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Towards best-practice approaches for CRISPR/Cas9 gene engineering

https://doi.org/10.1101/469544
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/1873-3468.12599openalex-snapshot
Enhanced CRISPR /Cas9‐mediated biallelic genome targeting with dual surrogate reporter‐integrated donors
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Chromatin accessibility and guide sequence secondary structure affect CRISPR ‐Cas9 gene editing efficiency
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Purified Cas9 Fusion Proteins for Advanced Genome Manipulation
inferredcites →https://doi.org/10.1007/s00239-004-0046-3openalex-snapshot
Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements
inferredcites →https://doi.org/10.1007/s00335-012-9418-yopenalex-snapshot
Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project
inferredcites →https://doi.org/10.1007/s00335-017-9697-4openalex-snapshot
CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools
inferredcites →https://doi.org/10.1007/s11248-016-9941-9openalex-snapshot
Hypomorphic phenotype of Foxn1 gene-modified rats by CRISPR/Cas9 system
inferredcites →https://doi.org/10.1016/b978-0-12-801185-0.00001-5openalex-snapshot
In Vitro Enzymology of Cas9
inferredcites →https://doi.org/10.1016/j.cell.2013.02.022openalex-snapshot
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
inferredcites →https://doi.org/10.1016/j.cell.2013.06.044openalex-snapshot
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
inferredcites →https://doi.org/10.1016/j.cell.2015.03.028openalex-snapshot
Efficient Intracellular Delivery of Native Proteins
inferredcites →https://doi.org/10.1016/j.cell.2015.09.038openalex-snapshot
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
inferredcites →https://doi.org/10.1016/j.cell.2015.11.015openalex-snapshot
High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities
inferredcites →https://doi.org/10.1016/j.cell.2018.02.033openalex-snapshot
Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
inferredcites →https://doi.org/10.1016/j.cell.2018.09.022openalex-snapshot
Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens
inferredcites →https://doi.org/10.1016/j.cell.2018.10.024openalex-snapshot
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
inferredcites →https://doi.org/10.1016/j.jbiotec.2015.04.024openalex-snapshot
Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection
inferredcites →https://doi.org/10.1016/j.jbiotec.2016.01.009openalex-snapshot
Comparison of surrogate reporter systems for enrichment of cells with mutations induced by genome editors
inferredcites →https://doi.org/10.1016/j.jmb.2018.03.019openalex-snapshot
CRISPys: Optimal sgRNA Design for Editing Multiple Members of a Gene Family Using the CRISPR System
inferredcites →https://doi.org/10.1016/j.omtm.2018.06.006openalex-snapshot
Prevalence of Pre-existing Antibodies to CRISPR-Associated Nuclease Cas9 in the USA Population
inferredcites →https://doi.org/10.1016/j.omtn.2017.08.005openalex-snapshot
The Chromatin Structure Differentially Impacts High-Specificity CRISPR-Cas9 Nuclease Strategies
inferredcites →https://doi.org/10.1016/j.stem.2014.06.011openalex-snapshot
Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs
inferredcites →https://doi.org/10.1021/acssynbio.5b00299openalex-snapshot
The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells
inferredcites →https://doi.org/10.1038/gt.2015.82openalex-snapshot
CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting
inferredcites →https://doi.org/10.1038/nature09886openalex-snapshot
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
inferredcites →https://doi.org/10.1038/nature14136openalex-snapshot
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
inferredcites →https://doi.org/10.1038/nature14299openalex-snapshot
In vivo genome editing using Staphylococcus aureus Cas9
inferredcites →https://doi.org/10.1038/nature14592openalex-snapshot
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
inferredcites →https://doi.org/10.1038/nature16526openalex-snapshot
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects
inferredcites →https://doi.org/10.1038/nature17946openalex-snapshot
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
inferredcites →https://doi.org/10.1038/nature23875openalex-snapshot
Discovery of stimulation-responsive immune enhancers with CRISPR activation
inferredcites →https://doi.org/10.1038/nature24268openalex-snapshot
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy
inferredcites →https://doi.org/10.1038/nbt.2507openalex-snapshot
Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
inferredcites →https://doi.org/10.1038/nbt.2623openalex-snapshot
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
inferredcites →https://doi.org/10.1038/nbt.2647openalex-snapshot
DNA targeting specificity of RNA-guided Cas9 nucleases
inferredcites →https://doi.org/10.1038/nbt.2808openalex-snapshot
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
inferredcites →https://doi.org/10.1038/nbt.2889openalex-snapshot
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
inferredcites →https://doi.org/10.1038/nbt.2908openalex-snapshot
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
inferredcites →https://doi.org/10.1038/nbt.2916openalex-snapshot
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
inferredcites →https://doi.org/10.1038/nbt.3081openalex-snapshot
Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo
inferredcites →https://doi.org/10.1038/nbt.3101openalex-snapshot
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
inferredcites →https://doi.org/10.1038/nbt.3117openalex-snapshot
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
inferredcites →https://doi.org/10.1038/nbt.3127openalex-snapshot
Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors
inferredcites →https://doi.org/10.1038/nbt.3149openalex-snapshot
A split-Cas9 architecture for inducible genome editing and transcription modulation
inferredcites →https://doi.org/10.1038/nbt.3235openalex-snapshot
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains
inferredcites →https://doi.org/10.1038/nbt.3437openalex-snapshot
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
inferredcites →https://doi.org/10.1038/nbt.3609openalex-snapshot
Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells
inferredcites →https://doi.org/10.1038/ncomms11750openalex-snapshot
Internal guide RNA interactions interfere with Cas9-mediated cleavage
inferredcites →https://doi.org/10.1038/ncomms13274openalex-snapshot
Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes
inferredcites →https://doi.org/10.1038/ncomms4378openalex-snapshot
Surrogate reporter-based enrichment of cells containing RNA-guided Cas9 nuclease-induced mutations
inferredcites →https://doi.org/10.1038/nmeth.3284openalex-snapshot
Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells
inferredcites →https://doi.org/10.1038/nmeth.4278openalex-snapshot
CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets
inferredcites →https://doi.org/10.1038/nmeth.4284openalex-snapshot
Mapping the genomic landscape of CRISPR–Cas9 cleavage
inferredcites →https://doi.org/10.1038/nrmicro.2016.184openalex-snapshot
Diversity and evolution of class 2 CRISPR–Cas systems
inferredcites →https://doi.org/10.1038/s41467-018-04252-2openalex-snapshot
The CRISPR tool kit for genome editing and beyond
inferredcites →https://doi.org/10.1038/s41467-018-05843-9openalex-snapshot
Cas9 immunity creates challenges for CRISPR gene editing therapies
inferredcites →https://doi.org/10.1038/s41467-019-09693-xopenalex-snapshot
Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes
inferredcites →https://doi.org/10.1038/s41589-018-0080-xopenalex-snapshot
Genome editing by natural and engineered CRISPR-associated nucleases
inferredcites →https://doi.org/10.1038/s41591-018-0326-xopenalex-snapshot
Identification of preexisting adaptive immunity to Cas9 proteins in humans
inferredcites →https://doi.org/10.1038/s41592-018-0048-5openalex-snapshot
An enhanced CRISPR repressor for targeted mammalian gene regulation
inferredcites →https://doi.org/10.1038/s41592-018-0149-1openalex-snapshot
Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells
inferredcites →https://doi.org/10.1038/s41598-017-12201-0openalex-snapshot
Production of immunodeficient rabbits by multiplex embryo transfer and multiplex gene targeting
inferredcites →https://doi.org/10.1038/s41598-018-19441-8openalex-snapshot
A Survey of Validation Strategies for CRISPR-Cas9 Editing
inferredcites →https://doi.org/10.1038/s41598-018-32714-6openalex-snapshot
Biolistic-delivery-based transient CRISPR/Cas9 expression enables in planta genome editing in wheat
inferredcites →https://doi.org/10.1038/srep40638openalex-snapshot
Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence
inferredcites →https://doi.org/10.1073/pnas.1208507109openalex-snapshot
Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
inferredcites →https://doi.org/10.1073/pnas.1308335110openalex-snapshot
Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
inferredcites →https://doi.org/10.1093/nar/gkv137openalex-snapshot
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
inferredcites →https://doi.org/10.1093/nar/gkv601openalex-snapshot
Development of an intein-mediated split–Cas9 system for gene therapy
inferredcites →https://doi.org/10.1093/nar/gkw524openalex-snapshot
Probing the impact of chromatin conformation on genome editing tools
inferredcites →https://doi.org/10.1093/nar/gkw660openalex-snapshot
An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting
inferredcites →https://doi.org/10.1093/nar/gkx1271openalex-snapshot
(Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed-cell super-resolution imaging of multiple genes
inferredcites →https://doi.org/10.1093/nar/gkx578openalex-snapshot
dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression
inferredcites →https://doi.org/10.1093/nar/gkx993openalex-snapshot
PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens
inferredcites →https://doi.org/10.1093/pcp/pcu154openalex-snapshot
Multigene Knockout Utilizing Off-Target Mutations of the CRISPR/Cas9 System in Rice
inferredcites →https://doi.org/10.1101/gr.162339.113openalex-snapshot
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
inferredcites →https://doi.org/10.1101/gr.171264.113openalex-snapshot
Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA
inferredcites →https://doi.org/10.1101/gr.171322.113openalex-snapshot
Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
inferredcites →https://doi.org/10.1101/gr.219089.116openalex-snapshot
Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degeneration
inferredcites →https://doi.org/10.1126/science.1138140openalex-snapshot
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
inferredcites →https://doi.org/10.1126/science.1225829openalex-snapshot
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
inferredcites →https://doi.org/10.1126/science.1231143openalex-snapshot
Multiplex Genome Engineering Using CRISPR/Cas Systems
inferredcites →https://doi.org/10.1126/science.1232033openalex-snapshot
RNA-Guided Human Genome Engineering via Cas9
inferredcites →https://doi.org/10.1126/science.1246981openalex-snapshot
Genetic Screens in Human Cells Using the CRISPR-Cas9 System
inferredcites →https://doi.org/10.1126/science.aac7041openalex-snapshot
Identification and characterization of essential genes in the human genome
inferredcites →https://doi.org/10.1126/science.aad5227openalex-snapshot
Rationally engineered Cas9 nucleases with improved specificity
inferredcites →https://doi.org/10.1126/science.aat1178openalex-snapshot
A molecular mechanism for Wnt ligand-specific signaling
inferredcites →https://doi.org/10.1186/s13059-016-1012-2openalex-snapshot
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR
inferredcites →https://doi.org/10.1186/s13104-018-3262-4openalex-snapshot
enChIP systems using different CRISPR orthologues and epitope tags
inferredcites →https://doi.org/10.1242/dev.123.1.1openalex-snapshot
The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio
inferredcites →https://doi.org/10.1242/dev.123.1.37openalex-snapshot
A genetic screen for mutations affecting embryogenesis in zebrafish
inferredcites →https://doi.org/10.1242/dev.123059openalex-snapshot
Reck enables cerebrovascular development by promoting canonical Wnt signaling
inferredcites →https://doi.org/10.1242/dev.134809openalex-snapshot
Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes.
inferredcites →https://doi.org/10.1371/journal.pgen.1006780openalex-snapshot
Genetic compensation: A phenomenon in search of mechanisms
inferredcites →https://doi.org/10.1371/journal.pone.0098186openalex-snapshot
Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs
inferredcites →https://doi.org/10.1371/journal.pone.0144970openalex-snapshot
Exploiting the CRISPR/Cas9 PAM Constraint for Single-Nucleotide Resolution Interventions
inferredcites →https://doi.org/10.1371/journal.pone.0155812openalex-snapshot
Novel Hypomorphic Alleles of the Mouse Tyrosinase Gene Induced by CRISPR-Cas9 Nucleases Cause Non-Albino Pigmentation Phenotypes
inferredcites →https://doi.org/10.1371/journal.pone.0182528openalex-snapshot
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish
inferredcites →https://doi.org/10.1371/journal.pone.0196238openalex-snapshot
Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)
inferredcites →https://doi.org/10.1534/g3.113.005777openalex-snapshot
The Genomic and Transcriptomic Landscape of a HeLa Cell Line
inferredcites →https://doi.org/10.1534/g3.114.015834openalex-snapshot
Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases
inferredcites →https://doi.org/10.7554/elife.06489openalex-snapshot
Tip cell-specific requirement for an atypical Gpr124- and Reck-dependent Wnt/β-catenin pathway during brain angiogenesis
inferredcites →https://doi.org/10.7554/elife.12677openalex-snapshot
Nucleosomes impede Cas9 access to DNA in vivo and in vitro
inferredcites →https://doi.org/10.7554/elife.13450openalex-snapshot
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
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