High‐efficiency prime editing enables new strategies for broad‐spectrum resistance to bacterial blight of rice

An engineered prime editor with enhanced editing efficiency in plants

(2022) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Efficient targeted insertion of large DNA fragments without DNA donors

(2022) Jinlin Wang et al.   NATURE METHODS

Improving the efficiency of prime editing with epegRNAs and high-temperature treatment in rice

(2022) Jinpeng Zou et al.   Science China-Life Sciences

Optimized prime editing efficiently generates glyphosate-resistant rice plants carrying homozygous TAP-IVS mutation in EPSPS

(2022) Yuanyuan Jiang et al.   Molecular Plant

Prime editing for precise and highly versatile genome manipulation

(2022) Peter J. Chen et al.   NATURE REVIEWS GENETICS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Engineering Broad-Spectrum Resistance to Bacterial Blight by CRISPR/Cas9-Mediated Precise Homology Directed Repair in Rice

(2021) Zheng Wei et al.   Molecular Plant

High-efficiency prime editing with optimized, paired pegRNAs in plants

(2021) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

Enhanced prime editing systems by manipulating cellular determinants of editing outcomes

(2021) Peter J. Chen et al.   CELL

Engineered pegRNAs improve prime editing efficiency

(2021) James W. Nelson et al.   NATURE BIOTECHNOLOGY

Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing

(2021) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Prime genome editing in rice and wheat

(2020) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome sequence of the model rice variety KitaakeX

(2019) Rashmi Jain et al.   BMC GENOMICS

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

(2019) Andrew V. Anzalone et al.   NATURE

Broad-spectrum resistance to bacterial blight in rice using genome editing

(2019) Ricardo Oliva et al.   NATURE BIOTECHNOLOGY

Diagnostic kit for rice blight resistance

(2019) Joon-Seob Eom et al.   NATURE BIOTECHNOLOGY

Plant–Pathogen Warfare under Changing Climate Conditions

(2018) André C. Velásquez et al.   CURRENT BIOLOGY

Induction of Xa10-like Genes in Rice Cultivar Nipponbare Confers Disease Resistance to Rice Bacterial Blight

(2017) Jun Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Processes Underlying a Reproductive Barrier in indica - japonica Rice Hybrids Revealed by Transcriptome Analysis

(2017) Yanfen Zhu et al.   PLANT PHYSIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello et al.   NATURE BIOTECHNOLOGY

Rice SNP-seek database update: new SNPs, indels, and queries

(2016) Locedie Mansueto et al.   NUCLEIC ACIDS RESEARCH

The broadly effective recessive resistance genexa5of rice is a virulence effector-dependent quantitative trait for bacterial blight

(2016) Sheng Huang et al.   PLANT JOURNAL

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XA23 Is an Executor R Protein and Confers Broad-Spectrum Disease Resistance in Rice

(2015) Chunlian Wang et al.   Molecular Plant

Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice

(2015) Junhui Zhou et al.   PLANT JOURNAL

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

Rice versus Xanthomonas oryzae pv. oryzae: a unique pathosystem

(2013) Haitao Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

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

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

Rice xa13 Recessive Resistance to Bacterial Blight Is Defeated by Induction of the Disease Susceptibility Gene Os-11N3

(2010) G. Antony et al.   PLANT CELL

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