Highly Parallel Profiling of Cas9 Variant Specificity

Genome engineering using the CRISPR-Cas9 system

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

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Rationally engineered Cas9 nucleases with improved specificity

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

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Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

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Enhanced proofreading governs CRISPR-Cas9 targeting accuracy

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

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Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

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Past, present, and future of CRISPR genome editing technologies

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The CRISPR-Cas toolbox and gene editing technologies

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Gaussian accelerated molecular dynamics: Principles and applications

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Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing

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Fanzor is a eukaryotic programmable RNA-guided endonuclease

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Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing

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Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering

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Unbiased investigation of specificities of prime editing systems in human cells

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Dual modes of CRISPR-associated transposon homing

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Genome-wide specificity of prime editors in plants

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Prediction of efficiencies for diverse prime editing systems in multiple cell types

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The NIH Somatic Cell Genome Editing program

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Human genetic diversity alters off-target outcomes of therapeutic gene editing

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Design of highly functional genome editors by modelling CRISPR–Cas sequences

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Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review

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CRISPR-based therapeutics: current challenges and future applications

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Cryo-EM structure of the transposon-associated TnpB enzyme

Nakagawa, R., Hirano, H., Omura, S. N., Nety, S. P., Kannan, S., Altae-Tran, H., Xiao, Y., Sakaguchi, Y., Ohira, T., Wu, W. Y., et al. (2023) · Nature · doi:10.1038/s41586-023-05933-9 · Cited by 99

CRISPR/Cas System and Factors Affecting Its Precision and Efficiency

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Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox

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CRISPR/Cas9 Landscape: Current State and Future Perspectives

Tyumentsev, A. I., Tyumentsev, A. I., & Акимкин, В. Г. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242216077 · Cited by 98

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences

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CRISPR-Cas9 library screening approach for anti-cancer drug discovery: overview and perspectives

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Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq

Malinin, N. L., Lee, G., Lazzarotto, C. R., Li, Y., Zheng, Z., Nguyen, N. T., Liebers, M. R., Topkar, V. V., Iafrate, A. J., Le, L. P., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00626-x · Cited by 91

Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

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Beyond the promise: evaluating and mitigating off-target effects in CRISPR gene editing for safer therapeutics

Lopes, R., & Prasad, M. K. (2024) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1339189 · Cited by 82

Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints

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Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription

Wilkinson, M. E., Frangieh, C. J., Macrae, R. K., & Zhang, F. (2023) · Science · doi:10.1126/science.adg7883 · Cited by 79

Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy

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Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells

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Prediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment

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Gene editing and its applications in biomedicine

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Recent advances in CRISPR-based genome editing technology and its applications in cardiovascular research

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In-depth assessment of the PAM compatibility and editing activities of Cas9 variants

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Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2

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Recent Advances in Improving Gene-Editing Specificity through CRISPR–Cas9 Nuclease Engineering

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Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA

Wilkinson, M. E., Li, D., Gao, L., Macrae, R. K., & Zhang, F. (2024) · Science · doi:10.1126/science.adq3977 · Cited by 61

Cas9 deactivation with photocleavable guide RNAs

Zou, R. S., Liu, Y., Wu, B., & Ha, T. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.02.007 · Cited by 61

Genome-wide detection of CRISPR editing in vivo using GUIDE-tag

Liang, S.-Q., Liu, P., Smith, J. L., Mintzer, E., Maitland, S., Dong, X., Yang, Q., Lee, J., Haynes, C. M., Zhu, L. J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28135-9 · Cited by 54

Pooled genetic perturbation screens with image-based phenotypes

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Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a

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Establishing the allosteric mechanism in CRISPR‐Cas9

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Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity

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Integrating machine learning and genome editing for crop improvement

Chen, L., Liu, G., & Zhang, T. (2024) · aBIOTECH · doi:10.1007/s42994-023-00133-5 · Cited by 60

Single-Base Resolution: Increasing the Specificity of the CRISPR-Cas System in Gene Editing

Rabinowitz, R., & Offen, D. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.11.009 · Cited by 58

History of genome editing: From meganucleases to CRISPR

Tröder, S. E., & Zevnik, B. (2021) · Laboratory Animals · doi:10.1177/0023677221994613 · Cited by 55

Recent Advances in Genome-Editing Technology with CRISPR/Cas9 Variants and Stimuli-Responsive Targeting Approaches within Tumor Cells: A Future Perspective of Cancer Management

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High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9

Skeens, E., Sinha, S., Ahsan, M., D’Ordine, A. M., Jogl, G., Palermo, G., & Lisi, G. P. (2024) · Science Advances · doi:10.1126/sciadv.adl1045 · Cited by 53

Rational engineering of minimally immunogenic nucleases for gene therapy

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Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity

Huang, H., Huang, G., Tan, Z., Hu, Y., Shan, L., Zhou, J., Zhang, X., Ma, S., Lv, W., Huang, T., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01296-1 · Cited by 46

Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing

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Putting CRISPR-Cas system in action: a golden window for efficient and precise genome editing for crop improvement

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Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

Schmidt, H., Zhang, M., Chakarov, D., Bansal, V., Mourelatos, H. A., Rivera, F. J. S., Lowe, S. W., Ventura, A., Leslie, C. S., & Pritykin, Y. (2025) · Genome biology · doi:10.1186/s13059-025-03488-8 · Cited by 48

Engineering of efficiency-enhanced Cas9 and base editors with improved gene therapy efficacies

Yin, S., Zhang, M., Liu, Y., Sun, X., Guan, Y., Chen, X., Yang, L., Huo, Y., Yang, J., Zhang, X., et al. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2022.11.014 · Cited by 47

SuperFi-Cas9 exhibits remarkable fidelity but severely reduced activity yet works effectively with ABE8e

Kulcsár, P. I., Tálas, A., Ligeti, Z., Krausz, S. L., & Welker, E. (2022) · Nature Communications · doi:10.1038/s41467-022-34527-8 · Cited by 46

Powerful CRISPR-Based Biosensing Techniques and Their Integration With Microfluidic Platforms

Chen, B., Li, Y., Xu, F., & Yang, X. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.851712 · Cited by 43

CRISPR-based strategies for targeted transgene knock-in and gene correction

Lau, C., Tin, C., & Suh, Y. (2020) · Faculty Reviews · doi:10.12703/r/9-20 · Cited by 46

CRISPRoffT: comprehensive database of CRISPR/Cas off-targets

Wang, G., Liu, X., Wang, A., Wen, J., Kim, P., Song, Q., Liu, X., & Zhou, X. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1025 · Cited by 42

Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria

Collias, D., Vialetto, E., Yu, J., Co, K., Almási, É. D. H., Rüttiger, A.-S., Achmedov, T., Strowig, T., & Beisel, C. L. (2023) · Nature Communications · doi:10.1038/s41467-023-36283-9 · Cited by 37

Paving the way towards precise and safe CRISPR genome editing

Śledziński, P., Dabrowska, M., Nowaczyk, M., & Olejniczak, M. (2021) · Biotechnology Advances · doi:10.1016/j.biotechadv.2021.107737 · Cited by 43

Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods

Saha, A., Arantes, P. R., & Palermo, G. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102400 · Cited by 39

Efficient protein tagging and cis-regulatory element engineering via precise and directional oligonucleotide-based targeted insertion in plants

Kumar, J., Char, S. N., Weiss, T. J., Liu, H., Liu, B., Yang, B., & Zhang, F. (2023) · The Plant Cell · doi:10.1093/plcell/koad139 · Cited by 35

Evolution-guided protein design of IscB for persistent epigenome editing in vivo

Kannan, S., Altae-Tran, H., Zhu, S., Xu, P., Strebinger, D., Oshiro, R., Faure, G., Moeller, L., Pham, J., Mears, K. S., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02655-3 · Cited by 40

Emerging Gene Therapeutics for Epidermolysis Bullosa under Development

Bischof, J., Hierl, M., & Koller, U. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25042243 · Cited by 36

Engineering Cas9 for human genome editing

Slaymaker, I. M., & Gaudelli, N. M. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.03.004 · Cited by 34

Targeted genome editing restores auditory function in adult mice with progressive hearing loss caused by a human microRNA mutation

Zhu, W., Du, W., Rameshbabu, A. P., Armstrong, A. M., Silver, S., Kim, Y., Wei, W., Shu, Y., Liu, X., Lewis, M. A., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adn0689 · Cited by 33

Modularity and diversity of target selectors in Tn7 transposons

Faure, G., Saito, M., Benler, S., Peng, I., Wolf, Y. I., Strecker, J., Altae-Tran, H., Neumann, E. N., Li, D., Makarova, K. S., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.05.013 · Cited by 30

Linking CRISPR–Cas9 double-strand break profiles to gene editing precision with BreakTag

Longo, G. M. C., Sayols, S., Kotini, A. G., Heinen, S., Möckel, M. M., Beli, P., & Roukos, V. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02238-8 · Cited by 32

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

Kurgan, G., Turk, R., Li, H., Roberts, N., Rettig, G. R., Jacobi, A. M., Tso, L., Sturgeon, M. L., Mertens, M., Noten, R., et al. (2021) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2021.03.024 · Cited by 31

Recent advances in methods for the diagnosis of Corona Virus Disease 2019

Guo, J., Ge, J., & Guo, Y. (2021) · Journal of Clinical Laboratory Analysis · doi:10.1002/jcla.24178 · Cited by 28

Graph theory approaches for molecular dynamics simulations

Patel, A. C., Sinha, S., & Palermo, G. (2024) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583524000143 · Cited by 33

Direct repeat region 3′ end modifications regulate Cas12a activity and expand its applications

Zhang, W., Zhong, Y., Wang, J., Zou, G., Chen, Q., & Liu, C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf040 · Cited by 32

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

Huang, H., Hu, Y., Huang, G., Ma, S., Feng, J., Wang, D., Lin, Y., Zhou, J., & Rong, Z. (2021) · Communications Biology · doi:10.1038/s42003-021-02351-3 · Cited by 28

Challenges of CRISPR/Cas-Based Cell Therapy for Type 1 Diabetes: How Not to Engineer a “Trojan Horse”

Karpov, D. S., Sosnovtseva, A. O., Pylina, S. V., Bastrich, A., Petrova, D. A., Kovalev, M. A., Shuvalova, A. I., Константиновна, Е. А., & Mokrysheva, N. G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242417320 · Cited by 30

Advances of engineered microfluidic biosensors via CRISPR/Cas in bacteria and virus monitoring

Li, X., Wang, T., Liu, X., Jiang, H., & Wang, X. (2024) · Chemical Engineering Journal · doi:10.1016/j.cej.2024.152038 · Cited by 27

Editing outside the body: Ex vivo gene-modification for β-hemoglobinopathy cellular therapy

Rosanwo, T. O., & Bauer, D. E. (2021) · Molecular Therapy · doi:10.1016/j.ymthe.2021.10.002 · Cited by 30

PINK1 gene mutation by pair truncated sgRNA/Cas9-D10A in cynomolgus monkeys

Chen, Z., 650500，中国, 昆. 昆., Wang, J.-Y., Kang, Y., Yang, Q., Gu, X.-Y., Zhi, D., Li, Y., Long, C., Shen, B., et al. (2021) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2021.023 · Cited by 27

Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing

Li, J., Wu, P., Cao, Z., Huang, G., Lu, Z., Yan, J., Zhang, H., Zhou, Y., Liu, R., Chen, H., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113765 · Cited by 26

SpCas9-HF1 enhances accuracy of cell cycle-dependent genome editing by increasing HDR efficiency, and by reducing off-target effects and indel rates

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Engineering Cas9: next generation of genomic editors

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