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

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Items 201–300 of 944

1. Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence
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2. Molecular biology at the cutting edge: A review on CRISPR/CAS9 gene editing for undergraduates
   Thurtle‐Schmidt, Deborah M., Lo, Te‐Wen · 2018 · Biochemistry and Molecular Biology Education
3. Inhibition of histone deacetylase reduces transcription of NADPH oxidases and ROS production and ameliorates pulmonary arterial hypertension
   Feng Chen, Xueyi Li, Emily Aquadro, Stephen B. Haigh, Jiliang Zhou, David W. Stepp, Neal L. Weintraub, Scott A. Barman, David J. Fulton · 2016 · Free Radical Biology and Medicine
4. Progress in Genome Editing Technology and Its Application in Plants
   Kai Zhang, Nadia Haingotiana Raboanatahiry, Bin Zhu, Maoteng Li · 2017 · Frontiers in Plant Science
5. Modeling Disease In Vivo With CRISPR/Cas9
   Lukas E. Dow · 2015 · Trends in Molecular Medicine
6. Resources for the design of CRISPR gene editing experiments
   Daniel B. Graham, David E. Root · 2015 · Genome biology
7. CRISPR/Cas9: an advanced tool for editing plant genomes
   Milan Kumar Samanta, Avishek Dey, Srimonta Gayen · 2016 · Transgenic Research
8. Enabling functional genomics with genome engineering
   Isaac B. Hilton, Charles A. Gersbach · 2015 · Genome Research
9. CRISPR/Cas9 for Human Genome Engineering and Disease Research
   Xin Xiong, Meng Chen, Wendell A. Lim, Dehua Zhao, Lei S. Qi · 2016 · Annual Review of Genomics and Human Genetics
10. Multiplex epigenome editing of MECP2 to rescue Rett syndrome neurons
    Junming Qian, Xiaonan Guan, Bing Xie, Chuanyun Xu, Jacqueline Niu, Xin Tang, Charles H. Li, Henry M. Colecraft, Rudolf Jaenisch, X. Shawn Liu · 2023 · Science Translational Medicine
11. CRISPR engineering in organoids for gene repair and disease modelling
    Geurts, Maarten H., Clevers, Hans · 2023 · Nature Reviews Bioengineering
12. CRISPR interference and priming varies with individual spacer sequences
    Chaoyou Xue, Arun Somwarpet Seetharam, Olga S. Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew Josef Severin, Dipali G. Sashital · 2015 · Nucleic Acids Research
13. Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)
    Meri I. E. Uusi-Mäkelä, Harlan R. Barker, Carina A. Bäuerlein, Tomi Häkkinen, Matti Nykter, Mika Rämet · 2018 · PLoS ONE
14. CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context
    Giulia Ilaria Corsi, Kunli Qu, Ferhat Alkan, Xiaoguang Pan, Yonglun Luo, Jan Gorodkin · 2022 · Nature Communications
15. CRISPR/Cas9-Mediated Gene Knock-Down in Post-Mitotic Neurons
    C. Straub, Adam J. Granger, Jessica L. Saulnier, Bernardo Luis Sabatini · 2014 · PLoS ONE
16. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation
    Christian Joerg Braun, Peter M. Bruno, Max A. Horlbeck, Luke A. Gilbert, Jonathan S. Weissman, Michael T. Hemann · 2016 · Proceedings of the National Academy of Sciences
17. CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers
    Franziska Wimmer, Chase L. Beisel · 2020 · Frontiers in Microbiology
18. CRISPR/dCas9-mediated Transcriptional Inhibition Ameliorates the Epigenetic Dysregulation at D4Z4 and Represses DUX4-fl in FSH Muscular Dystrophy
    Charis L. Himeda, Takako Iida Jones, Peter L. Jones · 2015 · Molecular Therapy
19. Epigenetic Regulation of Interleukin 6 by Histone Acetylation in Macrophages and Its Role in Paraquat-Induced Pulmonary Fibrosis
    Hu, Lingli, Yu, Yanfang, Huang, Huijie, Fan, Hanting, Hu, Li, Yin, Caiyong, Li, Kai, Fulton, David J. R., Chen, Feng · 2017 · Frontiers in Immunology
20. CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
    Joshua K. Young, Gina Zastrow‐Hayes, Stéphane Deschamps, Sergei K. Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris S. Schwartz, Vesna Djukanovic et al. · 2019 · Scientific Reports
21. Genome Editing Using Cas9 Nickases
    Alexandro E. Trevino, Feng Zhang · 2014 · Methods in enzymology on CD-ROM/Methods in enzymology
22. Messenger RNA Delivery for Tissue Engineering and Regenerative Medicine Applications
    Siddharth Patel, Avathamsa Athirasala, Paula dos Passos Menezes, N. Ashwanikumar, Ting Zou, Gaurav Sahay, Luiz E. Bertassoni · 2018 · Tissue Engineering Part A
23. Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair
    Kallimasioti Pazi, Keerthi T. Chathoth, Gillian C.A. Taylor, Alison M. Meynert, Tracy J. Ballinger, Martijn J. E. Kelder, Sébastien Lalevée, Ildem Sanli, Robert Feil, Andrew J. Wood · 2018 · PLoS Biology
24. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency
    Nasir Javaid, Sangdun Choi · 2021 · Frontiers in Cell and Developmental Biology
25. A universal deep-learning model for zinc finger design enables transcription factor reprogramming
    David M. Ichikawa, Osama Abdin, Nader Alerasool, Manjunatha Kogenaru, April L. Mueller, Han Wen, David O. Giganti, Gregory W. Goldberg, Samantha Adams, Jeffrey M. Spencer et al. · 2023 · Nature Biotechnology
26. Genetic screens and functional genomics using CRISPR /Cas9 technology
    Ella Hartenian, John G. Doench · 2015 · FEBS Journal
27. A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression
    Linghe Xi, Jens C. Schmidt, Arthur J. Zaug, Dante Ascarrunz, Thomas R. Cech · 2015 · Genome biology
28. Genome Editing in Human Stem Cells
    Susan M. Byrne, Prashant Mali, George McDonald Church · 2014 · Methods in enzymology on CD-ROM/Methods in enzymology
29. Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni
    Wannaporn Ittiprasert, Victoria H. Mann, Shannon E. Karinshak, Avril Coghlan, Gabriel Rinaldi, Geetha Sankaranarayanan, Apisit Chaidee, Toshihiko Tanno, Chutima Kumkhaek, Pannathee Prangtaworn et al. · 2019 · eLife
30. Off-target effects in CRISPR-Cas genome editing for human therapeutics: Progress and challenges
    Nechama Kalter, Carla Fuster‐García, Alfredo Silva, Víctor Ronco-Díaz, Stefano Roncelli, Giandomenico Turchiano, Jan Gorodkin, Toni Cathomen, Karim Benabdellah, Ciaran M. Lee et al. · 2025 · Molecular Therapy — Nucleic Acids
31. CRISPR/Cas9-based epigenome editing: An overview of dCas9-based tools with special emphasis on off-target activity
    Vanja Tadić, Goran Josipović, Vlatka Zoldoš, Aleksandar Vojta · 2019 · Methods
32. Strategies to reduce genetic mosaicism following CRISPR-mediated genome edition in bovine embryos
    Ismael Lamas‐Toranzo, Beatriz Galiano-Cogolludo, F. Cornudella-Ardiaca, J. Cobos-Figueroa, O. Ousinde, Pablo Bermejo‐Álvarez · 2019 · Scientific Reports
33. Epigenome engineering: new technologies for precision medicine
    Agustin Sgro, Pilar Blancafort · 2020 · Nucleic Acids Research
34. Achieving Plant CRISPR Targeting that Limits Off‐Target Effects
    Jeffrey D. Wolt, Kan Wang, Dipali G. Sashital, Carolyn J. Lawrence‐Dill · 2016 · The Plant Genome
35. CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
    Florian Heigwer, Tianzuo Zhan, Marco Breinig, Jan Winter, Dirk Brügemann, Svenja Leible, Michael Boutros · 2016 · Genome biology
36. Nonsense-mediated mRNA decay: a ‘nonsense’ pathway makes sense in stem cell biology
    Xin Han, Yanling Wei, Hua Wang, Feilong Wang, Zhenyu Ju, Tangliang Li · 2017 · Nucleic Acids Research
37. Activity and specificity of TRV-mediated gene editing in plants
    Zahir Ali, Aala Abdulaziz Abulfaraj, Marek J. Piatek, Magdy M. Mahfouz · 2015 · Plant Signaling & Behavior
38. CRISPR-Cas9 library screening approach for anti-cancer drug discovery: overview and perspectives
    Yau-Tuen Chan, Yuanjun Lu, Junyu Wu, Cheng Zhang, Hor‐Yue Tan, Zhaoxiang Bian, Ning Wang, Yibin Feng · 2022 · Theranostics
39. Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA
    Vladimir M. Mekler, Минахин Леонид Станиславович, Ekaterina Semenova, Konstantin D. Kuznedelov, Konstantin Severinov · 2016 · Nucleic Acids Research
40. CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes
    Yaojun Tong, Christopher M. Whitford, Kai Blin, Tue Sparholt Jørgensen, Tilmann Weber, Sang Yup Lee · 2020 · Nature Protocols
41. CRISPR-Cas based antiviral strategies against HIV-1
    Gang Wang, Na Zhao, Ben Berkhout, Atze T. Das · 2017 · Virus Research
42. Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9
    Daniel M. Sapozhnikov, Moshe Szyf · 2021 · Nature Communications
43. Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants
    Trevor J. Weiss, Peter A. Crisp, Krishan M Rai, Meredith Song, Nathan M. Springer, Feng Zhang · 2022 · PLANT PHYSIOLOGY
44. Guide RNA engineering for versatile Cas9 functionality
    Chance M. Nowak, Seth Lawson, Megan Zerez, Leonidas G. Bleris · 2016 · Nucleic Acids Research
45. Efficient CRISPR/Cas9-mediated biallelic gene disruption and site-specific knockin after rapid selection of highly active sgRNAs in pigs
    Xianlong Wang, Jinwei Zhou, Chunwei Cao, Jiaojiao Huang, Tang Hai, Yanfang Wang, Qiantao Zheng, Hongyong Zhang, Guosong Qin, Xiangnan Miao et al. · 2015 · Scientific Reports
46. CRISPR mediated somatic cell genome engineering in the chicken
    Véron, Nadège, Qu, Zhengdong, Kipen, Phoebe A.S., Hirst, Claire E., Marcelle, Christophe · 2015 · Developmental Biology
47. Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes
    Seok‐Man Ho, Brigham J. Hartley, Erin K. Flaherty, Prashanth Rajarajan, Rawan Abdelaal, Ifeanyi Obiorah, Natalie Barretto, Hamza Muhammad, Hemali P. Phatnani, Schahram Akbarian et al. · 2017 · Stem Cell Reports
48. Genomes in Focus: Development and Applications of CRISPR‐Cas9 Imaging Technologies
    Spencer C. Knight, Robert Tjian, Jennifer A. Doudna · 2017 · Angewandte Chemie International Edition
49. Hallmarks of cancer: The CRISPR generation
    Colette Moses, Benjamín García‐Bloj, Alan R. Harvey, Pilar Blancafort · 2018 · European Journal of Cancer
50. In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining
    Jonathan M. Geisinger, Sören Turan, Sophia Hernandez, Laura P. Spector, Michèle P. Calos · 2016 · Nucleic Acids Research
51. Deep learning improves the ability of sgRNA off-target propensity prediction
    Qiaoyue Liu, Xiang Cheng, Gan Liu, Bohao Li, Xiuqin Liu · 2020 · BMC Bioinformatics
52. Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity
    Rostain, William, Grebert, Theophile, Vyhovskyi, Danylo, Pizarro, Paula Thiel, Tshinsele-Van Bellingen, Gatwa, Cui, Lun, Bikard, David · 2023 · Nucleic Acids Research
53. Towards personalised allele-specific CRISPR gene editing to treat autosomal dominant disorders
    Kathleen A. Christie, David Courtney, Larry DeDionisio, Connie Chao-Shern, Shyamasree De Majumdar, Laura Mairs, M. Andrew Nesbit, Tara Moore · 2017 · Scientific Reports
54. Genome editing approaches: manipulating of lovastatin and taxol synthesis of filamentous fungi by CRISPR/Cas9 system
    Ashraf S. A. El‐Sayed, Salah E. Abdel‐Ghany, Gul Shad Ali · 2017 · Applied Microbiology and Biotechnology
55. Imaging Specific Genomic DNA in Living Cells
    Baohui Chen, Juan Guan, Bo Huang · 2016 · Annual Review of Biophysics
56. Efficiency Optimization of CRISPR/Cas9-Mediated Targeted Mutagenesis in Grape
    Fengrui Ren, Chong Ren, Zhan Zhang, Wei Duan, David Lecourieux, Shaohua Li, Zhenchang Liang · 2019 · Frontiers in Plant Science
57. Are the current gRNA ranking prediction algorithms useful for genome editing in plants?
    Fatima Naim, Kylie Shand, Satomi Hayashi, Martin O’Brien, James M. McGree, Alexander A. T. Johnson, Benjamin Dugdale, Peter M. Waterhouse · 2020 · PLoS ONE
58. Precision Modulation of Neurodegenerative Disease-Related Gene Expression in Human iPSC-Derived Neurons
    Sabrina M. Heman-Ackah, Andrew Roger Bassett, Matthew J. A. Wood · 2016 · Scientific Reports
59. Re-visiting the Protamine-2 locus: deletion, but not haploinsufficiency, renders male mice infertile
    Simon Schneider, Melanie Balbach, Jan F. Jikeli, Daniela Fietz, Daniel Nettersheim, Sina Jostes, Rovenna Schmidt, Monika Kressin, Martin Bergmann, Dagmar Wachten et al. · 2016 · Scientific Reports
60. Risk associated with off-target plant genome editing and methods for its limitation
    Hui Zhao, Jeffrey D. Wolt · 2017 · Emerging Topics in Life Sciences
61. Next stop for the CRISPR revolution: RNA‐guided epigenetic regulators
    Suhani Vora, Marcelle L. Tuttle, Jenny Yeuk‐Ki Cheng, George McDonald Church · 2016 · FEBS Journal
62. CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment
    Xiaojun Xu, Dongsheng Duan, Shi‐Jie Chen · 2017 · Scientific Reports
63. Targeted transcriptional modulation with type I CRISPR–Cas systems in human cells
    Adrian Pickar‐Oliver, Joshua B. Black, Mae M. Lewis, Kevin J. Mutchnick, Tyler S. Klann, Kylie A. Gilcrest, Madeleine J. Sitton, Christopher E. Nelson, Alejandro Barrera, Luke C. Bartelt et al. · 2019 · Nature Biotechnology
64. gRNA validation for wheat genome editing with the CRISPR-Cas9 system
    Taj Arndell, Niharika Sharma, Peter Langridge, Ute Baumann, Nathan S. Watson‐Haigh, Ryan Whitford · 2019 · BMC Biotechnology
65. In vivo locus-specific editing of the neuroepigenome
    Yim, Yun Young, Teague, Collin D., Nestler, Eric J. · 2020 · Nature Reviews Neuroscience
66. Complex Trait Loci in Maize Enabled by CRISPR-Cas9 Mediated Gene Insertion
    Huirong Gao, Jasdeep S. Mutti, Joshua K. Young, Meizhu Yang, Megan N. Schroder, Brian Lenderts, Lijuan Wang, Dave Peterson, Grace St. Clair, Spencer Jones et al. · 2020 · Frontiers in Plant Science
67. Evaluation of sgRNA Target Sites for CRISPR-Mediated Repression of TP53
    Ingrid E. B. Lawhorn, Joshua P. Ferreira, Clifford L. Wang · 2014 · PLoS ONE
68. The new CRISPR–Cas system: RNA-guided genome engineering to efficiently produce any desired genetic alteration in animals
    Davide Seruggia, Lluı́s Montoliu · 2014 · Transgenic Research
69. Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium
    Lee M, Scott E. Lindner, José-Juan Lopez-Rubio, Manuel Llinás · 2019 · Briefings in Functional Genomics
70. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy
    Andrew Atkins, Cheng-Han Chung, Alexander G. Allen, Will Dampier, Theodore E. Gurrola, Ilker Kudret Sariyer, Michael R. Nonnemacher, Brian L. Wigdahl · 2021 · Frontiers in Genome Editing
71. Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona
    Shashank Gandhi, Maximilian Haeussler, Florian Razy‐Krajka, Lionel Christiaen, Alberto Stolfi · 2017 · Developmental Biology
72. Synthetic epigenetics—towards intelligent control of epigenetic states and cell identity
    Tomasz Piotr Jurkowski, Mirunalini Ravichandran, Peter Stepper · 2015 · Clinical Epigenetics
73. Detection of target DNA with a novel Cas9/sgRNAs-associated reverse PCR (CARP) technique
    Beibei Zhang, Qiao Wang, Xinhui Xu, Qiang Xia, Feifei Long, Weiwei Li, Yingchun Shui, Xinyi Xia, Jinke Wang · 2018 · Analytical and Bioanalytical Chemistry
74. Distinct patterns of Cas9 mismatch tolerancein vitroandin vivo
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75. Modulating the expression of long non‐coding RNAs for functional studies
    Siyuan John Liu, Daniel A. Lim · 2018 · EMBO Reports
