Off-target Effects in CRISPR/Cas9-mediated Genome Engineering

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

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Multiplex Genome Engineering Using CRISPR/Cas Systems

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Genome engineering using the CRISPR-Cas9 system

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RNA-Guided Human Genome Engineering via Cas9

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The new frontier of genome engineering with CRISPR-Cas9

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Development and Applications of CRISPR-Cas9 for Genome Engineering

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Improved vectors and genome-wide libraries for CRISPR screening

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Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

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

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DNA targeting specificity of RNA-guided Cas9 nucleases

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CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

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Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity

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High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells

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DNA methylation: roles in mammalian development

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Genetic screens in human cells using the CRISPR-Cas9 system

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Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

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Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

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CRISPR/Cas, the Immune System of Bacteria and Archaea

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RNA-guided editing of bacterial genomes using CRISPR-Cas systems

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Crystal structure of Cas9 in complex with guide RNA and target DNA

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

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Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

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Optogenetics

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Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

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Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

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DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

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CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

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Engineered CRISPR-Cas9 nucleases with altered PAM specificities

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Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation

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Short motif sequences determine the targets of the prokaryotic CRISPR defence system

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High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487 · see citing works

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.162339.113 · Cited by 1,356 · see citing works

Therapeutic genome editing: prospects and challenges

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Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

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CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

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CRISPR RNA–guided activation of endogenous human genes

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Structures of Cas9 endonucleases reveal RNA-mediated conformational activation

Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230 · see citing works

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

Maruyama, T., Dougan, S. K., Truttmann, M. C., Bilate, A. M., Ingram, J. R., & Ploegh, H. L. (2015) · Nature Biotechnology · doi:10.1038/nbt.3190 · Cited by 1,137 · see citing works

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

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Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

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Digenome-seq: Genome-wide profiling of CRISPR-cas9 off-target effects in human cells

Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H. R., Hwang, J., Kim, J.-I., & Kim, J.-S. (2015) · Nature Methods · doi:10.1038/nmeth.3284 · Cited by 992 · see citing works

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

Tsai, S. Q., Wyvekens, N., Khayter, C., Foden, J. A., Thapar, V., Reyon, D., Goodwin, M. J., Aryee, M. J., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2908 · Cited by 952 · see citing works

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

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E-CRISP: fast CRISPR target site identification

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Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

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

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Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects

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Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

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Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

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A split-Cas9 architecture for inducible genome editing and transcription modulation

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Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

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Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA

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Heritable gene targeting in the mouse and rat using a CRISPR-Cas system

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A light-inducible CRISPR-Cas9 system for control of endogenous gene activation

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The interaction of closed circular DNA with intercalative dyes

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Generation of gene-modified mice via Cas9/RNA-mediated gene targeting

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An unbiased genome-wide analysis of zinc-finger nuclease specificity

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Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

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Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly

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One-step generation of knockout pigs by zygote injection of CRISPR/Cas system

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Small molecules enhance CRISPR genome editing in pluripotent stem cells

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

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Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs

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Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila

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TALEN-based Gene Correction for Epidermolysis Bullosa

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Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

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Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells

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Off-target mutations are rare in Cas9-modified mice

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Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs

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Quantifying on- and off-target genome editing

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Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing

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Genome-wide identification of CRISPR/Cas9 off-targets in human genome

Duan, J., Lu, G., Xie, Z., Lou, M., Luo, J., Guo, L., & Zhang, Y. (2014) · Cell Research · doi:10.1038/cr.2014.87 · Cited by 137 · see citing works

Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage

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Trends in large-scale mouse mutagenesis: from genetics to functional genomics

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One-step generation of p53 gene biallelic mutant Cynomolgus monkey via the CRISPR/Cas system

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Genome Editing Technologies: Defining a Path to Clinic

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Expansion of the CRISPR–Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs

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Genome-Wide Mutation Avalanches Induced in Diploid Yeast Cells by a Base Analog or an APOBEC Deaminase

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Mapping the precision of genome editing

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A pre-screening FISH-based method to detect CRISPR/Cas9 off-targets in mouse embryonic stem cells

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Next-generation CRISPRs

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CRISPR technology: A decade of genome editing is only the beginning

Wang, J. Y., & Doudna, J. A. (2023) · Science · doi:10.1126/science.add8643 · Cited by 1,058 · see citing works

DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins

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CRISPR Gene Therapy: Applications, Limitations, and Implications for the Future

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Huntington disease: new insights into molecular pathogenesis and therapeutic opportunities

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CRISPR/Cas system: recent advances and future prospects for genome editing

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Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

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Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing

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CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off‐Target Evaluation, and Strategies to Mitigate Off‐Target Effects

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Precise plant genome editing using base editors and prime editors

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Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning

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Editing streptomycete genomes in the CRISPR/Cas9 age

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Orthologous CRISPR/Cas9 systems for specific and efficient degradation of covalently closed circular DNA of hepatitis B virus

Kostyushev, D. S., Brezgin, S., Kostyusheva, A., Zarifyan, D., Goptar, I. A., & Chulanov, V. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03021-8 · Cited by 90 · see citing works

CRISPR/Cas9 revitalizes adoptive T-cell therapy for cancer immunotherapy

Ghaffari, S., Khalili, N., & Rezaei, N. (2021) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-021-02076-5 · Cited by 89 · see citing works

Biomaterials-mediated CRISPR/Cas9 delivery: recent challenges and opportunities in gene therapy

Dubey, A. K., & Mostafavi, E. (2023) · Frontiers in Chemistry · doi:10.3389/fchem.2023.1259435 · Cited by 89 · see citing works

Transgene-free Genome Editing in Plants

Gu, X., Liu, L., & Zhang, H. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.805317 · Cited by 88 · see citing works

Recent advances in the delivery and applications of nonviral CRISPR/Cas9 gene editing

Sinclair, F., Begum, A. A., Dai, C. C., Tóth, I., & Moyle, P. M. (2023) · Drug Delivery and Translational Research · doi:10.1007/s13346-023-01320-z · Cited by 88 · see citing works

CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies

Roy, R. K., Debashree, I., Srivastava, S., Rishi, N., & Srivastava, A. (2021) · Current Bioinformatics · doi:10.2174/1574893616666210708150439 · Cited by 7 · see citing works

Progress of application and off-target effects of CRISPR/Cas9.

Zheng, W., & Gu, F. (2015) · PubMed · doi:10.16288/j.yczz.15-070 · Cited by 10 · see citing works

Emerging strategies to minimize the off-target effects in CRISPR/Cas9 system

Ouyang, C. (2024) · International Conference on Biological Engineering and Medical Science (ICBioMed) · doi:10.1117/12.3013214 · Cited by 1 · see citing works

Off-target effects in CRISPR/Cas9 gene editing

Guo, C., Ma, X., Gao, F., & Guo, Y. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1143157 · Cited by 625 · see citing works

Off-target interactions in the CRISPR-Cas9 Machinery: mechanisms and outcomes

Kanazhevskaya, L. Y., Zhdanova, P. V., Chernonosov, A. А., & Koval, V. V. (2025) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2025.102134 · Cited by 4 · see citing works