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Pacesa M, Nickel L, Schellhaas C, Schmidt J, Pyatova E, Kissling L, Barendse P, Choudhury J, Kapoor S, Alcaraz-Serna A, Cho Y, Ghamary KH, Vinué L, Yachnin BJ, Wollacott AM, Buckley S, Westphal AH, Lindhoud S, Georgeon S, Goverde CA, Hatzopoulos GN, Gönczy P, Muller YD, Schwank G, Swarts DC, Vecchio AJ, Schneider BL, Ovchinnikov S, Correia BE. BindCraft: one-shot design of functional protein binders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.30.615802. [PMID: 39677777 PMCID: PMC11642741 DOI: 10.1101/2024.09.30.615802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
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Marquart KF, Mathis N, Mollaysa A, Müller S, Kissling L, Rothgangl T, Schmidheini L, Kulcsár PI, Allam A, Kaufmann MM, Matsushita M, Haenggi T, Cathomen T, Kopf M, Krauthammer M, Schwank G. Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs. Nat Methods 2024;21:2084-2093. [PMID: 39313558 DOI: 10.1038/s41592-024-02418-z] [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: 10/04/2023] [Accepted: 08/18/2024] [Indexed: 09/25/2024]
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Raimondi F, Siow KM, Wrona D, Fuster-García C, Pastukhov O, Schmitz M, Bargsten K, Kissling L, Swarts DC, Andrieux G, Cathomen T, Modlich U, Jinek M, Siler U, Reichenbach J. Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Commun Biol 2024;7:1291. [PMID: 39384978 PMCID: PMC11464842 DOI: 10.1038/s42003-024-06959-z] [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: 09/30/2022] [Accepted: 09/24/2024] [Indexed: 10/11/2024]  Open
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Mathis N, Allam A, Tálas A, Kissling L, Benvenuto E, Schmidheini L, Schep R, Damodharan T, Balázs Z, Janjuha S, Ioannidi EI, Böck D, van Steensel B, Krauthammer M, Schwank G. Publisher Correction: Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nat Biotechnol 2024:10.1038/s41587-024-02383-0. [PMID: 39134755 DOI: 10.1038/s41587-024-02383-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
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Mathis N, Allam A, Tálas A, Kissling L, Benvenuto E, Schmidheini L, Schep R, Damodharan T, Balázs Z, Janjuha S, Ioannidi EI, Böck D, van Steensel B, Krauthammer M, Schwank G. Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nat Biotechnol 2024:10.1038/s41587-024-02268-2. [PMID: 38907037 DOI: 10.1038/s41587-024-02268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
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Böck D, Revers IM, Bomhof ASJ, Hillen AEJ, Boeijink C, Kissling L, Egli S, Moreno-Mateos MA, van der Knaap MS, van Til NP, Schwank G. In vivo base editing of a pathogenic Eif2b5 variant improves vanishing white matter phenotypes in mice. Mol Ther 2024;32:1328-1343. [PMID: 38454603 PMCID: PMC11081866 DOI: 10.1016/j.ymthe.2024.03.009] [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: 10/17/2023] [Revised: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/09/2024]  Open
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Weber Y, Böck D, Ivașcu A, Mathis N, Rothgangl T, Ioannidi EI, Blaudt AC, Tidecks L, Vadovics M, Muramatsu H, Reichmuth A, Marquart KF, Kissling L, Pardi N, Jinek M, Schwank G. Enhancing prime editor activity by directed protein evolution in yeast. Nat Commun 2024;15:2092. [PMID: 38453904 PMCID: PMC10920827 DOI: 10.1038/s41467-024-46107-z] [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: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]  Open
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Schmidheini L, Mathis N, Marquart KF, Rothgangl T, Kissling L, Böck D, Chanez C, Wang JP, Jinek M, Schwank G. Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nat Chem Biol 2024;20:333-343. [PMID: 37735239 PMCID: PMC7616171 DOI: 10.1038/s41589-023-01427-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
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Mathis N, Allam A, Kissling L, Marquart KF, Schmidheini L, Solari C, Balázs Z, Krauthammer M, Schwank G. Predicting prime editing efficiency and product purity by deep learning. Nat Biotechnol 2023;41:1151-1159. [PMID: 36646933 PMCID: PMC7614945 DOI: 10.1038/s41587-022-01613-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/15/2022] [Indexed: 01/18/2023]
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Möller L, Aird EJ, Schröder MS, Kobel L, Kissling L, van de Venn L, Corn JE. Recursive Editing improves homology-directed repair through retargeting of undesired outcomes. Nat Commun 2022;13:4550. [PMID: 35931681 PMCID: PMC9356142 DOI: 10.1038/s41467-022-31944-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 12/30/2022]  Open
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Rothgangl T, Dennis MK, Lin PJC, Oka R, Witzigmann D, Villiger L, Qi W, Hruzova M, Kissling L, Lenggenhager D, Borrelli C, Egli S, Frey N, Bakker N, Walker JA, Kadina AP, Victorov DV, Pacesa M, Kreutzer S, Kontarakis Z, Moor A, Jinek M, Weissman D, Stoffel M, van Boxtel R, Holden K, Pardi N, Thöny B, Häberle J, Tam YK, Semple SC, Schwank G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 2021;39:949-957. [PMID: 34012094 PMCID: PMC8352781 DOI: 10.1038/s41587-021-00933-4] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
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Dumeau CE, Monfort A, Kissling L, Swarts DC, Jinek M, Wutz A. Introducing gene deletions by mouse zygote electroporation of Cas12a/Cpf1. Transgenic Res 2019;28:525-535. [PMID: 31482512 PMCID: PMC6848045 DOI: 10.1007/s11248-019-00168-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2019] [Indexed: 11/10/2022]
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Kissling L, Monfort A, Swarts DC, Wutz A, Jinek M. Preparation and electroporation of Cas12a/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells. Methods Enzymol 2019;616:241-263. [PMID: 30691645 DOI: 10.1016/bs.mie.2018.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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