Mapping the genomic landscape of CRISPR-Cas9 cleavage

Cited by (454)

Items 201–300 of 454

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2. Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity
   Kevin A. Peterson, Sam Khalouei, Nour Hanafi, Joshua A. Wood, Denise Grant Lanza, Lauri G. Lintott, Brandon Willis, John R. Seavitt, Robert E. Braun, Mary E. Dickinson et al. · 2023 · Communications Biology
3. From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases
   Pandey, Manish, Ojha, Divya, Bansal, Sakshi, Rode, Ambadas B., Chawla, Geetanjali · 2021 · Molecular Aspects of Medicine
4. Synthetic gRNA/Cas9 ribonucleoprotein targeting HBV DNA inhibits viral replication
   Jinyu Zhang, Yi Zhang, Sushant Khanal, Dechao Cao, Juan Zhao, Xindi Dang, Lam Ngoc Thao Nguyen, Madison Schank, Xiao Y. Wu, Yong Jiang et al. · 2023 · Journal of Medical Virology
5. Generating, modeling and evaluating a large-scale set of CRISPR/Cas9 off-target sites with bulges
   Ofir Yaish, Yaron Orenstein · 2024 · Nucleic Acids Research
6. Evaluation of off-targets predicted by sgRNA design tools
   Jaspreet Kaur Dhanjal, Samvit Dammalapati, Shreya Pal, Durai Sundar · 2020 · Genomics
7. Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On‐ and Off‐Target Damage
   Anthony Newman, Lora M. Starrs, Gaétan Burgio · 2020 · BioEssays
8. Gene therapy in cardiac and vascular diseases: a review of approaches to treat genetic and common cardiovascular diseases with novel gene-based therapeutics
   P. Musolino, Susan J. Rosser, M. Brittan, D. E. Newby, C. Berry, Paul R Riley, Mauro Giacca, R. Hajjar, A. Baker · 2025 · Cardiovascular Research
9. Next-generation T cell immunotherapies engineered with CRISPR base and prime editing: challenges and opportunities
   Karl Petri, Elvira D’Ippolito, Annette Künkele, Ulrike Koehl, Dirk Hans Busch, Hermann Einsele, Michael Hudecek · 2025 · Nature Reviews Clinical Oncology
10. An unbiased method for evaluating the genome-wide specificity of base editors in rice
    Shuai Jin, Qiang Gao, Caixia Gao · 2020 · Nature Protocols
11. Genome-wide specificity of plant genome editing by both CRISPR–Cas9 and TALEN
    Nadia Bessoltane, Florence Charlot, Anouchka Guyon‐Debast, Delphine Charif, Kostlend Mara, Cécile Collonnier, Pierre‐François Perroud, Mark Tepfer, Fabien Nogué · 2022 · Scientific Reports
12. Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs
    Özden, Furkan, Minary, Peter · 2024 · Nucleic Acids Research
13. Position of Deltaproteobacteria Cas12e nuclease cleavage sites depends on spacer length of guide RNA
    Polina Selkova, Aleksandra Vasileva, Georgii E. Pobegalov, Olga S. Musharova, Anatolii Arseniev, Maksim Kazalov, Tatyana Zyubko, Nataliia Shcheglova, Tatyana Artamonova, Mikhail A. Khodorkovskii et al. · 2020 · RNA Biology
14. Evaluation of two in vitro assays for tumorigenicity assessment of CRISPR-Cas9 genome-edited cells
    Myriam Lemmens, Benoit Fischer, Michael Zogg, Lindsey Ulkus Rodrigues, Gráinne Kerr, Alberto Del Río-Espínola, Fanny Schaeffer, Danilo Maddalo, Valérie Dubost, Alessandro Piaia et al. · 2021 · Molecular Therapy — Methods & Clinical Development
15. Prediction of CRISPR-Cas9 off-target activities with mismatches and indels based on hybrid neural network
    Yanpeng Yang, Jian Li, Quan Zou, Yaoping Ruan, Hailin Feng · 2023 · Computational and Structural Biotechnology Journal
16. CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy
    Mingming Qin, Chunhao Deng, Liewei Wen, Guoqun Luo, Ya Meng · 2024 · Journal of Translational Medicine
17. Quantifying CRISPR off-target effects
    Soragia Athina Gkazi · 2019 · Emerging Topics in Life Sciences
18. Identification of Guide-Intrinsic Determinants of Cas9 Specificity
    Nicholas C. Huston, Josh Tycko, Eric L. Tillotson, Christopher J. Wilson, Vic E. Myer, Hariharan Jayaram, Barrett E. Steinberg · 2019 · The CRISPR Journal
19. A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
    Yaish, Ofir, Asif, Maor, Orenstein, Yaron · 2022 · Briefings in Bioinformatics
20. Breaking Yield Ceiling in Wheat: Progress and Future Prospects
    Neeraj Pal, Dinesh Kumar Saini, Sundip Kumar · 2022 · IntechOpen eBooks
21. Genome editing in cancer: Challenges and potential opportunities
    Dor Breier, Dan Peer · 2022 · Bioactive Materials
22. Advances in Recombinant Adeno-Associated Virus Vectors for Neurodegenerative Diseases
    Leyao Li, Lakshmy Vasan, Bryan Kartono, Kevan P. Clifford, Ahmadreza Attarpour, Raghav Sharma, Matthew Mandrozos, Ain Kim, Wenda Zhao, Ari Belotserkovsky et al. · 2023 · Biomedicines
23. The application of CRISPR/Cas9–based genome-wide screening to disease research
    Xiuqin Chen, Min Zheng, Su Lin, Meiqing Huang, Shaoying Chen, Shilong Chen · 2024 · Molecular and Cellular Probes
24. Debugging the genetic code: Non-viral in vivo delivery of therapeutic genome editing technologies
    Alexandra S. Piotrowski-Daspit, Peter M. Glazer, W. Mark Saltzman · 2018 · Current Opinion in Biomedical Engineering
25. Genome-wide detection and analysis of CRISPR-Cas off-targets
    Tomás Rodríguez, Sina Dadafarin, Henry Pratt, Pengpeng Liu, Nadia Amrani, Lihua Julie Zhu · 2021 · Progress in molecular biology and translational science
26. Novel Strategies in Transplantation: Genetic Engineering and Vascularized Composite Allotransplantation
    Martin Kauke‐Navarro, Olivier F. Noel, Leonard Knoedler, Samuel A. Knoedler, Adriana Christine Panayi, Viola Antonia Stögner, Lioba Franziska Huelsboemer, Bohdan Pomahač · 2023 · Journal of Surgical Research
27. CRISPR to the Rescue: Advances in Gene Editing for the FMR1 Gene
    Carolyn M. Yrigollen, Beverly L. Davidson · 2019 · Brain Sciences
28. Cytosine Deaminase Base Editing to Restore COL7A1 in Dystrophic Epidermolysis Bullosa Human: Murine Skin Model
    Gaetano Naso, Soragia Athina Gkazi, Christos Georgiadis, Vignesh Jayarajan, J. Jackow, Roland A. Fleck, Leanne Allison, Olumide Kayode Ogunbiyi, John Alexander McGrath, Duško Ilić et al. · 2023 · JID Innovations
29. Homology-Directed-Repair-Based Genome Editing in HSPCs for the Treatment of Inborn Errors of Immunity and Blood Disorders
    Daniel G. Allen, Nechama Kalter, Michael Rosenberg, Ayal Hendel · 2023 · Pharmaceutics
30. 2022 White Paper on Recent Issues in Bioanalysis: Fda Draft Guidance on Immunogenicity Information in Prescription Drug Labeling, Lnp & Viral Vectors Therapeutics/Vaccines Immunogenicity, Prolongation Effect, Ada Affinity, Risk-Based Approaches, Ngs, Qpcr, Ddpcr Assays ( Part 3 – Recommendations on Gene Therapy, Cell Therapy, Vaccines Immunogenicity & Technologies; Immunogenicity & Risk Assessment of Biotherapeutics and Novel Modalities; NAb Assays Integrated Approach)
    Luying Pan, Johanna R. Mora, Karl Walravens, Leslie Wagner, Shirley Hopper, LiNa Loo, David J. Bettoun, Sarah Bond, Francis J. Dessy, Sean Downing et al. · 2023 · Bioanalysis
31. In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster
    Yuwei Zhang, Guofang Zhao, Fatma Yislam Hadi Ahmed, Tianfei Yi, Shiyun Hu, Ting Cai, Qi Liao · 2020 · Frontiers in Oncology
32. CRISPR, animals, and FDA oversight: Building a path to success
    Laura R. Epstein, Stella S. Lee, Mayumi F. Miller, Heather A. Lombardi · 2021 · Proceedings of the National Academy of Sciences
33. Perfecting Targeting in CRISPR
    Hainan Zhang, Tong Li, Yidi Sun, Hui Yang · 2021 · Annual Review of Genetics
34. Artificial intelligence and machine learning in veterinary medicine: a regulatory perspective on current initiatives and future prospects
    Hesha Jani Duggirala, Jennifer Leigh Johnson, Daniel A. Tadesse, Chih-Hao Hsu, Alexis L. Norris, Joseph Faust, Linda A Walter-Grimm, Tristan J. Colonius · 2025 · American Journal of Veterinary Research
35. Precision gene editing: The power of CRISPR-Cas in modern genetics
    Jeong H. Joo, Soogene Lee, Keun Pil Kim · 2025 · Molecular Therapy — Nucleic Acids
36. Solid-State Nanopore Real-Time Assay for Monitoring Cas9 Endonuclease Reactivity
