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
- Lessons From Using Genome Editing to Create a Faithful Model of a Novel Congenital AnemiaXiaoli Mi · 2018 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
- Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Šalovská, Yansheng Liu · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Target DNA mutagenesis-based fluorescence assessment of off-target activity of the CRISPR-Cas9 systemDan Wang, Cuili Niu, Jingxin Han, Dejun Ma, Zhen Xi · 2019 · RSC Advances
- Towards best-practice approaches for CRISPR/Cas9 gene engineeringClaude 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)
- Integrative Modeling and Novel Technologies in Human GenomicsPaulina Carmona-Mora, Juan I. Young · 2019 · Elsevier eBooks
- Current Capabilities, Precision, and Risks of Genome Editing Techniques in Agricultural SystemsMorgan Carter · 2020 · Preprints.org
- Bioanalytical Challenges and Strategies of Crispr Genome EditorsMikko Hölttä, Roberto Nitsch, Neil Henderson · 2021 · Bioanalysis
- Ultra-deep sequencing reveals no evidence of oncogenic mutations or enrichment by ex vivo CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cellsM. 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)
- Crispr-Embedding: CRISPR/Cas9 Off-Target Activity Prediction Using DNA k-Mer EmbeddingSwakkhar Shatabda, Anika Tahsin, Zarin Tasnim, Muneera Chowdhury, Kangkhita Hassin, Galib Hossain Meraz, Kazi Farzana Aziz · 2022 · SSRN Electronic Journal
- Molecular Mechanisms of Type II CRISPR ‐ Cas SystemsTautvydas Karvelis, Virginijus Šikšnys · 2022 · Wiley eBooks
- Plant Genome EditingNaoki Wada, Yuriko Osakabe, Keishi Osakabe · 2022 · CABI eBooks
- Gene Therapy and Gene EditingBasel T. Assaf, Claudia G. Harper, Jonathan A. Phillips · 2023 · Elsevier eBooks
- Understanding genetic heterogeneity in gene-edited hematopoietic stem cell productsH. Becker, Satoshi Yamazaki · 2023 · Experimental Hematology
- 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
- Protocol for optimizing culture conditions for ex vivo activation during CRISPR-Cas9 gene editing in human hematopoietic stem and progenitor cellsLucrezia della Volpe, Roberta Vacca, Raffaella Di Micco · 2025 · STAR Protocols
- SANTON: Sequencing Analysis Toolkits for Off-target NominationHuan Qiu, Ruijia Wang, Shu Wang, Aymen Maqsood Mulbagal, Eric Anderson, Huanying Gary Ge · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Development of new increased fidelity SpCas9 variantsPéter István Kulcsár · 2019
- Off-target sequence variations driven by the intrinsic properties of the Cas–sgRNA–DNA complex in genome editingCeline Kurniawan, Takeshi Itoh · 2025 · PLoS ONE
- 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editorsJacob 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
- Weighted Off-target and Efficiency Scoring Reveal Genome Composition-Dependent Optimal CRISPR/Cas9 Guide DesignY K Yathu Krishna · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistanceDreyton Amador, James M. Powers, Ashley G. Njiru, Zahra Ansari, Yvon Woappi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cellsTong Wang, Selin Jessa, Georgi K. Marinov, Sandy L. Klemm, Anshul Bharat Kundaje, William James Greenleaf · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome Editing as Genetic Engineering Tool: Potential Applications in Production of Microbial Foods for Food SecurityOluwafemi S. Obayori, Oluwaseun Oyetunji Olasunkanmi · 2025 · Springer eBooks
- CRISPR System and AI ApplicationsMuhammad Nabeel Asim, Sheraz Ahmed, Andreas Dengel · 2025 · Springer eBooks
- Multilevel characterization of genome editor nuclease activity with BreakTagGabriel M. C. Longo, Sergi Sayols, Vassilis Roukos · 2025 · Nature Protocols
- 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 approachesJeonghun 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
- 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 editingCamilo Ayala Breton, Peter Clark, Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
- 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 editingCamilo Ayala Breton, Clark, Peter M., Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
- 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 editingCamilo Ayala Breton, Peter Clark, Wang, Lili, Jenny A. Greig, James M. Wilson · 2020 · Figshare
- Additional file 2 of CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mappingGeorgi 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
- Additional file 1 of CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mappingGeorgi 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
- Additional file 1 of CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in miceTanaka, Masayuki, Yokoyama, Keiko, Hayashi, Hideki, Sanae Isaki, Kanae Kitatani, Wang, Ting, Hisako Kawata, Hideyuki Matsuzawa, Gurumurthy, Channabasavaiah B., Hiromi Miura et al. · 2022 · Figshare
- 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 approachesJeonghun 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
- Additional file 1 of Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activityIda 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
- Additional file 2 of CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in miceTanaka, Masayuki, Yokoyama, Keiko, Hayashi, Hideki, Sanae Isaki, Kanae Kitatani, Wang, Ting, Hisako Kawata, Hideyuki Matsuzawa, Gurumurthy, Channabasavaiah B., Hiromi Miura et al. · 2022 · Figshare
- 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 approachesJeonghun 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
- 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 approachesJeonghun 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
- Additional file 13 of Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activityIda 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
- Tracking-seq: a universal off-target detection approach for CRISPR–Cas genome editingRunda Xu, Tingting Cong, Junsong Yuan, Xuancheng Chen, Yinqing Li, Xun Lan, Ming Zhu · 2026 · Nature Protocols
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assaysJingzhi Luo, Fanyu Zhao, Shuyan Lin, Yang Liu · 2026 · Medical Review
- A Potent CRISPR-Cas12l Double-Strand Break Gene EditorTomas 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
- CRISPR-MBTF: a multi-branch transformer fusion framework for CRISPR-Cas9 off-target predictionAli Jahangiri-Sisakht, Leila Safari, Roghayyeh Alipanahi · 2026 · Briefings in Bioinformatics
- CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screensSamuel 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
- EHNN: enhanced hybrid neural network for CRISPR-Cas9 gRNA off-target predictionAkhtar Sayed, Kifayat Ullah, Muzammil Khan, Rayed A. Alakhtar, Huda Alsobhi · 2026 · PeerJ Computer Science
- abCRISPR: deep learning-based design of abasic gRNA sequences for specific CRISPR-Cas9 genome editingGeun-Woo D. Kim, Dowoon Gu, Mingyo Park, Sung Wook Chi · 2026 · Bioinformatics
- Genomic repeats for single-cell molecular recordingRachel 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)
- Future landscape of CRISPR and AI in plant gene editingOseias Rodrigues Feitosa-Junior · 2026 · Elsevier eBooks
- Navigating off-target effects in CRISPR-based genome editing for safer gene therapiesAnuradha Bhardwaj · 2026 · Discover Genetics and Evolution
- Beyond Precision: A Multidimensional Framework for Selecting Genetic Medicine PlatformsJared Wieland, Peyton Jackson, William Penrod, Spencer Nadauld, Jared James Barrott · 2026 · Cells
- CRISPR-Based Genome Editing and Delivery Systems: Advances, Challenges and Future DirectionsAnroop Kaur, Ritika Chanan, Mehga Sharma, Shailja Sharma, Devender Sharma · 2026 · IntechOpen eBooks
- Analysis of Sp Cas9 on- and off-target effects in high efficiency multiplex editing in ArabidopsisJohannes 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)
- Evolution of Gene Therapy in HematologyRobyn H. Loves, Donald B. Kohn · 2026 · Seminars in Hematology
- Nonclinical Evaluation of Gene-Editing Products2026 · Elsevier eBooks
- Integration Site Analysis and Off-target Analysis of Cellular and Gene Therapy Products2026 · Elsevier eBooks