Mapping the genomic landscape of CRISPR-Cas9 cleavage

Cameron, Peter, Fuller, Chris K, Donohoue, Paul D, Jones, Brittnee N, Thompson, Matthew S, Carter, Matthew M, Gradia, Scott, Vidal, Bastien +13 more·2017·Nature Methods

Cited by (454)

Items 401–454 of 454

  1. Lessons From Using Genome Editing to Create a Faithful Model of a Novel Congenital Anemia
    Xiaoli Mi · 2018 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
  2. Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1
    Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Šalovská, Yansheng Liu · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Target DNA mutagenesis-based fluorescence assessment of off-target activity of the CRISPR-Cas9 system
    Dan Wang, Cuili Niu, Jingxin Han, Dejun Ma, Zhen Xi · 2019 · RSC Advances
  4. Towards best-practice approaches for CRISPR/Cas9 gene engineering
    Claude Van Campenhout, Pauline Cabochette, Anne-Clémence Veillard, Miklós Laczik, Agnieszka Zelisko-Schmidt, Céline Sabatel, Maxime Dhainaut, Benoît Vanhollebeke, Cyril Gueydan, Véronique Kruys · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Integrative Modeling and Novel Technologies in Human Genomics
    Paulina Carmona-Mora, Juan I. Young · 2019 · Elsevier eBooks
  6. Current Capabilities, Precision, and Risks of Genome Editing Techniques in Agricultural Systems
    Morgan Carter · 2020 · Preprints.org
  7. Bioanalytical Challenges and Strategies of Crispr Genome Editors
    Mikko Hölttä, Roberto Nitsch, Neil Henderson · 2021 · Bioanalysis
  8. Ultra-deep sequencing reveals no evidence of oncogenic mutations or enrichment by ex vivo CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells
    M. Kyle Cromer, Valentin V. Barsan, Erich B. Jaeger, Mengchi Wang, Jessica P. Hampton, Feng Chen, Drew Kennedy, Irina Khrebtukova, Ana Granat, Tiffany Truong et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Crispr-Embedding: CRISPR/Cas9 Off-Target Activity Prediction Using DNA k-Mer Embedding
    Swakkhar Shatabda, Anika Tahsin, Zarin Tasnim, Muneera Chowdhury, Kangkhita Hassin, Galib Hossain Meraz, Kazi Farzana Aziz · 2022 · SSRN Electronic Journal
  10. Molecular Mechanisms of Type II CRISPR ‐ Cas Systems
    Tautvydas Karvelis, Virginijus Šikšnys · 2022 · Wiley eBooks
  11. Plant Genome Editing
    Naoki Wada, Yuriko Osakabe, Keishi Osakabe · 2022 · CABI eBooks
  12. Gene Therapy and Gene Editing
    Basel T. Assaf, Claudia G. Harper, Jonathan A. Phillips · 2023 · Elsevier eBooks
  13. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products
    H. Becker, Satoshi Yamazaki · 2023 · Experimental Hematology
  14. Precise Mapping of Physiological DSBs Using In-Suspension Break Labeling In Situ and Sequencing (sBLISS)
    Osama Hidmi, Sara K. Oster, Diala Shatleh, Jonathan Monin, Rami I. Aqeilan · 2025 · Methods in molecular biology
  15. Protocol for optimizing culture conditions for ex vivo activation during CRISPR-Cas9 gene editing in human hematopoietic stem and progenitor cells
    Lucrezia della Volpe, Roberta Vacca, Raffaella Di Micco · 2025 · STAR Protocols
  16. SANTON: Sequencing Analysis Toolkits for Off-target Nomination
    Huan Qiu, Ruijia Wang, Shu Wang, Aymen Maqsood Mulbagal, Eric Anderson, Huanying Gary Ge · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Development of new increased fidelity SpCas9 variants
    Péter István Kulcsár · 2019
  18. Off-target sequence variations driven by the intrinsic properties of the Cas–sgRNA–DNA complex in genome editing
    Celine Kurniawan, Takeshi Itoh · 2025 · PLoS ONE
  19. 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
    Jacob Stewart-Ornstein, Matthew J. Irby, Marina Korinne Lilieholm, Dylan Laprise, Maria Donaldson Collier, Thomas R. Aunins, Dewi Harjanto, Aaron N. Chang, Deepak Reyon, Jeremy S. Duffield · 2025 · Genome Research
  20. Weighted Off-target and Efficiency Scoring Reveal Genome Composition-Dependent Optimal CRISPR/Cas9 Guide Design
    Y K Yathu Krishna · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  21. RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistance
    Dreyton Amador, James M. Powers, Ashley G. Njiru, Zahra Ansari, Yvon Woappi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells
    Tong Wang, Selin Jessa, Georgi K. Marinov, Sandy L. Klemm, Anshul Bharat Kundaje, William James Greenleaf · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  23. Genome Editing as Genetic Engineering Tool: Potential Applications in Production of Microbial Foods for Food Security
    Oluwafemi S. Obayori, Oluwaseun Oyetunji Olasunkanmi · 2025 · Springer eBooks
  24. CRISPR System and AI Applications
    Muhammad Nabeel Asim, Sheraz Ahmed, Andreas Dengel · 2025 · Springer eBooks
  25. Multilevel characterization of genome editor nuclease activity with BreakTag
    Gabriel M. C. Longo, Sergi Sayols, Vassilis Roukos · 2025 · Nature Protocols
  26. Additional file 4 of Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches
    Jeonghun Kwon, Kim, Minyoung, Hwang, Woochang, Anna Jo, Hwang, Gue-Ho, Jung, Minhee, Kim, Un Gi, Gang Cui, Heon Seok Kim, Eom, Joon-Ho et al. · 2023 · Figshare
  27. Additional file 2 of ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing
    Camilo Ayala Breton, Peter Clark, Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
  28. Additional file 1 of ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing
    Camilo Ayala Breton, Clark, Peter M., Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
  29. Additional file 3 of ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing
    Camilo Ayala Breton, Peter Clark, Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
  30. Additional file 2 of 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 · Figshare
  31. Additional file 1 of 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 · Figshare
  32. Additional file 1 of CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice
    Tanaka, Masayuki, Yokoyama, Keiko, Hayashi, Hideki, Sanae Isaki, Kanae Kitatani, Wang, Ting, Hisako Kawata, Hideyuki Matsuzawa, Gurumurthy, Channabasavaiah B., Hiromi Miura et al. · 2022 · Figshare
  33. Additional file 1 of Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches
    Jeonghun Kwon, Kim, Minyoung, Hwang, Woochang, Anna Jo, Hwang, Gue-Ho, Jung, Minhee, Kim, Un Gi, Gang Cui, Heon Seok Kim, Eom, Joon-Ho et al. · 2023 · Figshare
  34. Additional file 1 of Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
    Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chin, Chen-Shan, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Bondeson, Marie-Louise et al. · 2020 · Figshare
  35. Additional file 2 of CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice
    Tanaka, Masayuki, Yokoyama, Keiko, Hayashi, Hideki, Sanae Isaki, Kanae Kitatani, Wang, Ting, Hisako Kawata, Hideyuki Matsuzawa, Gurumurthy, Channabasavaiah B., Hiromi Miura et al. · 2022 · Figshare
  36. Additional file 6 of Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches
    Jeonghun Kwon, Kim, Minyoung, Hwang, Woochang, Anna Jo, Hwang, Gue-Ho, Jung, Minhee, Kim, Un Gi, Gang Cui, Heon Seok Kim, Eom, Joon-Ho et al. · 2023 · Figshare
  37. Additional file 3 of Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches
    Jeonghun Kwon, Kim, Minyoung, Woo Chang Hwang, Anna Jo, Hwang, Gue-Ho, Jung, Minhee, Kim, Un Gi, Gang Cui, Heon Seok Kim, Eom, Joon-Ho et al. · 2023 · Figshare
  38. Additional file 13 of Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
    Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chin, Chen-Shan, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Bondeson, Marie-Louise et al. · 2020 · Figshare
  39. Tracking-seq: a universal off-target detection approach for CRISPR–Cas genome editing
    Runda Xu, Tingting Cong, Junsong Yuan, Xuancheng Chen, Yinqing Li, Xun Lan, Ming Zhu · 2026 · Nature Protocols
  40. Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays
    Jingzhi Luo, Fanyu Zhao, Shuyan Lin, Yang Liu · 2026 · Medical Review
  41. A Potent CRISPR-Cas12l Double-Strand Break Gene Editor
    Tomas Urbaitis, Laima Trinkuniene, Ieva Lenkaite, Monika Petrauskytė, Renatas Krasauskas, Migle Stitilyte, Modestas Sabaliauskas, Giedrius Sasnauskas, Giedrė Tamulaitienė, Joshua K. Young et al. · 2026 · The CRISPR Journal
  42. CRISPR-MBTF: a multi-branch transformer fusion framework for CRISPR-Cas9 off-target prediction
    Ali Jahangiri-Sisakht, Leila Safari, Roghayyeh Alipanahi · 2026 · Briefings in Bioinformatics
  43. CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screens
    Samuel Coleman, Jacob Tye, Daxton Furniss, Robert Sainsbury, Abhay Rastogi, Xincen Xi, Balázs Murnyák, Jason Bell, Joseph G. Skeate, Minjing Wang et al. · 2026 · BMC Bioinformatics
  44. EHNN: enhanced hybrid neural network for CRISPR-Cas9 gRNA off-target prediction
    Akhtar Sayed, Kifayat Ullah, Muzammil Khan, Rayed A. Alakhtar, Huda Alsobhi · 2026 · PeerJ Computer Science
  45. abCRISPR: deep learning-based design of abasic gRNA sequences for specific CRISPR-Cas9 genome editing
    Geun-Woo D. Kim, Dowoon Gu, Mingyo Park, Sung Wook Chi · 2026 · Bioinformatics
  46. Genomic repeats for single-cell molecular recording
    Rachel K. Dveirin, Jessica D. Lin, Preeti Vyas, Jiaxi Lu, Yuqing Yan, Jennifer J. Lee, Xinzhong Dong, Sujatha Kannan, Ben Langmead, Sashank Reddy et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  47. Future landscape of CRISPR and AI in plant gene editing
    Oseias Rodrigues Feitosa-Junior · 2026 · Elsevier eBooks
  48. Navigating off-target effects in CRISPR-based genome editing for safer gene therapies
    Anuradha Bhardwaj · 2026 · Discover Genetics and Evolution
  49. Beyond Precision: A Multidimensional Framework for Selecting Genetic Medicine Platforms
    Jared Wieland, Peyton Jackson, William Penrod, Spencer Nadauld, Jared James Barrott · 2026 · Cells
  50. CRISPR-Based Genome Editing and Delivery Systems: Advances, Challenges and Future Directions
    Anroop Kaur, Ritika Chanan, Mehga Sharma, Shailja Sharma, Devender Sharma · 2026 · IntechOpen eBooks
  51. Analysis of Sp Cas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis
    Johannes Stuttmann, Jens Keilwagen, Philippe Ortet, Fang Shiang Lim, Thomas Schmutzer, Christel Llauro, Assane Mbodj, Marie Mirouze, Frank Hartung, Ralf Wilhelm · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Evolution of Gene Therapy in Hematology
    Robyn H. Loves, Donald B. Kohn · 2026 · Seminars in Hematology
  53. Nonclinical Evaluation of Gene-Editing Products
    2026 · Elsevier eBooks
  54. Integration Site Analysis and Off-target Analysis of Cellular and Gene Therapy Products
    2026 · Elsevier eBooks