A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing

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

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

Continuous evolution of SpCas9 variants compatible with non-G PAMs

(2020) Shannon M. Miller et al.   NATURE BIOTECHNOLOGY

Burkholderia cenocepacia utilizes a type VI secretion system for bacterial competition

(2019) Helena L. Spiewak et al.   MicrobiologyOpen

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

The Type VI secretion system: a versatile bacterial weapon

(2019) Sarah Coulthurst   MICROBIOLOGY-SGM

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Analysis and minimization of cellular RNA editing by DNA adenine base editors

(2019) Holly A. Rees et al.   Science Advances

Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria

(2019) Anna V Kotrys et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Andrew V. Anzalone et al.   NATURE

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

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma

(2018) Raj K. Gopal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands

(2018) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mitochondrial Genome Engineering: The Revolution May Not Be CRISPR-Ized

(2018) Payam A. Gammage et al.   TRENDS IN GENETICS

Linear mitochondrial DNA is rapidly degraded by components of the replication machinery

(2018) Viktoriya Peeva et al.   Nature Communications

The mitochondrial DNA polymerase gamma degrades linear DNA fragments precluding the formation of deletions

(2018) Nadee Nissanka et al.   Nature Communications

Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma

(2018) Raj K. Gopal et al.   CANCER CELL

MitoTALEN reduces mutant mtDNA load and restores tRNAAla levels in a mouse model of heteroplasmic mtDNA mutation

(2018) Sandra R. Bacman et al.   NATURE MEDICINE

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

The effect of increasing numbers of repeats on TAL effector DNA binding specificity

(2017) Fabio C. Rinaldi et al.   NUCLEIC ACIDS RESEARCH

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

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

(2016) Alexis C. Komor et al.   NATURE

Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations inEscherichia coli

(2016) Ashok S. Bhagwat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

(2016) K. Nishida et al.   SCIENCE

Mitochondrial dysfunction remodels one-carbon metabolism in human cells

(2016) Xiaoyan Robert Bao et al.   eLife

In-Frame and Unmarked Gene Deletions in Burkholderia cenocepacia via an Allelic Exchange System Compatible with Gateway Technology

(2015) Mustafa Fazli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Crystal Structure of Staphylococcus aureus Cas9

(2015) Hiroshi Nishimasu et al.   CELL

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition

(2015) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease

(2015) James B. Stewart et al.   NATURE REVIEWS GENETICS

Mitochondrially targeted ZFNs for selective degradation of pathogenic mitochondrial genomes bearing large-scale deletions or point mutations

(2014) P. A. Gammage et al.   EMBO Molecular Medicine

Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition

(2014) Sandra R Richardson et al.   eLife

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs

(2013) Sandra R Bacman et al.   NATURE MEDICINE

Base Excision Repair

(2013) H. E. Krokan et al.   Cold Spring Harbor Perspectives in Biology

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

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

Mitochondrial disorders as windows into an ancient organelle

(2012) Scott B. Vafai et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

(2011) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria

(2010) Rachel D. Hood et al.   Cell Host & Microbe

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS