An unbiased method for evaluating the genome-wide specificity of base editors in rice

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

(2020) Jordan L. Doman et al.   NATURE BIOTECHNOLOGY

Genome-wide profiling of adenine base editor specificity by EndoV-seq

(2019) Puping Liang et al.   Nature Communications

Genome-wide target specificity of CRISPR RNA-guided adenine base editors

(2019) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

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

(2018) Chao Feng et al.   PLANT BIOTECHNOLOGY JOURNAL

No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice

(2018) Vivek Iyer et al.   PLoS Genetics

Mutation frequency is not increased in CRISPR–Cas9-edited mice

(2018) Michaela Willi et al.   NATURE METHODS

DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA

(2018) Daesik Kim et al.   GENOME RESEARCH

Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A

(2018) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

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

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

(2017) Nicole M. Gaudelli et al.   NATURE

Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion

(2017) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Highly efficient RNA-guided base editing in mouse embryos

(2017) Kyoungmi Kim et al.   NATURE BIOTECHNOLOGY

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

Anything impossible with CRISPR/Cas9?

(2017) Renjie Jiao et al.   Science China-Life Sciences

Effective gene editing by high-fidelity base editor 2 in mouse zygotes

(2017) Puping Liang et al.   Protein & Cell

Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion

(2017) Vladimir Nekrasov et al.   Scientific Reports

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

(2016) Daesik Kim et al.   GENOME RESEARCH

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

(2016) Josh Tycko et al.   MOLECULAR CELL

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

(2016) Shengdar Q. Tsai et al.   NATURE REVIEWS GENETICS

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

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

Teleseismic S wave microseisms

(2016) K. Nishida et al.   SCIENCE

Rice: The First Crop Genome

(2016) Scott A. Jackson   Rice

A global reference for human genetic variation

(2015) Richard A. Gibbs 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

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

Genome editing in rice and wheat using the CRISPR/Cas system

(2014) Qiwei Shan et al.   Nature Protocols

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

Rapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs

(2013) Qiwei Shan et al.   Molecular Plant

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

(2013) Nicola Crosetto et al.   NATURE METHODS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

High-efficiency TALEN-based gene editing produces disease-resistant rice

(2012) Ting Li et al.   NATURE BIOTECHNOLOGY

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

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

(2012) M. Jinek et al.   SCIENCE

An unbiased genome-wide analysis of zinc-finger nuclease specificity

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Targeted Genome Editing Across Species Using ZFNs and TALENs

(2011) Andrew J. Wood et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

High-frequency modification of plant genes using engineered zinc-finger nucleases

(2009) Jeffrey A. Townsend et al.   NATURE

Precise genome modification in the crop species Zea mays using zinc-finger nucleases

(2009) Vipula K. Shukla et al.   NATURE

Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed

(2008) Yukoh Hiei et al.   Nature Protocols