Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

RNA-guided retargeting of Sleeping Beauty transposition in human cells

(2020) Adrian Kovač et al.   eLife

Highly Parallel Profiling of Cas9 Variant Specificity

(2020) Jonathan L. Schmid-Burgk et al.   MOLECULAR CELL

CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

(2020) Cicera R. Lazzarotto et al.   NATURE BIOTECHNOLOGY

Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases

(2019) Daesik Kim et al.   Annual Review of Biochemistry

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A highly soluble Sleeping Beauty transposase improves control of gene insertion

(2019) Irma Querques et al.   NATURE BIOTECHNOLOGY

Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion

(2018) Jia Shou et al.   MOLECULAR CELL

DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA

(2018) Daesik Kim et al.   GENOME RESEARCH

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

(2017) Tom Smith et al.   GENOME RESEARCH

Mapping the genomic landscape of CRISPR–Cas9 cleavage

(2017) Peter Cameron et al.   NATURE METHODS

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets

(2017) Shengdar Q Tsai et al.   NATURE METHODS

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

DNA Breaks and End Resection Measured Genome-wide by End Sequencing

(2016) Andres Canela et al.   MOLECULAR CELL

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Open-source guideseq software for analysis of GUIDE-seq data

(2016) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

(2016) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

DSBCapture: in situ capture and sequencing of DNA breaks

(2016) Stefanie V Lensing et al.   NATURE METHODS

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

(2015) Xiaoling Wang et al.   NATURE BIOTECHNOLOGY

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs

(2014) Cory Smith et al.   Cell Stem Cell

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

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

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

High-resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome

(2010) Jason S Iacovoni et al.   EMBO JOURNAL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS