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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

MicroRNAs: Target Recognition and Regulatory Functions

Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386

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

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116

Multiplex Genome Engineering Using CRISPR/Cas Systems

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339

WebLogo: A Sequence Logo Generator: Figure 1Preprint

Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,418

RNA-Guided Human Genome Engineering via Cas9

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210

Genome-scale CRISPR-Cas9 knockout screening in human cells

Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science · doi:10.1126/science.1247005 · Cited by 5,234

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

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016

DNA targeting specificity of RNA-guided Cas9 nucleases

Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741

Systematic in vitro specificity profiling reveals nicking defects in natural and engineered CRISPR–Cas9 variants

Murugan, K., Suresh, S. K., Seetharam, A. S., Severin, A. J., & Sashital, D. G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab163 · Cited by 25

Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity

Mak, J. K., Störtz, F., & Mináry, P. (2022) · BMC Genomics · doi:10.1186/s12864-022-09012-7 · Cited by 24

Synthetic genome readers target clustered binding sites across diverse chromatin states

Erwin, G. S., Grieshop, M. P., Bhimsaria, D., Do, T. J., Rodríguez‐Martínez, J. A., Mehta, C., Khanna, K., Swanson, S. A., Stewart, R. M., Thomson, J. A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604847113 · Cited by 24

In vivo gene therapy potentials of CRISPR-Cas9

Xue, H.-Y., Zhang, X., Wang, Y., Lu, X., Dai, W.-J., & Xu, Y. C. (2016) · Gene Therapy · doi:10.1038/gt.2016.25 · Cited by 24

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

Malik, A., Gul, A., Munir, F., Amir, R., Alipour, H., Babar, M. M., Bakhtiar, S. M., Paracha, R. Z., Khalid, Z., & Hayat, M. Q. (2021) · PeerJ · doi:10.7717/peerj.11409 · Cited by 23

Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae

Antony, J. S., Hinz, J. M., & Wyrick, J. J. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.924914 · Cited by 24

The Application of CRISPR/Cas9 for the Treatment of Retinal Diseases.

Peddle, C. F., & MacLaren, R. E. (2017) · PubMed · Cited by 23

TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome

Cenik, B. K., Aoi, Y., Iwanaszko, M., Howard, B. C., Morgan, M. A., Andersen, G. D., Bartom, E. T., & Shilatifard, A. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.007 · Cited by 22

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening

Köferle, A., Worf, K., Breunig, C., Baumann, V., Herrero, J., Wiesbeck, M. F., Hutter, L. H., Götz, M., Fuchs, C., Beck, S., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-3268-z · Cited by 20

Insights into the molecular mechanisms of CRISPR/Cas9-mediated gene targeting at multiple loci in Arabidopsis

Zhang, Z., Zeng, W., Zhang, W., Li, J., Kong, D., Zhang, L., Wang, R., Peng, F., Kong, Z., Ke, Y., et al. (2022) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiac431 · Cited by 22

Guide-specific loss of efficiency and off-target reduction with Cas9 variants

Zhang, L., He, W., Fu, R., Wang, S., Chen, Y., & Xu, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad702 · Cited by 27

Adapting CRISPR/Cas9 for Functional Genomics Screens

Malina, A., Katigbak, A., Cencic, R., Maïga, R. I., Robert, F., Miura, H., & Pelletier, J. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-801185-0.00010-6 · Cited by 22

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

Kim, J. H., Titus, K. R., Gong, W., Beagan, J. A., Cao, Z., & Phillips‐Cremins, J. E. (2018) · Methods · doi:10.1016/j.ymeth.2018.05.005 · Cited by 21

How to start your monocot CRISPR/Cas project: plasmid design, efficiency detection, and offspring analysis

Yue, J.-J., Hong, C., Wei, P., Tsai, Y., & Lin, C. (2020) · Rice · doi:10.1186/s12284-019-0354-2 · Cited by 22

Determination of Cas9/dCas9 associated toxicity in microbesPreprint

Misra, C. S., Bindal, G., Sodani, M., Wadhawan, S., Kulkarni, S., Gautam, S., Mukhopadhyaya, R., & Rath, D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/848135 · Cited by 22

Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

Schep, R., Trauernicht, M., Vergara, X., Friskes, A., Morris, B., Gregoricchio, S., Manzo, S. G., Zwart, W. T., Beijersbergen, R. L., Medema, R. H., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae570 · Cited by 21

Single-Molecule Insight Into Target Recognition by CRISPR–Cas Complexes

Rutkauskas, M., Krivoy, A., Szczelkun, M. D., Rouillon, C., & Seidel, R. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.001 · Cited by 20

Targeted genome editing in Caenorhabditis elegans using CRISPR /Cas9

Farboud, B. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.287 · Cited by 20

Mastering targeted genome engineering of GC-rich oleaginous yeast for tailored plant oil alternatives for the food and chemical sector

Shaigani, P., Fuchs, T., Graban, P., Prem, S., Haack, M., Masri, M. A., Mehlmer, N., & Brueck, T. (2023) · Microbial Cell Factories · doi:10.1186/s12934-023-02033-1 · Cited by 23

The promise and peril of CRISPR gene drives

Zentner, G. E., & Wade, M. J. (2017) · BioEssays · doi:10.1002/bies.201700109 · Cited by 21

The prospects of CRISPR-based genome engineering in the treatment of neurodegenerative disorders

Shin, J. W., & Lee, J. (2017) · Therapeutic Advances in Neurological Disorders · doi:10.1177/1756285617741837 · Cited by 21

CRISPR/Cas9 Based Knockout of miR-145 Affects Intracellular Fatty Acid Metabolism by Targeting INSIG1 in Goat Mammary Epithelial Cells

Huang, L., Tian, H., Luo, J., Song, N., & Wu, J. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c00845 · Cited by 21

CRISPR Guide RNA Design Guidelines for Efficient Genome Editing

Schindele, P., Wolter, F., & Puchta, H. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0712-1_19 · Cited by 25

Gating and ion selectivity of Channelrhodopsins are critical for photo-activated orientation of Chlamydomonas as shown by in vivo point mutation

Baidukova, O., Oppermann, J., Kelterborn, S., Lahore, R. G. F., Schumacher, D., Evers, H., Kamrani, Y. Y., & Hegemann, P. (2022) · Nature Communications · doi:10.1038/s41467-022-35018-6 · Cited by 20

Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment

Chen, Y., Luo, X. L., Kang, R., Cui, K., Ou, J., Zhang, X., & Liang, P. (2023) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2023.07.007 · Cited by 23

Polycomb Responds to Low Levels of Transcription

Berrozpe, G., Bryant, G. O., Warpinski, K., Spagna, D., Narayan, S., Shah, S., & Ptashne, M. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.076 · Cited by 20

Applications of CRISPR systems in respiratory health: Entering a new ‘red pen’ era in genome editing

Moses, C., & Kaur, P. (2019) · Respirology · doi:10.1111/resp.13527 · Cited by 22

Identification of Guide-Intrinsic Determinants of Cas9 Specificity

Huston, N. C., Tycko, J., Tillotson, E. L., Wilson, C. J., Myer, V. E., Jayaram, H., & Steinberg, B. E. (2019) · The CRISPR Journal · doi:10.1089/crispr.2019.0009 · Cited by 20

Generation of Gene-Knockout Mongolian Gerbils via CRISPR/Cas9 System

Wang, Y., Zhao, P., Song, Z., Du, X., Huo, X., Lü, J., Liu, X., Lv, J., Li, C., Guo, M., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00780 · Cited by 20

Advancements in genome editing tools for genetic studies and crop improvement

Ahmadikhah, A., Zarabizadeh, H., Nayeri, S., & Abbasi, M. S. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2024.1370675 · Cited by 21

Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression

Sapozhnikov, D. M., & Szyf, M. (2022) · Nature Protocols · doi:10.1038/s41596-022-00741-3 · Cited by 21

CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids

Yang, H., Eremeeva, E., Abramov, M., Jacquemyn, M., Groaz, E., Daelemans, D., & Herdewijn, P. A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1147 · Cited by 19

Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research

Raper, A. T., Stephenson, A. A., & Suo, Z. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b05469 · Cited by 19

HLA DR Genome Editing with TALENs in Human iPSCs Produced Immune-Tolerant Dendritic Cells

Kwon, Y., Ahn, H.-S., Lee, J. W., Yang, H., Cho, H., Kim, S. J., Lee, S.-H., Yang, H.-M., Jang, H.-D., Kim, S. J., et al. (2021) · Stem Cells International · doi:10.1155/2021/8873383 · Cited by 19

CRISPR-Cas9 Genome Engineering: Trends in Medicine and Health

Zaib, S., Khan, I. A., & Saleem, M. A. (2021) · Mini-Reviews in Medicinal Chemistry · doi:10.2174/1389557521666210913112030 · Cited by 20

Genome engineering of isogenic human ES cells to model autism disorders

Martinez, R. A., Stein, J. L., Krostag, A.-R., Nelson, A. M., Marken, J., Menon, V., May, R., Yao, Z., Kaykas, A., Geschwind, D. H., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv164 · Cited by 20

Genome Editing Fidelity in the Context of DNA Sequence and Chromatin Structure

Chechik, L. L., Martin, O. A., & Soutoglou, E. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00319 · Cited by 16

A Scaled Framework for CRISPR Editing of Human Pluripotent Stem Cells to Study Psychiatric Disease

Hazelbaker, D. Z., Beccard, A., Bara, A. M., Dabkowski, N., Messana, A., Mazzucato, P., Lam, D., Manning, D. K., Eggan, K. C., & Barrett, L. E. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.09.006 · Cited by 19

Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm

Zhou, H., Zhou, M., Li, D., Manthey, J., Lioutikova, E., Wang, H., & Zeng, X. (2017) · BMC Genomics · doi:10.1186/s12864-017-4225-1 · Cited by 18

CRISPR/Cas: An intriguing genomic editing tool with prospects in treating neurodegenerative diseases

Rahman, S., Datta, M., Kim, J., & Jan, A. T. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.05.014 · Cited by 19

Gene Editing and Gene-Based Therapeutics for Cardiomyopathies

Ohiri, J. C., & McNally, E. M. (2018) · Heart Failure Clinics · doi:10.1016/j.hfc.2017.12.006 · Cited by 17

A Novel Cre/lox-Based Genetic Tool for Repeated, Targeted and Markerless Gene Integration in Yarrowia lipolytica

Zhou, Q., Jiao, L., Li, W., Hu, Z., Li, Y., Zhang, H., Yang, M., Xu, L., & Yan, Y. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910739 · Cited by 17

Epigenetics in the Diagnosis and Therapy of Malignant Melanoma

Santourlidis, S., Schulz, W. A., Araúzo-Bravo, M. J., Daniela Gerovska, D., Ott, P., Bendhack, M. L., Hassan, M., & Erichsen, L. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031531 · Cited by 20

BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models

Zarate, O. A., Yang, Y., Wang, X., & Wang, J.-P. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04998-z · Cited by 17

The impact of nucleosome structure on CRISPR/Cas9 fidelity

Handelmann, C. R., Tsompana, M., Samudrala, R., & Buck, M. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad021 · Cited by 17

Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds

Bush, K. B., Corsi, G. I., Yan, A. C., Haynes, K., Layzer, J. M., Zhou, J. H., Llanga, T., Gorodkin, J., & Sullenger, B. A. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.06.007 · Cited by 18

Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies

Cottingham, H., Judd, L. M., Wisniewski, J. A., Wick, R. R., Stanton, T. D., Vezina, B., Maćešić, N., Peleg, A. Y., Okeke, I. N., Holt, K. E., et al. (2025) · mSystems · doi:10.1128/msystems.01413-24 · Cited by 17

To Crispr And Beyond: The Evolution Of Genome Editing In Stem Cells

Chen, K.-Y. M., & Knoepfler, P. S. (2016) · Regenerative Medicine · doi:10.2217/rme-2016-0107 · Cited by 18

Precise editing of plant genomes – Prospects and challenges

Satheesh, V., Zhang, H., Wang, X., & Lei, M. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.04.010 · Cited by 17

Genetically Engineering the Nervous System with CRISPR-Cas

Sandoval, A., Elahi, H., & Ploski, J. E. (2020) · eNeuro · doi:10.1523/eneuro.0419-19.2020 · Cited by 18

Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits

Yu, L., & Marchisio, M. A. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.575393 · Cited by 18

Perfecting Targeting in CRISPR

Zhang, H., Li, T., Sun, Y., & Yang, H. (2021) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-030438 · Cited by 18

Modularization of genetic elements promotes synthetic metabolic engineering

Qi, H., Li, B., Zhang, W., Liu, D., & Yuan, Y. (2015) · Biotechnology Advances · doi:10.1016/j.biotechadv.2015.04.002 · Cited by 18

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

Zhang, X., Bhattacharya, A., Pu, C., Dai, Y., Liu, J., Rao, L., & Tian, C. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.05.010 · Cited by 16

Improving the on-target activity of high-fidelity Cas9 editors by combining rational design and random mutagenesis

Spasskaya, D. S., Davletshin, A. I., Bachurin, S. S., Tutyaeva, V. V., Garbuz, D. G., & Karpov, D. S. (2023) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-023-12469-5 · Cited by 16

Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes

Liu, Z., Liu, J., Yang, Z., Zhū, L., Zhu, Z., Huang, H., & Jiang, L. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108241 · Cited by 16

Seed sequences mediate off-target activity in the CRISPR-interference system

Rohatgi, N., Fortin, J., Lau, T., Ying, Y., Zhang, Y., Lee, B. L., Costa, M. R., & Reja, R. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100693 · Cited by 19

CRISPR/Cas9 in the Chicken Embryo

Morin, V., Véron, N., & Marcelle, C. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7216-6_7 · Cited by 16

DMSO increases efficiency of genome editing at two non-coding loci

Stratigopoulos, G., Rosa, M. C. D., LeDuc, C. A., Leibel, R. L., & Doege, C. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198637 · Cited by 15

CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity

Jiang, W., Singh, J. K., Allen, A., Li, Y., Kathiresan, V., Qureshi, O. A., Tangprasertchai, N. S., Zhang, X., Parameshwaran, H. P., Rajan, R., et al. (2019) · ACS Omega · doi:10.1021/acsomega.9b01469 · Cited by 16

CRISPR/Cas9 Guide RNA Design Rules for Predicting Activity

Hiranniramol, K., Chen, Y., & Wang, X. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0290-4_19 · Cited by 16

Valproic Acid Significantly Improves CRISPR/Cas9-Mediated Gene Editing

Park, H., Shin, J., Choi, H. G., Cho, B., & Kim, J. (2020) · Cells · doi:10.3390/cells9061447 · Cited by 16

CRISPR GENOME SURGERY IN THE RETINA IN LIGHT OF OFF-TARGETING

Cho, G. Y., Schaefer, K. A., Bassuk, A. G., Tsang, S. H., & Mahajan, V. B. (2018) · Retina · doi:10.1097/iae.0000000000002197 · Cited by 15

Overcoming the Limitations of CRISPR-Cas9 Systems in Saccharomyces cerevisiae: Off-Target Effects, Epigenome, and Mitochondrial Editing

Sato, G. E., & Kuroda, K. (2023) · Microorganisms · doi:10.3390/microorganisms11041040 · Cited by 16

CRISPR-Cas9 Based Genome Engineering: Opportunities in Agri-Food-Nutrition and Healthcare

Rajendran, S. R. C. K., Yau, Y., Pandey, D., & Kumar, A., V (2015) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2015.0023 · Cited by 17

RNA‐Generated and Gene‐Edited Induced Pluripotent Stem Cells for Disease Modeling and Therapy

Kehler, J., Greco, M., Martino, V., Manickam, P., Yokoe, H., Chen, A. P., Yang, M., Auerbach, J., Jessee, J. A., Götte, M., et al. (2016) · Journal of Cellular Physiology · doi:10.1002/jcp.25597 · Cited by 15

Defective heart chamber growth and myofibrillogenesis after knockout of adprhl1 gene function by targeted disruption of the ancestral catalytic active site

Smith, S. J., Towers, N., Demetriou, K., & Mohun, T. J. (2020) · PLoS ONE · doi:10.1371/journal.pone.0235433 · Cited by 16

Designing Safer CRISPR/Cas9 Therapeutics for HIV: Defining Factors That Regulate and Technologies Used to Detect Off-Target Editing

Sullivan, N. T., Allen, A. G., Atkins, A., Chung, C.-H., Dampier, W., Nonnemacher, M. R., & Wigdahl, B. L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01872 · Cited by 16

Toxic metal pollution and ecological risk assessment in superficial soils of “rural-agricultural and coastal-urban” of Monastir region, Eastern Tunisia

Chabbi, I., Baati, H., Dammak, R., Bahloul, M. M., & Azri, C. (2020) · Human and Ecological Risk Assessment An International Journal · doi:10.1080/10807039.2020.1732189 · Cited by 15

Characterization of Cas9–Guide RNA OrthologsPreprint

Braff, J. L., Yaung, S. J., Esvelt, K. M., & Church, G. M. (2016) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top086793 · Cited by 15

Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9

Okada, K., Aoki, K., Tabei, T., Sugio, K., Imai, K., Bonkohara, Y., & Kamachi, Y. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac100 · Cited by 14

Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches

Singh, D., & Ha, T. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00905 · Cited by 14

Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line

Fujita, T., Kitaura, F., Yuno, M., Suzuki, Y., Sugano, S., & Fujii, H. (2017) · DNA Research · doi:10.1093/dnares/dsx023 · Cited by 14

Restoration of dystrophin expression and correction of Duchenne muscular dystrophy by genome editing

Aslesh, T., Erkut, E. J. N., & Yokota, T. (2021) · Expert Opinion on Biological Therapy · doi:10.1080/14712598.2021.1872539 · Cited by 15

An FYVE-Domain-Containing Protein, PsFP1, Is Involved in Vegetative Growth, Oxidative Stress Response and Virulence of Phytophthora sojae

Zhang, J., Du, X., Zhou, X., Jin, D., Miao, J., & Liu, X. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22126601 · Cited by 14

Pioneer Factor Improves CRISPR‐Based C‐To‐G and C‐To‐T Base Editing

Yang, C., Dong, X., Ma, Z., Li, B., Bi, C., & Zhang, X. (2022) · Advanced Science · doi:10.1002/advs.202202957 · Cited by 15

CRISPR mediated transactivation in the human disease vector Aedes aegypti

Bui, M., Benetta, E. D., Dong, Y., Zhao, Y., Yang, T., Li, M., Antoshechkin, I. A., Buchman, A. B., Bottino-Rojas, V., James, A. A., et al. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1010842 · Cited by 14

CRISPR-engineered genome editing for the next generation neurological disease modeling

Feng, W., Liu, H., & Kawauchi, D. (2017) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2017.05.019 · Cited by 15

The epigenome editors: How tools such as CRISPR offer new details about epigenetics

Willyard, C. (2017) · Nature Medicine · doi:10.1038/nm0817-900 · Cited by 13

Eukaryotic-driven directed evolution of Cas9 nucleases

(2024) · doi:10.1186/s13059-024-03215-9 · Cited by 15

An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools

Yuan, H., Song, C., Xu, H., Sun, Y., Anthon, C., Bolund, L., Lin, L., Benabdellah, K., Lee, C. M., Hou, Y., et al. (2025) · The CRISPR Journal · doi:10.1089/crispr.2024.0058 · Cited by 13

Site‐Specific m6A Erasing via Conditionally Stabilized CRISPR‐Cas13b Editor

Xu, Y., Wang, Y., & Liang, F. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202309291 · Cited by 13

Genetic therapies and potential therapeutic applications of CRISPR activators in the eye

Ng, B., Kaukonen, M. K., McClements, M. E., Shamsnajafabadi, H., MacLaren, R. E., & Cehajic‐Kapetanovic, J. (2024) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2024.101289 · Cited by 13

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

Soczek, K. M., Cofsky, J. C., Tuck, O. T., Shi, H., & Doudna, J. A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1192 · Cited by 13

Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides

Xu, H., Shi, L., Boob, A. G., Park, W., Tan, S., Tran, V. G., Schultz, J. C., & Zhao, H. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.02.004 · Cited by 13

Modeling cancer processes with CRISPR-Cas9

Lu, X., Qi, X., Zheng, D., & Ji, L.-J. (2015) · Trends in biotechnology · doi:10.1016/j.tibtech.2015.03.007 · Cited by 13

Gene editing in the context of an increasingly complex genome

Blighe, K., DeDionisio, L., Christie, K. A., Chawes, B., Shareef, S., Kakouli‐Duarte, T., Chao-Shern, C., Harding, V., Kelly, R. S., Castellano, L., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4963-8 · Cited by 13

Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems

Antao, A. M., Karapurkar, J. K., Lee, D. R., Kim, K.-S., & Ramakrishna, S. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.026 · Cited by 14

T cell-specific inactivation of mouse CD2 by CRISPR/Cas9

Beil-Wagner, J., Dössinger, G., Schober, K., Berg, J. V., Tresch, A., Grandl, M., Palle, P., Mair, F., Gerhard, M., Becher, B., et al. (2016) · Scientific Reports · doi:10.1038/srep21377 · Cited by 13

Off-target effects of CRISPRa on interleukin-6 expression

Soubeyrand, S., Lau, P., Peters, V., & McPherson, R. (2019) · PLoS ONE · doi:10.1371/journal.pone.0224113 · Cited by 13

Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering

Lamothe, R. C., Storlie, M. D., Espinosa, D. A., Rudlaff, R. M., Browne, P. J., Liu, J., Rivas, A., Devoto, A. E., Oki, J., Khoubyari, A., et al. (2023) · The CRISPR Journal · doi:10.1089/crispr.2022.0089 · Cited by 12

Non-replicative phage particles delivering CRISPR-Cas9 to target major blaCTX-M variants

Nittayasut, N., Yata, T., Chirakul, S., Techakriengkrai, N., & Chanchaithong, P. (2024) · PLoS ONE · doi:10.1371/journal.pone.0303555 · Cited by 15

OliTag-seq enhances in cellulo detection of CRISPR-Cas9 off-targets

Yang, Z.-X., Deng, D.-H., Gao, Z.-Y., Zhang, Z.-K., Fu, Y.-W., Wen, W., Zhang, F., Li, X., Li, H., Zhang, J., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06360-w · Cited by 17

Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms

Ohtani, H., Liu, M., Liang, G., Jang, H. J., & Jones, P. A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae498 · Cited by 13

Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies

Fujita, T., & Fujii, H. (2016) · Gene Regulation and Systems Biology · doi:10.4137/grsb.s32520 · Cited by 12

Epigenetic Editing in Prostate Cancer: Challenges and Opportunities

Pacheco, M. B., Camilo, V., Henrique, R., & Jerónimo, C. (2021) · Epigenetics · doi:10.1080/15592294.2021.1939477 · Cited by 12

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping

Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02930-z · Cited by 12

DNA-binding of the Tet-transactivator curtails antigen-induced lymphocyte activation in mice

Ottina, E., Peperzak, V., Schoeler, K., Carrington, E. M., Sgonc, R., Pellegrini, M., Preston, S., Herold, M. J., Strasser, A., & Villunger, A. (2017) · Nature Communications · doi:10.1038/s41467-017-01022-4 · Cited by 12

Convolution neural network model for predicting single guide RNA efficiency in CRISPR/Cas9 system

Shrawgi, H., & Sisodia, D. S. (2019) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2019.04.008 · Cited by 12

Comprehensive Analysis of CRISPR/Cas9-Mediated Mutagenesis in Arabidopsis thaliana by Genome-Wide Sequencing

Xu, W., Fu, W., Zhu, P., Li, Z., Wang, C., Wang, C., Zhang, Y., & Zhu, S. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20174125 · Cited by 13

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

Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777

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

Cencic, R., Miura, H., Malina, A., Robert, F., Ethier, S., Schmeing, T. M., Dostie, J., & Pelletier, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109213 · Cited by 117

Mechanistic studies of CRISPR proteins in living cells

Knight, S. C. (2017) · eScholarship (California Digital Library)

Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)Preprint

Marinov, G. K., Kim, S. H., Bagdatli, S. T., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., Kundaje, A. B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.16.440202 · Cited by 3

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping

Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02930-z · Cited by 12