    Chalmers Chi Cheng Chau, Nicole E. Weckman, Emma E. Thomson, Paolo Actis · 2025 · ACS Nano
37. Rheostatic Control of Cas9-Mediated DNA Double Strand Break (DSB) Generation and Genome Editing
    John C. Rose, Jason J. Stephany, Cindy T. Wei, Douglas M. Fowler, Dustin J. Maly · 2017 · ACS Chemical Biology
38. CrisPR/CRIS systems are highly effective and useful for genomic manipulation. Despite this, cardiac treatment remains difficult due to existing genome editing and delivery processes.
    Moataz Dowaidar · 2021
39. Aspects of Gene Therapy Products Using Current Genome-Editing Technology in Japan
    Teruhide Yamaguchi, Eriko Uchida, Takashi Okada, Keiya Ozawa, Masafumi Onodera, Akihiro Kume, Takashi Shimada, Satoru Takahashi, Kenzaburo Tani, Yasutomo Nasu et al. · 2020 · Human Gene Therapy
40. Therapeutic development for Canavan disease using patient iPSCs introduced with the wild-type ASPA gene
    Jianfei Chao, Lizhao Feng, Peng Ye, Xianwei Chen, Qi Cui, Guihua Sun, Tao Zhou, Erpo Tian, Wendong Li, Weidong Hu et al. · 2022 · iScience
41. Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model
    Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li, Hailin Feng · 2024 · PLoS Computational Biology
42. Exploring the SSBreakome: genome‐wide mapping of DNA single‐strand breaks by next‐generation sequencing
    Nicola Zilio, Helle D. Ulrich · 2020 · FEBS Journal
43. Emerging Technologies for Genome-Wide Profiling of DNA Breakage
    Matthew J. Rybin, Melina Ramic, Natalie R. Ricciardi, Philipp Kapranov, Claes Wahlestedt, Zane R. Zeier · 2021 · Frontiers in Genetics
44. Frequent, context-dependent effects of human genetic variation on Cas9 activity revealed by population-scale GUIDE-seq-2 and deep combinatorial CHANCE-seq profiling
    Ashley R. Flory, Cícera Regina Lazzarotto, Yichao Li, Jacqueline Chyr, Muyu Yang, Varun Katta, Elizabeth Urbina, GaHyun Lee, Rachael K. Wood, Azusa Matsubara et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. Structural basis of Cas9 DNA interrogation with a 5′ truncated sgRNA
    Kaitlyn A. Kiernan, Jieun Kwon, Bradley J. Merrill, Miljan Simonović · 2024 · Nucleic Acids Research
46. Deep Learning Based Models for CRISPR/Cas Off‐Target Prediction
    Mingming Cao, Alexander Brennan, Ciaran M. Lee, So‐Hyun Park, Gang Bao · 2025 · Small Methods
47. Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning
    Aidan R. O’Brien, Denis C. Bauer, Gaétan Burgio · 2023 · PLoS ONE
48. Non-clinical safety assessment of novel drug modalities: Genome safety perspectives on viral-, nuclease- and nucleotide-based gene therapies
    Myriam Lemmens, Lena Dorsheimer, Andreas Zeller, Yasmin Dietz · 2024 · Mutation Research/Genetic Toxicology and Environmental Mutagenesis
49. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems
    Ainsley Mike Antao, Janardhan Keshav Karapurkar, Dong Ryul Lee, Kye-Seong Kim, Suresh Ramakrishna · 2020 · Computational and Structural Biotechnology Journal
50. Technical considerations towards commercialization of porcine respiratory and reproductive syndrome (PRRS) virus resistant pigs
    A. Mark Cigan, Pieter W. Knap · 2022 · CABI Agriculture and Bioscience
51. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments
    Matthew C. Canver, Maximilian Haeussler, Daniel E. Bauer, Stuart H. Orkin, Neville E. Sanjana, Ophir Shalem, Guo‐Cheng Yuan, Feng Zhang, Jean‐Paul Concordet, Luca Pinello · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
52. Measurement and clinical interpretation of CRISPR off-targets
    Ariella Angelini Stewart, Rebecca C. Ahrens‐Nicklas, Shengdar Q. Tsai, Kiran Musunuru, Petros Giannikopoulos, Claire Dudley Clelland · 2025 · Nature Genetics
53. Monitoring biological effects of somatic cell genome editing
    Benjamin Freedman, Jeff W. M. Bulte, Bruce R. Conklin, Luke M. Judge, Melinda R. Dwinell, Aron M. Geurts, Madeleine J. Sitton, Vineet Mahajan, Samira Kiani, Charles A. Gersbach et al. · 2026 · Nature Reviews Genetics
54. CRISPR/Cas systems usher in a new era of disease treatment and diagnosis
    Ruiting Li, Qin Wang, Kaiqin She, Fang Lu, Yang Yang · 2022 · Molecular Biomedicine
55. A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets
    Péter István Kulcsár, András Tálas, Zoltán Ligeti, Eszter Tóth, Zsófia Rakvács, Zsuzsa Bartos, Sarah Laura Krausz, Ágnes Welker, Vanessza Laura Végi, Krisztina Huszár et al. · 2023 · Nature Communications
56. CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases
    Desh Deepak Singh, R. David Hawkins, Riitta Lahesmaa, Subhash Kumar Tripathi · 2019 · Seminars in Cell and Developmental Biology
57. CRISPcut: A novel tool for designing optimal sgRNAs for CRISPR/Cas9 based experiments in human cells
    Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar · 2018 · Genomics
58. VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9
    Laurence O. W. Wilson, Sara Hetzel, Christopher Pockrandt, Knut Reinert, Denis C. Bauer · 2019 · BMC Biotechnology
59. The origin of unwanted editing byproducts in gene editing
    Jianhang Yin, Jiazhi Hu · 2022 · Acta Biochimica et Biophysica Sinica
60. Synthetic gRNA/Cas9 Ribonucleoprotein Inhibits HIV Reactivation and Replication
    Sushant Khanal, Dechao Cao, Jinyu Zhang, Yi Zhang, Madison Schank, Xindi Dang, Lam Ngoc Thao Nguyen, Xiao Y. Wu, Yong Jiang, Shunbin Ning et al. · 2022 · Viruses
61. The Evolution of Nucleic Acid–Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design
    Shruti Sarika Chakraborty, Jayati Ray Dutta, Ramakrishnan Ganesan, Péter Mináry · 2024 · Methods in molecular biology
62. Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing
    Nechama Kalter, Saurabh Gulati, Michael Rosenberg, Qawer Ayaz, Joanne Nguyen, Shu Wang, Benjamin Schroeder, Chieh-Yuan Li, Ayal Hendel · 2025 · Molecular Therapy — Methods & Clinical Development
63. CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping
    Georgi K. Marinov, Samuel H. Kim, S. Tansu Bagdatli, Soon Il Higashino, Alexandro E. Trevino, Josh Tycko, Tong Wu, Lacramioara Bintu, Michael Cory Bassik, Chuan He et al. · 2023 · Genome biology
64. Systems-level interference strategies to decipher host factors involved in bacterial pathogen interaction: from RNAi to CRISPRi
    Maxime Québatte, Christoph Dehio · 2017 · Current Opinion in Microbiology
65. CRISPR/Cas-based Human T cell Engineering: Basic Research and Clinical Application
    Bettina E. Bernard, Emmanuelle Landmann, Lukas T. Jeker, Kathrin Schumann · 2022 · Immunology Letters
66. Predicting CRISPR-Cas9 off-target effects in human primary cells using bidirectional LSTM with BERT embedding
    Orhan Sari, Ziying Liu, Youlian Pan, Xiaojian Shao · 2024 · Bioinformatics Advances
67. CRISPR‐mediated mutation of cytokinin signaling genes ( SlHP2 and SlHP3 ) in tomato: Morphological, physiological, and molecular characterization
    Abdullah Aydin, Bayram Ali Yerlikaya, Seher Yerlikaya, Nisa Nur Yılmaz, Musa Kavas · 2025 · The Plant Genome
68. CRISPR-MFH: A Lightweight Hybrid Deep Learning Framework with Multi-Feature Encoding for Improved CRISPR-Cas9 Off-Target Prediction
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69. Delivery Methods, Resources and Design Tools in CRISPR/Cas
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70. Multiplexed functional genomic assays to decipher the noncoding genome
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71. CRISPR/Cas9-mediated genome editing in naïve human embryonic stem cells
    Eva Jacobs, Sharat Warrier, Pieter‐Jan Volders, Eva D’haene, Eva Van Lombergen, Lies Vantomme, Margot Van der Jeught, Björn Heindryckx, Björn Menten, Sarah Vergult · 2017 · Scientific Reports
72. NmeCas9 is an intrinsically high-fidelity genome editing platform
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73. Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0
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74. Treating genetic blood disorders in the era of CRISPR-mediated genome editing
    Alhomidi Almotiri, Ahmed Abogosh, Ali Abdelfattah, Dalya Alowaisy, Neil P. Rodrigues · 2025 · Molecular Therapy
75. TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors
    Min Duan, Pan Gao, Yi-Zhou Zhang, Yu-Long Hu, Lei Zhou, Zhong-Chen Xu, Hou-Yuan Qiu, Xiaohan Tong, Rui-Jin Ji, Xin-Lin Lei et al. · 2025 · Nature Chemical Biology
76. Methods for detecting off-target effects of CRISPR/Cas9
    Yingying Xu, Shengmei Zhou, Lu-Yan Wang, Rong Zhang, Kai Li, Zhiyuan Qian, Xiao Li · 2025 · Biotechnology Advances
77. Assessing off-target effects in CRISPR/Cas9: challenges and strategies for precision DNA editing
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78. Mechanisms of the Specificity of the CRISPR/Cas9 System in Genome Editing
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79. Tracking CRISPR’s Footprints
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80. Efficient generation of bone morphogenetic protein 15-edited Yorkshire pigs using CRISPR/Cas9†
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81. Discovering the Genome-Wide Activity of CRISPR-Cas Nucleases
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82. New Breeding Techniques: Detection and Identification of the Techniques and Derived Products
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83. Genome-wide CRISPR off-target DNA break detection by the BLISS method
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84. Regulatory Considerations for Genome-Edited T-cell Therapies
    Julie K. Jadlowsky, Ju-Fang Chang, David H. Spencer, John M. Warrington, Bruce L. Levine, Carl H. June, Joseph A. Fraietta, Nathan Singh · 2024 · Cancer Immunology Research
85. Direct delivery of Cas-embedded cytosine base editors as ribonucleoprotein complexes for efficient and accurate editing of clinically relevant targets
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86. A precision gene-engineered B cell medicine producing sustained levels of active factor IX for hemophilia B therapy
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87. ENDO-Pore: high-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing
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88. A massively parallel approach for assessing CRISPR off-targets in vitro
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89. Recent advances in genome engineering by CRISPR technology
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90. CRISPR-based genetic screens advance cancer immunology
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91. Dynamic sampling of a surveillance state enables DNA proofreading by Cas9
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92. Unlocking the potential of CRISPR-Cas9 for cystic fibrosis: A systematic literature review
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93. Chemical and Biological Approaches to Interrogate off-Target Effects of Genome Editing Tools
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94. Development of Toolboxes for Precision Genome/Epigenome Editing and Imaging of Epigenetics
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95. Analysis of CRISPR/Cas9 Guide RNA Efficiency and Specificity Against Genetically Diverse HIV-1 Isolates
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96. Genome Editing: Insights from Chemical Biology to Support Safe and Transformative Therapeutic Applications
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97. Ligand-modified rAAV6 vectors with nanoblades allow high-level gene knockin in HSPCs without compromising cell survival
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98. A long journey towards genome editing technologies in plants: a technical and critical review of genome editing technologies
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99. CRISPR technology in human diseases
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100. CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies
     Roshan Kumar Roy, Ipsita Debashree, Sonal Srivastava, Narayan Rishi, Ashish Srivastava · 2021 · Current Bioinformatics