Improved plant cytosine base editors with high editing activity, purity, and specificity

Base-Editing-Mediated Artificial Evolution of OsALS1 In Planta to Develop Novel Herbicide-Tolerant Rice Germplasms

(2020) Yongjie Kuang et al.   Molecular Plant

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

(2020) Chao Li et al.   NATURE BIOTECHNOLOGY

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

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

Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

(2020) Zhaohui Zhong et al.   Rice

Expanding the genome-targeting scope and the site selectivity of high-precision base editors

(2020) Junjie Tan et al.   Nature Communications

Dual base editor catalyzes both cytosine and adenine base conversions in human cells

(2020) Xiaohui Zhang et al.   NATURE BIOTECHNOLOGY

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

(2020) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Base editors for simultaneous introduction of C-to-T and A-to-G mutations

(2020) Rina C. Sakata et al.   NATURE BIOTECHNOLOGY

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

(2020) Erwei Zuo et al.   NATURE METHODS

A Cas9 with PAM recognition for adenine dinucleotides

(2020) Pranam Chatterjee et al.   Nature Communications

Rationally Designed APOBEC3B Cytosine Base Editors with Improved Specificity

(2020) Shuai Jin et al.   MOLECULAR CELL

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Base editing with high efficiency in allotetraploid oilseed rape by A3A‐PBE system

(2020) Hongtao Cheng et al.   PLANT BIOTECHNOLOGY JOURNAL

Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects

(2020) Sangsin Lee et al.   Science Advances

Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants

(2020) Juan Li et al.   Molecular Plant

Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG

(2019) Zhaohui Zhong et al.   Molecular Plant

Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice

(2019) Wang Bo et al.   Rice Science

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

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

Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing

(2019) Qiurong Ren et al.   Frontiers in Plant Science

CRISPRMatch: An Automatic Calculation and Visualization Tool for High-throughput CRISPR Genome-editing Data Analysis

(2018) Qi You et al.   International Journal of Biological Sciences

Improved Base Editor for Efficiently Inducing Genetic Variations in Rice with CRISPR/Cas9-Guided Hyperactive hAID Mutant

(2018) Bin Ren et al.   Molecular Plant

Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems

(2018) Levi G. Lowder et al.   Molecular Plant

Plant Genome Editing Using FnCpf1 and LbCpf1 Nucleases at Redefined and Altered PAM Sites

(2018) Zhaohui Zhong et al.   Molecular Plant

Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion

(2018) Xiao Wang et al.   NATURE BIOTECHNOLOGY

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

Multiplex QTL editing of grain-related genes improves yield in elite rice varieties

(2018) Jianping Zhou et al.   PLANT CELL REPORTS

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

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

(2018) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing

(2018) Xu Tang et al.   PLANT BIOTECHNOLOGY JOURNAL

Developing a highly efficient and wildly adaptive CRISPR ‐ Sa Cas9 toolset for plant genome editing

(2018) Ruying Qin et al.   PLANT BIOTECHNOLOGY JOURNAL

Precise Editing of a Target Base in the Rice Genome Using a Modified CRISPR/Cas9 System

(2017) Yuming Lu et al.   Molecular Plant

Generation of Targeted Point Mutations in Rice by a Modified CRISPR/Cas9 System

(2017) Jingying Li et al.   Molecular Plant

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

(2017) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion

(2017) Zenpei Shimatani et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas9 Based Genome Editing Reveals New Insights into MicroRNA Function and Regulation in Rice

(2017) Jianping Zhou et al.   Frontiers in Plant Science

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

A Single Transcript CRISPR-Cas9 System for Efficient Genome Editing in Plants

(2016) Xu Tang et al.   Molecular Plant

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

(2016) Alexis C. Komor et al.   NATURE

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism

(2016) Xuelian Zheng et al.   PLANT CELL REPORTS

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

(2016) K. Nishida et al.   SCIENCE

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

(2015) Levi G. Lowder et al.   PLANT PHYSIOLOGY

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

Glyphosate resistance: state of knowledge

(2014) Robert Douglas Sammons et al.   PEST MANAGEMENT SCIENCE

Resistance to AHAS inhibitor herbicides: current understanding

(2013) Qin Yu et al.   PEST MANAGEMENT SCIENCE

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

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

Control of grain size, shape and quality by OsSPL16 in rice

(2012) Shaokui Wang et al.   NATURE GENETICS

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

Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering

(2012) Y. Zhang et al.   PLANT PHYSIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

(2010) Yongqing Jiao et al.   NATURE GENETICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH