Comprehensive Analysis of CRISPR/Cas9-Mediated Mutagenesis in Arabidopsis thaliana by Genome-wide Sequencing

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

(2019) Benjamin L. Oakes et al.   CELL

Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion

(2018) Jia Shou et al.   MOLECULAR CELL

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

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

(2018) Qiang Zhang et al.   PLANT MOLECULAR BIOLOGY

Concerns regarding ‘off-target’ activity of genome editing endonucleases

(2018) Ulhas Sopanrao Kadam et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

CRISPR for Crop Improvement: An Update Review

(2018) Deepa Jaganathan et al.   Frontiers in Plant Science

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

(2018) Pinar Akcakaya et al.   NATURE

Genome editing technologies and their applications in crop improvement

(2018) Rukmini Mishra et al.   Plant Biotechnology Reports

Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants

(2018) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR/Cas9 genome editing in wheat

(2017) Dongjin Kim et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

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

(2017) Shengdar Q Tsai et al.   NATURE METHODS

Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice

(2017) Xiangbing Meng et al.   Science China-Life Sciences

CRISPR/Cas9 in Genome Editing and Beyond

(2016) Haifeng Wang et al.   Annual Review of Biochemistry

Naturally Occurring Off-Switches for CRISPR-Cas9

(2016) April Pawluk et al.   CELL

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

(2016) Daesik Kim et al.   GENOME RESEARCH

Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System

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

Gene-edited CRISPR mushroom escapes US regulation

(2016) Emily Waltz   NATURE

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

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

(2016) Juan C. Oliveros et al.   NUCLEIC ACIDS RESEARCH

ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions

(2016) Jinrui Shi et al.   PLANT BIOTECHNOLOGY JOURNAL

Enhanced Rice Blast Resistance by CRISPR/Cas9-Targeted Mutagenesis of the ERF Transcription Factor Gene OsERF922

(2016) Fujun Wang et al.   PLoS One

Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis

(2016) Brenda A. Peterson et al.   PLoS One

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos 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

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

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

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

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

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem Cell

Improving the specificity and efficacy of CRISPR/CAS9 and gRNA through target specific DNA reporter

(2014) Jian-Hua Zhang et al.   JOURNAL OF BIOTECHNOLOGY

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

(2014) Xuebing Wu 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

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

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

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

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

(2014) Luhan Yang et al.   Nature Communications

Genotyping with CRISPR-Cas-derived RNA-guided endonucleases

(2014) Jong Min Kim et al.   Nature Communications

Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells

(2014) Yilan Zhang et al.   Scientific Reports

Efficient genome editing in plants using a CRISPR/Cas system

(2013) Zhengyan Feng et al.   CELL 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

Heritable gene targeting in the mouse and rat using a CRISPR-Cas system

(2013) Dali Li et al.   NATURE BIOTECHNOLOGY

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS