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For: DeWeirdt PC, McGee AV, Zheng F, Nwolah I, Hegde M, Doench JG. Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening. Nat Commun 2022;13:5255. [PMID: 36068235 DOI: 10.1038/s41467-022-33024-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/30/2022] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
Lodewijk GA, Kozuki S, Guiltinan C, Topacio BR, Shariati SA. Application of CRISPR-Based Epigenome Editing Tools for Engineering Programmable Embryo Models. Methods Mol Biol 2025. [PMID: 40397277 DOI: 10.1007/7651_2025_637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025]
2
Riesenberg S, Kanis P, Karlic R, Maricic T. Robust prediction of synthetic gRNA activity and cryptic DNA repair by disentangling cellular CRISPR cleavage outcomes. Nat Commun 2025;16:4717. [PMID: 40399255 PMCID: PMC12095496 DOI: 10.1038/s41467-025-59947-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 05/08/2025] [Indexed: 05/23/2025]  Open
3
Chapdelaine-Trépanier V, Shenoy S, Masud W, Minju-Op A, Bérubé MA, Schönherr S, Forer L, Fradet-Turcotte A, Taliun D, Cuella-Martin R. CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens. Nucleic Acids Res 2025:gkaf382. [PMID: 40377102 DOI: 10.1093/nar/gkaf382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 04/15/2025] [Accepted: 04/24/2025] [Indexed: 05/18/2025]  Open
4
Cabré-Romans JJ, Cuella-Martin R. CRISPR-dependent base editing as a therapeutic strategy for rare monogenic disorders. Front Genome Ed 2025;7:1553590. [PMID: 40242216 PMCID: PMC12000063 DOI: 10.3389/fgeed.2025.1553590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Accepted: 03/17/2025] [Indexed: 04/18/2025]  Open
5
Yuan H, Song C, Xu H, Sun Y, Anthon C, Bolund L, Lin L, Benabdellah K, Lee C, Hou Y, Gorodkin J, Luo Y. An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools. CRISPR J 2025;8:89-104. [PMID: 40151952 DOI: 10.1089/crispr.2024.0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2025]  Open
6
Godbout K, Dugas M, Reiken SR, Ramezani S, Falle A, Rousseau J, Wronska AE, Lamothe G, Canet G, Lu Y, Planel E, Marks AR, Tremblay JP. Universal Prime Editing Therapeutic Strategy for RyR1-Related Myopathies: A Protective Mutation Rescues Leaky RyR1 Channel. Int J Mol Sci 2025;26:2835. [PMID: 40243436 PMCID: PMC11988564 DOI: 10.3390/ijms26072835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/18/2025] [Accepted: 03/19/2025] [Indexed: 04/18/2025]  Open
7
Lukasiak S, Kalinka A, Gupta N, Papadopoulos A, Saeed K, McDermott U, Hannon GJ, Ross-Thriepland D, Walter D. A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency. BMC Genomics 2025;26:198. [PMID: 40011813 PMCID: PMC11863645 DOI: 10.1186/s12864-025-11386-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 02/19/2025] [Indexed: 02/28/2025]  Open
8
Chey YCJ, Gierus L, Lushington C, Arudkumar JC, B Geiger A, Staker LG, Robertson LJ, Pfitzner C, Kennedy JG, Lee RHB, Godahewa GI, Adikusuma F, Thomas PQ. Optimal SpCas9- and SaCas9-mediated gene editing by enhancing gRNA transcript levels through scaffold poly-T tract reduction. BMC Genomics 2025;26:138. [PMID: 39939860 PMCID: PMC11823040 DOI: 10.1186/s12864-025-11317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 02/03/2025] [Indexed: 02/14/2025]  Open
9
Ashkin EL, Tang YJ, Xu H, Hung KL, Belk JA, Cai H, Lopez SS, Dolcen DN, Hebert JD, Li R, Ruiz PA, Keal T, Andrejka L, Chang HY, Petrov DA, Dixon JR, Xu Z, Winslow MM. A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis. J Exp Med 2025;222:e20240765. [PMID: 39652422 PMCID: PMC11627241 DOI: 10.1084/jem.20240765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 09/16/2024] [Accepted: 10/30/2024] [Indexed: 12/12/2024]  Open
10
Asadi Sarabi P, Shabanpouremam M, Eghtedari AR, Barat M, Moshiri B, Zarrabi A, Vosough M. AI-Based solutions for current challenges in regenerative medicine. Eur J Pharmacol 2024;984:177067. [PMID: 39454850 DOI: 10.1016/j.ejphar.2024.177067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 10/20/2024] [Accepted: 10/20/2024] [Indexed: 10/28/2024]
11
Viswanatha R, Entwisle S, Hu C, Reap K, Butnaru M, Mohr SE, Perrimon N. Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using Integration and Anti-CRISPR (IntAC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613976. [PMID: 39345359 PMCID: PMC11429967 DOI: 10.1101/2024.09.19.613976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
12
Sanchez HM, Lapidot T, Shalem O. High-throughput optimized prime editing mediated endogenous protein tagging for pooled imaging of protein localization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613361. [PMID: 39345511 PMCID: PMC11429766 DOI: 10.1101/2024.09.16.613361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
13
Clark T, Waller MA, Loo L, Moreno CL, Denes CE, Neely GG. CRISPR activation screens: navigating technologies and applications. Trends Biotechnol 2024;42:1017-1034. [PMID: 38493051 DOI: 10.1016/j.tibtech.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
14
Chen L, Liu G, Zhang T. Integrating machine learning and genome editing for crop improvement. ABIOTECH 2024;5:262-277. [PMID: 38974863 PMCID: PMC11224061 DOI: 10.1007/s42994-023-00133-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/18/2023] [Indexed: 07/09/2024]
15
McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Escude Velasco B, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. CELL GENOMICS 2024;4:100519. [PMID: 38484704 PMCID: PMC10943585 DOI: 10.1016/j.xgen.2024.100519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/31/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
16
Ito Y, Inoue S, Nakashima T, Zhang H, Li Y, Kasuya H, Matsukawa T, Wu Z, Yoshikawa T, Kataoka M, Ishikawa T, Kagoya Y. Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells. Nucleic Acids Res 2024;52:141-153. [PMID: 37985205 PMCID: PMC10783505 DOI: 10.1093/nar/gkad1076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]  Open
17
McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Velasco BE, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564061. [PMID: 37961518 PMCID: PMC10634825 DOI: 10.1101/2023.10.25.564061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
18
Zhang L, He W, Fu R, Wang S, Chen Y, Xu H. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. Nucleic Acids Res 2023;51:9880-9893. [PMID: 37615574 PMCID: PMC10570041 DOI: 10.1093/nar/gkad702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]  Open
19
Zhang L, He W, Fu R, Xu H. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532856. [PMID: 36993488 PMCID: PMC10055116 DOI: 10.1101/2023.03.16.532856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
20
Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022;13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]  Open
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