Comprehensive Analysis of CRISPR-Cas9 Editing Outcomes in Yeast Xanthophyllomyces dendrorhous

The promise and challenge of therapeutic genome editing

(2020) Jennifer A. Doudna   NATURE

A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break repair choice

(2020) Paris Roidos et al.   Nature Communications

Controlling and enhancing CRISPR systems

(2020) Haridha Shivram et al.   Nature Chemical Biology

Catalytically inactive Cas9 impairs DNA replication fork progression to induce focal genomic instability

(2020) Goro Doi et al.   NUCLEIC ACIDS RESEARCH

Target-dependent nickase activities of the CRISPR–Cas nucleases Cpf1 and Cas9

(2019) Becky Xu Hua Fu et al.   Nature Microbiology

Cooperation between non-essential DNA polymerases contributes to genome stability in Saccharomyces cerevisiae

(2019) Damon Meyer et al.   DNA REPAIR

Microhomologies are prevalent at Cas9-induced larger deletions

(2019) Dominic D G Owens et al.   NUCLEIC ACIDS RESEARCH

The mismatch repair-dependent DNA damage response: Mechanisms and implications

(2019) Dipika Gupta et al.   DNA REPAIR

Adenine base editors catalyze cytosine conversions in human cells

(2019) Heon Seok Kim et al.   NATURE BIOTECHNOLOGY

Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing

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

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair

(2018) Tomoko Kato-Inui et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles

(2018) Brenda R. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas immunity, DNA repair and genome stability

(2018) Andrew Cubbon et al.   BIOSCIENCE REPORTS

20 Years of Mre11 Biology: No End in Sight

(2018) Tanya T. Paull   MOLECULAR CELL

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

R-loop formation by dCas9 is mutagenic in Saccharomyces cerevisiae

(2018) Marian F Laughery et al.   NUCLEIC ACIDS RESEARCH

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

(2017) Nicholas R. Pannunzio et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2017) Nicole M. Gaudelli et al.   NATURE

Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR–Cas9 genome-editing efficiency

(2017) Marella D Canny et al.   NATURE BIOTECHNOLOGY

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Consider the workhorse: Nonhomologous end-joining in budding yeast

(2016) Charlene H. Emerson et al.   Biochemistry and Cell Biology

Multiplex gene editing of the Yarrowia lipolytica genome using the CRISPR-Cas9 system

(2016) Shuliang Gao et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

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

(2016) Alexis C. Komor et al.   NATURE

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina

(2015) Rahul Sharma et al.   BMC GENOMICS

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns et al.   NATURE

Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

(2015) Takeshi Maruyama et al.   NATURE BIOTECHNOLOGY

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells

(2015) Van Trung Chu et al.   NATURE BIOTECHNOLOGY

DNA polymerases δ and λ cooperate in repairing double-strand breaks by microhomology-mediated end-joining inSaccharomyces cerevisiae

(2015) Damon Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Red yeasts and carotenoid production: outlining a future for non-conventional yeasts of biotechnological interest

(2015) Ilaria Mannazzu et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System

(2013) Andrew R. Bassett et al.   Cell Reports

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Proteomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous

(2011) Pilar Martinez-Moya et al.   BMC MICROBIOLOGY

Multiple end joining mechanisms repair a chromosomal DNA break in fission yeast

(2011) Peng Li et al.   DNA REPAIR

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Mechanism of Eukaryotic Homologous Recombination

(2008) Joseph San Filippo et al.   Annual Review of Biochemistry