CRISPAltRations: A validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing

Template plasmid integration in germline genome-edited cattle

(2020) Alexis L. Norris et al.   NATURE BIOTECHNOLOGY

CRISPR-engineered T cells in patients with refractory cancer

(2020) Edward A. Stadtmauer et al.   SCIENCE

Highly Parallel Profiling of Cas9 Variant Specificity

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

Extinction of all infectious HIV in cell culture by the CRISPR-Cas12a system with only a single crRNA

(2020) Zongliang Gao et al.   NUCLEIC ACIDS RESEARCH

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

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

Increasing CRISPR Efficiency and Measuring Its Specificity in HSPCs Using a Clinically Relevant System

(2020) Jenny Shapiro et al.   Molecular Therapy-Methods & Clinical Development

A New Class of Medicines through DNA Editing

(2019) Matthew H. Porteus   NEW ENGLAND JOURNAL OF MEDICINE

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

(2019) Benjamin P. Kleinstiver et al.   NATURE BIOTECHNOLOGY

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Accurate analysis of genuine CRISPR editing events with ampliCan

(2019) Kornel Labun et al.   GENOME RESEARCH

High efficiency error suppression for accurate detection of low-frequency variants

(2019) Ting Ting Wang et al.   NUCLEIC ACIDS RESEARCH

Microhomologies are prevalent at Cas9-induced larger deletions

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

Evaluation and Reduction of CRISPR Off-Target Cleavage Events

(2019) Christopher A. Vakulskas et al.   Nucleic Acid Therapeutics

Enhancing gene editing specificity by attenuating DNA cleavage kinetics

(2019) Jeffrey C. Miller et al.   NATURE BIOTECHNOLOGY

Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

(2019) Ryan T. Leenay et al.   NATURE BIOTECHNOLOGY

Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining

(2019) Joost Schimmel et al.   TRENDS IN GENETICS

Challenges and recommendations to improve the installability and archival stability of omics computational tools

(2019) Serghei Mangul et al.   PLOS BIOLOGY

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

(2019) Andrew V. Anzalone et al.   NATURE

High levels of AAV vector integration into CRISPR-induced DNA breaks

(2019) Killian S. Hanlon et al.   Nature Communications

A Mechanism to Minimize Errors during Non-homologous End Joining

(2019) Benjamin M. Stinson et al.   MOLECULAR CELL

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data

(2018) Nick Kamps-Hughes et al.   PLoS One

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

A Survey of Validation Strategies for CRISPR-Cas9 Editing

(2018) Monica F. Sentmanat et al.   Scientific Reports

Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a

(2018) Isabel Strohkendl et al.   MOLECULAR CELL

A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells

(2018) Christopher A. Vakulskas et al.   NATURE MEDICINE

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

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes

(2017) Ashley M. Jacobi et al.   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

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

CrispRVariants charts the mutation spectrum of genome engineering experiments

(2016) Helen Lindsay et al.   NATURE BIOTECHNOLOGY

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

Cancer: hunting rare somatic mutations

(2016) Vivien Marx   NATURE METHODS

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

C-Brick: A New Standard for Assembly of Biological Parts Using Cpf1

(2016) Shi-Yuan Li et al.   ACS Synthetic Biology

A somatic reference standard for cancer genome sequencing

(2016) David W. Craig et al.   Scientific Reports

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

(2015) Bernd Zetsche et al.   CELL

High-throughput genotyping of CRISPR/Cas9-mediated mutants using fluorescent PCR-capillary gel electrophoresis

(2015) Muhammad Khairul Ramlee et al.   Scientific Reports

Genome Engineering with Targetable Nucleases

(2014) Dana Carroll   Annual Review of Biochemistry

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications

(2014) John C. Mu et al.   BIOINFORMATICS

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

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

(2014) Thomas J Cradick et al.   Molecular Therapy-Nucleic Acids

Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays

(2013) Satoshi Ota et al.   GENES TO CELLS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

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

(2010) Michael R. Lieber   Annual Review of Biochemistry

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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