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

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

(2019) Puping Liang et al.   Nature Communications

A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes

(2019) A. St. Martin et al.   Scientific Reports

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors

(2019) Tony P. Huang et al.   NATURE BIOTECHNOLOGY

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing

(2019) Erica McGrath et al.   Nature Communications

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC–Cas9 or cleavage by Cas9 in living cells

(2018) Amber St. Martin et al.   NUCLEIC ACIDS RESEARCH

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

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

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

BE-FLARE: a fluorescent reporter of base editing activity reveals editing characteristics of APOBEC3A and APOBEC3B

(2018) Matthew A. Coelho et al.   BMC BIOLOGY

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

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

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

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Highly efficient RNA-guided base editing in mouse embryos

(2017) Kyoungmi Kim et al.   NATURE BIOTECHNOLOGY

Genome-wide target specificities of CRISPR RNA-guided programmable deaminases

(2017) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

(2017) Xiao Dong et al.   NATURE METHODS

APOBEC3 induces mutations during repair of CRISPR–Cas9-generated DNA breaks

(2017) Liqun Lei et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differences between germline and somatic mutation rates in humans and mice

(2017) Brandon Milholland et al.   Nature Communications

Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system

(2017) Yihan Zhang et al.   Nature Communications

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

(2017) Holly A. Rees et al.   Nature Communications

APOBEC3 induces mutations during repair of CRISPR–Cas9-generated DNA breaks

(2017) Liqun Lei et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2016) Alexis C. Komor et al.   NATURE

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning

(2016) Jennifer L. Hazen et al.   NEURON

Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

(2016) Monica K. Akre et al.   PLoS One

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

(2016) K. Nishida et al.   SCIENCE

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

Timing, rates and spectra of human germline mutation

(2015) Raheleh Rahbari et al.   NATURE GENETICS

Development of potent in vivo mutagenesis plasmids with broad mutational spectra

(2015) Ahmed H. Badran et al.   Nature Communications

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

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

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

Methylcytosine and Normal Cytosine Deamination by the Foreign DNA Restriction Enzyme APOBEC3A

(2012) Michael A. Carpenter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A nucleoside kinase as a dual selector for genetic switches and circuits

(2010) Yohei Tashiro et al.   NUCLEIC ACIDS RESEARCH

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Portable Hot Spot Recognition Loop Transfers Sequence Preferences from APOBEC Family Members to Activation-induced Cytidine Deaminase

(2009) Rahul M. Kohli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY