Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

Identifying Novel Enhancer Elements with CRISPR-Based Screens

(2018) Jason C. Klein et al.   ACS Chemical Biology

FlashFry: a fast and flexible tool for large-scale CRISPR target design

(2018) Aaron McKenna et al.   BMC BIOLOGY

Bidirectional Degradation of DNA Cleavage Products Catalyzed by CRISPR/Cas9

(2018) Anthony A. Stephenson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

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

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Target-Specific Precision of CRISPR-Mediated Genome Editing

(2018) Anob M. Chakrabarti et al.   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

Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing

(2018) Mehmet Fatih Bolukbasi et al.   Nature Communications

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

(2018) Eirini M. Kallimasioti-Pazi et al.   PLOS BIOLOGY

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

(2017) Xuebing Wu et al.   NUCLEIC ACIDS RESEARCH

Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus

(2017) Anne Bothmer et al.   Nature Communications

DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining

(2017) Michael P. Conlin et al.   Cell Reports

Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency

(2016) Howard H. Y. Chang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Probing the impact of chromatin conformation on genome editing tools

(2016) Xiaoyu Chen et al.   NUCLEIC ACIDS RESEARCH

Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease

(2016) Jason M. Wolfs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

(2016) F. Jiang et al.   SCIENCE

Sources of Error in Mammalian Genetic Screens

(2016) Laura Magill Sack et al.   G3-Genes Genomes Genetics

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway?

(2015) Agnel Sfeir et al.   TRENDS IN BIOCHEMICAL SCIENCES

An Inducible Lentiviral Guide RNA Platform Enables the Identification of Tumor-Essential Genes and Tumor-Promoting Mutations In Vivo

(2015) Brandon J. Aubrey et al.   Cell Reports

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Non-homologous end joining often uses microhomology: Implications for alternative end joining

(2014) Nicholas R. Pannunzio et al.   DNA REPAIR

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

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

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

Microhomology-based choice of Cas9 nuclease target sites

(2014) Sangsu Bae et al.   NATURE METHODS

Is Non-Homologous End-Joining Really an Inherently Error-Prone Process?

(2014) Mireille Bétermier et al.   PLoS Genetics

Modernizing the Nonhomologous End-Joining Repertoire: Alternative and Classical NHEJ Share the Stage

(2013) Ludovic Deriano et al.   Annual Review of Genetics

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

(2013) J. Zhang et al.   BIOINFORMATICS

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology

(2012) Duran Ustek et al.   INFECTION GENETICS AND EVOLUTION

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

(2012) M. Jinek et al.   SCIENCE

The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway

(2010) Michael R. Lieber   Annual Review of Biochemistry

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Lentiviral integration preferences in transgenic mice

(2008) Shang-Hsun Yang et al.   GENESIS