Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods

Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins

(2021) Liwei Chen et al.   Nature Communications

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

(2020) Jordan L. Doman 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

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

(2020) Mandana Arbab et al.   CELL

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

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

Sequence-specific prediction of the efficiencies of adenine and cytosine base editors

(2020) Myungjae Song et al.   NATURE BIOTECHNOLOGY

Prediction of the sequence-specific cleavage activity of Cas9 variants

(2020) Nahye Kim et al.   NATURE BIOTECHNOLOGY

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

GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos

(2020) Erwei Zuo et al.   Nature Protocols

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

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

(2019) Changyang Zhou et al.   NATURE

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

(2019) Andrew V. Anzalone et al.   NATURE

Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos

(2018) Bin Gu et al.   NATURE BIOTECHNOLOGY

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

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

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

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

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

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

(2017) Gaelen T. Hess et al.   MOLECULAR CELL

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

(2017) Nicole M. Gaudelli et al.   NATURE

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

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

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

(2017) Puping Liang et al.   Protein & Cell

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

(2016) Alexis C. Komor et al.   NATURE

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

APOBEC3G Inhibits HIV-1 RNA Elongation by Inactivating the Viral Trans-Activation Response Element

(2014) Roni Nowarski et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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