76. Efficient BoPDS Gene Editing in Cabbage by the CRISPR/Cas9 System
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77. Single and multiple gene knockouts by CRISPR–Cas9 in maize
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78. High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation
    Mateusz Legut, Zharko Daniloski, Xinhe Xue, Dayna McKenzie, Xinyi Guo, Hans‐Hermann Wessels, Neville E. Sanjana · 2020 · Cell Reports
79. Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio
    Lijiang Long, Hong Guo, Di Yao, Kai Xiong, Yongjun Li, Pengpeng Liu, Zuoyan Zhu, Dong Liu · 2015 · Cell Research
80. Determining the Specificities of TALENs, Cas9, and Other Genome-Editing Enzymes
    Vikram Pattanayak, John P. Guilinger, David R. Liu · 2014 · Methods in enzymology on CD-ROM/Methods in enzymology
81. The applications of CRISPR /Cas system in molecular detection
    Li Zhou, Rongxue Peng, Rui Zhang, Jinming Li · 2018 · Journal of Cellular and Molecular Medicine
82. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency
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83. Ten decadal advances in fungal biology leading towards human well-being
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84. Scarless Genome Editing of Human Pluripotent Stem Cells via Transient Puromycin Selection
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85. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation
    Matthew Grimmer, Sabine Stolzenburg, Ethan Ford, Ryan Lister, Pilar Blancafort, Peggy Farnham · 2014 · Nucleic Acids Research
86. Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?
    Akbar Hasanzadeh, Michael Richard Hamblin, Jafar Kiani, Hamid Noori, Joseph Michael Hardie, Mahdi Karimi, Hadi Shafiee · 2022 · Nano Today
87. Inactivation of GDP‐fucose transporter gene (Slc35c1) in CHO cells by ZFNs, TALENs and CRISPR‐Cas9 for production of fucose‐free antibodies
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88. Fine-Tuning Next-Generation Genome Editing Tools
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89. Guidelines for Optimized Gene Knockout Using CRISPR/Cas9
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90. Gene-Specific Targeting of DNA Methylation in the Mammalian Genome
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91. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies
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92. Landscape of target:guide homology effects on Cas9-mediated cleavage
    Becky Xu Hua Fu, Loren L Hansen, Karen L. Artiles, Michael L. Nonet, Andrew Z. Fire · 2014 · Nucleic Acids Research
93. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes
    Michael Wierer, Matthias Mann · 2016 · Human Molecular Genetics
94. CRISPR/Cas-Based Biosensor As a New Age Detection Method for Pathogenic Bacteria
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95. From bench to bedside: cutting-edge applications of base editing and prime editing in precision medicine
    Weihui Xu, Shiyao Zhang, Huan Qin, Kai Yao · 2024 · Journal of Translational Medicine
96. Integrating gene delivery and gene-editing technologies by adenoviral vector transfer of optimized CRISPR-Cas9 components
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97. Bacterial CRISPR/Cas DNA endonucleases: A revolutionary technology that could dramatically impact viral research and treatment
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98. Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers
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99. Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects
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100. The genome editing revolution: A CRISPR‐Cas TALE off‐target story
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