by carbon-ion irradiation in Arabidopsis

(2018) Yoshihiro Hase et al.   Scientific Reports

Lycopene Is Enriched in Tomato Fruit by CRISPR/Cas9-Mediated Multiplex Genome Editing

(2018) Xindi Li et al.   Frontiers in Plant Science

HorTILLUS—A Rich and Renewable Source of Induced Mutations for Forward/Reverse Genetics and Pre-breeding Programs in Barley (Hordeum vulgare L.)

(2018) Miriam E. Szurman-Zubrzycka et al.   Frontiers in Plant Science

Simultaneous Editing of Two Copies of Gh14-3-3d Confers Enhanced Transgene-Clean Plant Defense Against Verticillium dahliae in Allotetraploid Upland Cotton

(2018) Zhennan Zhang et al.   Frontiers in Plant Science

In vivo CRISPR editing with no detectable genome-wide off-target mutations

(2018) Pinar Akcakaya et al.   NATURE

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

The Enhancement of Plant Disease Resistance Using CRISPR/Cas9 Technology

(2018) Virginia M. G. Borrelli et al.   Frontiers in Plant Science

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

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

The initiation, propagation and dynamics of CRISPR-SpyCas9 R-loop complex

(2017) Yan Zeng et al.   NUCLEIC ACIDS RESEARCH

High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum ) using CRISPR/Cas9 system

(2017) Pengcheng Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress

(2017) Chantal LeBlanc et al.   PLANT JOURNAL

Contributions of Zea mays subspecies mexicana haplotypes to modern maize

(2017) Ning Yang et al.   Nature Communications

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence

(2017) Ting Zheng 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

CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment

(2017) Xiaojun Xu et al.   Scientific Reports

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants

(2016) Justin E. Anderson et al.   BMC BIOTECHNOLOGY

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

Targeted mutagenesis of a conserved anther-expressed P450 gene confers male sterility in monocots

(2016) A. Mark Cigan et al.   PLANT BIOTECHNOLOGY JOURNAL

Somaclonal variation does not preclude the use of rice transformants for genetic screening

(2016) Fu-Jin Wei et al.   PLANT JOURNAL

Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes

(2016) Sergei Svitashev et al.   Nature Communications

Achieving Plant CRISPR Targeting that Limits Off-Target Effects

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

Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection

(2015) Xiquan Liang et al.   JOURNAL OF BIOTECHNOLOGY

Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

(2015) Sergei Svitashev et al.   PLANT PHYSIOLOGY

Rationally engineered Cas9 nucleases with improved specificity

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

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms

(2014) Christopher Y. Park et al.   BIOINFORMATICS

CasOT: a genome-wide Cas9/gRNA off-target searching tool

(2014) A. Xiao 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

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

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

(2014) S. Kim et al.   GENOME RESEARCH

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

(2014) Yanpeng Wang 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

Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis

(2014) Z. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

(2014) Steven Lin et al.   eLife

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

(2013) J. B. Hiatt 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

Male-sterile maize plants produced by targeted mutagenesis of the cytochrome P450-like gene (MS26) using a re-designed I-CreI homing endonuclease

(2013) Vesna Djukanovic et al.   PLANT JOURNAL

Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding

(2013) Nancy Podevin et al.   TRENDS IN BIOTECHNOLOGY

An Integrated Approach to Crop Genetic ImprovementF

(2012) Martin A. J. Parry et al.   Journal of Integrative Plant Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. Jinek et al.   SCIENCE

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Massively parallel exon capture and library-free resequencing across 16 genomes

(2009) Emily H Turner et al.   NATURE METHODS

Heritable targeted mutagenesis in maize using a designed endonuclease

(2009) Huirong Gao et al.   PLANT JOURNAL

LAP3, a novel plant protein required for pollen development, is essential for proper exine formation

(2009) Anna A. Dobritsa et al.   SEXUAL PLANT REPRODUCTION

Artificial chromosome formation in maize (Zea mays L.)

(2008) Evgueni V. Ananiev et al.   CHROMOSOMA

Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

(2008) R. Batista et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA